Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo-Cross-LinkingClick to copy article linkArticle link copied!
- Shantam KalraShantam KalraDepartment of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Shantam Kalra
- Amber DonnellyAmber DonnellyDepartment of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Amber Donnelly
- Nishtha SinghNishtha SinghDepartment of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Nishtha Singh
- Daniel MatthewsDaniel MatthewsDepartment of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Daniel Matthews
- Rafael Del Villar-GuerraRafael Del Villar-GuerraDepartment of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Rafael Del Villar-Guerra
- Victoria BemmerVictoria BemmerCentre for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, U.K.More by Victoria Bemmer
- Cyril DominguezCyril DominguezDepartment of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Cyril Dominguez
- Natalie AllcockNatalie AllcockCore Biotechnology Services Electron Microscopy Facility, University of Leicester, Leicester LE1 7RH, U.K.More by Natalie Allcock
- Dmitry ChernyDmitry ChernyDepartment of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Dmitry Cherny
- Andrey Revyakin*Andrey Revyakin*E-mail: [email protected]Department of Molecular and Cell Biology, and Leicester Institute of Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.More by Andrey Revyakin
- David A. Rusling*David A. Rusling*E-mail: [email protected]School of Medicine, Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K.More by David A. Rusling
Abstract
Here, we present a cross-linking approach to covalently functionalize and stabilize DNA origami structures in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands, so that, upon assembly of the origami structure, the extensions form short hairpin duplexes targetable by psoralen-labeled triplex-forming oligonucleotides bearing other functional groups (pso-TFOs). Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO (and attached group) to the origami with ca. 80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates “superstaples” that improve the structural integrity of the functionalized complex. We show that directing cross-linking to regions outside of the origami core dramatically reduces sensitivity of the structures to thermal denaturation and disassembly by T7 RNA polymerase. We also show that the underlying duplex regions of the origami core are digested by DNase I and thus remain accessible to read-out by DNA-binding proteins. Our strategy is scalable and cost-effective, as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen-modified oligonucleotide.
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You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
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License Summary*
You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
Creative Commons (CC): This is a Creative Commons license.
Attribution (BY): Credit must be given to the creator.
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Introduction
Results
Design of TFO-Targetable Hairpin-Modified Origami
HP-Origami Are Targetable by Unmodified and Modified pso-TFOs
Mechanism and Specificity of TFO-Directed Photo-Cross-Linking
Improving the Structural Integrity of Functionalized Origami
Discussion
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.4c03413.
Contains experimental methods, oligonucleotide and staple sequences, and additional AGE, PAGE, TEM, and AFM data (PDF)
Terms & Conditions
Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.
Acknowledgments
We thank Ian Eperon and Glenn Burley for advice on experimental design, Paul Rothemund and Shawn Douglas for advice on DNA origami design, and Olga Makarova for advice on DNA origami purification. We would also like to thank Catarina Prates Rosado for help with running supplementary gels investigating the short triplex oligonucleotides. A.R. thanks the University of Leicester and the BBSRC (BB/L021730/1) for support.
References
This article references 62 other publications.
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- 5Knappe, G. A.; Wamhoff, E.-C.; Bathe, M. Functionalizing DNA Origami to Investigate and Interact with Biological Systems. Nat. Rev. Mater. 2023, 8 (2), 123– 138, DOI: 10.1038/s41578-022-00517-xGoogle Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XjtF2gsrvP&md5=6769af788ee460c1b00f9246194f148aFunctionalizing DNA origami to investigate and interact with biological systemsKnappe, Grant A.; Wamhoff, Eike-Christian; Bathe, MarkNature Reviews Materials (2023), 8 (2), 123-138CODEN: NRMADL; ISSN:2058-8437. (Nature Portfolio)A review. Abstr. DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophys. studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromol. cargos. Here, we review methods developed to functionalize, purify and characterize DNA origami nanostructures. We identify remaining challenges such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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- 8Ramezani, H.; Dietz, H. Building Machines with DNA Molecules. Nat. Rev. Genet. 2020, 21 (1), 5– 26, DOI: 10.1038/s41576-019-0175-6Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvF2ru7%252FN&md5=3d18110085ea649fbd537c4db681b0b5Building machines with DNA moleculesRamezani, Hamid; Dietz, HendrikNature Reviews Genetics (2020), 21 (1), 5-26CODEN: NRGAAM; ISSN:1471-0056. (Nature Research)A review. In nature, DNA mols. carry the hereditary information. But DNA has phys. and chem. properties that make it attractive for uses beyond heredity. In this Review, we discuss the potential of DNA for creating machines that are both encoded by and built from DNA mols. We review the main methods of DNA nanostructure assembly, describe recent advances in building increasingly complex mol. structures and discuss strategies for creating machine-like nanostructures that can be actuated and move. We highlight opportunities for applications of custom DNA nanostructures as scientific tools to address challenges across biol., chem. and engineering.
- 9Zhang, Q.; Jiang, Q.; Li, N.; Dai, L.; Liu, Q.; Song, L.; Wang, J.; Li, Y.; Tian, J.; Ding, B.et al. DNA Origami as an In Vivo Drug Delivery Vehicle for Cancer Therapy. ACS Nano 2014, 8 (7), 6633– 6643, DOI: 10.1021/nn502058jGoogle Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVCru7bL&md5=3e6a85ec691c013ac04041221c67a87fDNA origami as an in vivo drug delivery vehicle for cancer therapyZhang, Qian; Jiang, Qiao; Li, Na; Dai, Luru; Liu, Qing; Song, Linlin; Wang, Jinye; Li, Yaqian; Tian, Jie; Ding, Baoquan; Du, YangACS Nano (2014), 8 (7), 6633-6643CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)Many chemotherapeutics used for cancer treatments encounter issues during delivery to tumors in vivo and may have high levels of systemic toxicity due to their nonspecific distribution. Various materials have been explored to fabricate nanoparticles as drug carriers to improve delivery efficiency. However, most of these materials suffer from multiple drawbacks, such as limited biocompatibility and inability to engineer spatially addressable surfaces that can be utilized for multifunctional activity. Here, we demonstrate that DNA origami possessed enhanced tumor passive targeting and long-lasting properties at the tumor region. Particularly, the triangle-shaped DNA origami exhibits optimal tumor passive targeting accumulation. The delivery of the known anticancer drug doxorubicin into tumors by self-assembled DNA origami nanostructures was performed, and this approach showed prominent therapeutic efficacy in vivo. The DNA origami carriers were prepd. through the self-assembly of M13mp18 phage DNA and hundreds of complementary DNA helper strands; the doxorubicin was subsequently noncovalently intercalated into these nanostructures. After conducting fluorescence imaging and safety evaluation, the doxorubicin-contg. DNA origami exhibited remarkable antitumor efficacy without observable systemic toxicity in nude mice bearing orthotopic breast tumors labeled with green fluorescent protein. Our results demonstrated the potential of DNA origami nanostructures as innovative platforms for the efficient and safe drug delivery of cancer therapeutics in vivo.
- 10Steinhauer, C.; Jungmann, R.; Sobey, T.; Simmel, F.; Tinnefeld, P. DNA Origami as a Nanoscopic Ruler for Super-Resolution Microscopy. Angew. Chem., Int. Ed. 2009, 48 (47), 8870– 8873, DOI: 10.1002/anie.200903308Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtl2rs7bF&md5=1393182cb421cb86eb2a6acd2965f861DNA Origami as a Nanoscopic Ruler for Super-Resolution MicroscopySteinhauer, Christian; Jungmann, Ralf; Sobey, Thomas L.; Simmel, Friedrich C.; Tinnefeld, PhilipAngewandte Chemie, International Edition (2009), 48 (47), 8870-8873, S8870/1-S8870/6CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Resolving the distances: Rectangular DNA origami labeled with fluorophores at specific positions has been used as a nanoscopic ruler. Super-resoln. microscopy based on the subsequent localization of single mols. enables two fluorophores at a distance of about 90 nm to be optically resolved. This combination of subdiffraction imaging and DNA nanotechnol. opens up new avenues for studying nanostructures and their dynamics.
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- 12Kramm, K.; Schröder, T.; Gouge, J.; Vera, A. M.; Gupta, K.; Heiss, F. B.; Liedl, T.; Engel, C.; Berger, I.; Vannini, A.et al. DNA Origami-Based Single-Molecule Force Spectroscopy Elucidates RNA Polymerase III Pre-Initiation Complex Stability. Nat. Commun. 2020, 11 (1), 2828, DOI: 10.1038/s41467-020-16702-xGoogle Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtFahsb%252FI&md5=356bf10ead928725a76a074b250d3e07DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stabilityKramm, Kevin; Schroeder, Tim; Gouge, Jerome; Vera, Andres Manuel; Gupta, Kapil; Heiss, Florian B.; Liedl, Tim; Engel, Christoph; Berger, Imre; Vannini, Alessandro; Tinnefeld, Philip; Grohmann, DinaNature Communications (2020), 11 (1), 2828CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Abstr.: The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the addnl. initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-mol. level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilize TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.
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- 14Shen, W.; Zhong, H.; Neff, D.; Norton, M. L. NTA Directed Protein Nanopatterning on DNA Origami Nanoconstructs. J. Am. Chem. Soc. 2009, 131 (19), 6660– 6661, DOI: 10.1021/ja901407jGoogle Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXltFemsbs%253D&md5=e54508dad59565401422d1c46ea0422eNTA Directed Protein Nanopatterning on DNA Origami NanoconstructsShen, Wanqiu; Zhong, Hong; Neff, David; Norton, Michael L.Journal of the American Chemical Society (2009), 131 (19), 6660-6661CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Precisely patterning proteins and other mols. at the nanoscale is crucial to future biosensing and optoelectronic applications. One- and two-dimensional DNA nanoconstructs have proven to be useful scaffolds for nanopatterning. This paper demonstrates the application of nitrilotriacetic acid (NTA) forming chelate complexes to localize histidine (His) tagged proteins via Ni2+ ions onto DNA based structures. Particularly, enhanced green fluorescent protein (EGFP) was directed to sp. surface locations on a designed DNA Origami nanoconstruct, and the resulting EGFP nanopattern was visualized using at. force microscopy (AFM).
- 15Voigt, N. V.; To̷rring, T.; Rotaru, A.; Jacobsen, M. F.; Ravnsbæk, J. B.; Subramani, R.; Mamdouh, W.; Kjems, J.; Mokhir, A.; Besenbacher, F.et al. Single-Molecule Chemical Reactions on DNA Origami. Nat. Nanotechnol. 2010, 5 (3), 200– 203, DOI: 10.1038/nnano.2010.5Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXislais78%253D&md5=5ae93254bf59d7cd04b18ce8e48724eeSingle-molecule chemical reactions on DNA origamiVoigt, Niels V.; Torring, Thomas; Rotaru, Alexandru; Jacobsen, Mikkel F.; Ravnsbaek, Jens B.; Subramani, Ramesh; Mamdouh, Wael; Kjems, Jorgen; Mokhir, Andriy; Besenbacher, Flemming; Gothelf, Kurt VesteragerNature Nanotechnology (2010), 5 (3), 200-203CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)DNA nanotechnol. and particularly DNA origami, in which long, single-stranded DNA mols. are folded into predetd. shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chem., optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomols. can also be integrated into DNA nanostructures and imaged. Here, we show that chem. reactions with single mols. can be performed and imaged at a local position on a DNA origami scaffold by at. force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions obsd. in these expts. demonstrate the feasibility of post-assembly chem. modification of DNA nanostructures and their potential use as locally addressable solid supports.
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- 17Chhabra, R.; Sharma, J.; Ke, Y.; Liu, Y.; Rinker, S.; Lindsay, S.; Yan, H. Spatially Addressable Multiprotein Nanoarrays Templated by Aptamer-Tagged DNA Nanoarchitectures. J. Am. Chem. Soc. 2007, 129 (34), 10304– 10305, DOI: 10.1021/ja072410uGoogle Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXos1Sksbs%253D&md5=16c7e974dcc65bae02b3d40a479478ccSpatially Addressable Multiprotein Nanoarrays Templated by Aptamer-Tagged DNA NanoarchitecturesChhabra, Rahul; Sharma, Jaswinder; Ke, Yonggang; Liu, Yan; Rinker, Sherri; Lindsay, Stuart; Yan, HaoJournal of the American Chemical Society (2007), 129 (34), 10304-10305CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Here the authors generalize a highly programmable strategy to self-assemble multiprotein nanoarrays with deterministic positional addressability. These protein nanoarrays were templated by aptamer-tagged DNA nanoarchitectures. Arrays of proteins with precisely controlled positions and interprotein spacings offer great potential in proteomics, tissue engineering, and medical diagnostics.
- 18Nakata, E.; Liew, F. F.; Uwatoko, C.; Kiyonaka, S.; Mori, Y.; Katsuda, Y.; Endo, M.; Sugiyama, H.; Morii, T. Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures. Angew. Chem., Int. Ed. 2012, 51 (10), 2421– 2424, DOI: 10.1002/anie.201108199Google ScholarThere is no corresponding record for this reference.
- 19Linko, V.; Keller, A. Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions. Small 2023, 19, 2301935, DOI: 10.1002/smll.202301935Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXosVKks7s%253D&md5=5f0c2287247b9a22089da60e3befe444Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular InteractionsLinko, Veikko; Keller, AdrianSmall (2023), 19 (34), 2301935CODEN: SMALBC; ISSN:1613-6810. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. Programmable, custom-shaped, and nanometer-precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnol. and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiol. conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct mol.-level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Addnl., specific issues demanding further investigation are identified. This review - through its specific viewpoint - may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiol. media.
- 20Rajendran, A.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-Assembly. J. Am. Chem. Soc. 2011, 133 (37), 14488– 14491, DOI: 10.1021/ja204546hGoogle Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtV2isbfO&md5=1e105ad880f0f23a80749ac9733b4e83Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-AssemblyRajendran, Arivazhagan; Endo, Masayuki; Katsuda, Yousuke; Hidaka, Kumi; Sugiyama, HiroshiJournal of the American Chemical Society (2011), 133 (37), 14488-14491CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Heat tolerance of DNA origami structures has been improved about 30 °C by photo-crosslinking of 8-methoxypsoralen. To demonstrate one of its applications, the crosslinked origami were used for higher-temp. self-assembly, which markedly increased the yield of the assembled product when compared to the self-assembly of non-crosslinked origami at lower-temp. By contrast, at higher-temp. annealing, native non-crosslinked tiles did not self-assemble to yield the desired product; however, they formed a non-specific broken structure.
- 21Ramakrishnan, S.; Krainer, G.; Grundmeier, G.; Schlierf, M.; Keller, A. Structural Stability of DNA Origami Nanostructures in the Presence of Chaotropic Agents. Nanoscale 2016, 8 (19), 10398– 10405, DOI: 10.1039/C6NR00835FGoogle Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xms1Wju74%253D&md5=71250697b13ab6e2b46195da7beb959fStructural stability of DNA origami nanostructures in the presence of chaotropic agentsRamakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, AdrianNanoscale (2016), 8 (19), 10398-10405CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)DNA origami represent powerful platforms for single-mol. investigations of biomol. processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concn. and temp. At room temp., the DNA origami triangles are stable up to at least 24 h in both denaturants at concns. as high as 6 M. At elevated temps., however, structural stability is governed by variations in the melting temp. of the individual staple strands. Therefore, the global melting temp. of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temp., its attack results in less structural damage than obsd. for urea under equiv. conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual exptl. requirements. Overall, their high stability renders DNA origami promising platforms for biomol. studies in the presence of chaotropic agents, including single-mol. protein folding or structural switching.
- 22Martin, T. G.; Dietz, H. Magnesium-Free Self-Assembly of Multi-Layer DNA Objects. Nat. Commun. 2012, 3 (1), 1103, DOI: 10.1038/ncomms2095Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3s%252FitF2guw%253D%253D&md5=25e8a9da6130f0460adad1d8ddb557b5Magnesium-free self-assembly of multi-layer DNA objectsMartin Thomas G; Dietz HendrikNature communications (2012), 3 (), 1103 ISSN:.Molecular self-assembly with DNA offers a route for building user-defined nanoscale objects, but an apparent requirement for magnesium in solution has limited the range of conditions for which practical utility of such objects may be achieved. Here we report conditions for assembling templated multi-layer DNA objects in the presence of monovalent ions, showing that neither divalent cations in general or magnesium in particular are essential ingredients for the successful assembly of such objects. The percentage of DNA strands in an object that do not form thermally stable double-helical DNA domains (T(m)>45 °C) with the template molecule correlated with the sodium requirements for obtaining folded objects. Minimizing the fraction of such weakly binding strands by rational design choices enhanced the yield of folding. The results support the view that DNA-based nanodevices may be designed and produced for a variety of target environments.
- 23Kim, H.; Surwade, S. P.; Powell, A.; O’Donnell, C.; Liu, H. Stability of DNA Origami Nanostructure under Diverse Chemical Environments. Chem. Mater. 2014, 26 (18), 5265– 5273, DOI: 10.1021/cm5019663Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVSrtb%252FI&md5=b676d6d7c7e79549f9fe5adb5137a1d4Stability of DNA Origami Nanostructure under Diverse Chemical EnvironmentsKim, Hyojeong; Surwade, Sumedh P.; Powell, Anna; O'Donnell, Christina; Liu, HaitaoChemistry of Materials (2014), 26 (18), 5265-5273CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)The authors report the effect of chem. and phys. treatments on the structural stability of DNA origami nanostructures. The DNA nanostructure maintains its shape under harsh processing conditions, including thermal annealing up to 200°C for 10 min, immersing in a wide range of org. solvents for up to 24 h, brief exposure to alk. aq. solns., and 5 min exposure to UV/O3. These results suggest that the application window of DNA nanostructure is significantly wider than previously believed.
- 24Chandrasekaran, A. R. Nuclease Resistance of DNA Nanostructures. Nat. Rev. Chem. 2021, 5 (4), 225– 239, DOI: 10.1038/s41570-021-00251-yGoogle Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXosFers70%253D&md5=699982fbddaa5e245fee0d6091d45a65Nuclease resistance of DNA nanostructuresChandrasekaran, Arun RichardNature Reviews Chemistry (2021), 5 (4), 225-239CODEN: NRCAF7; ISSN:2397-3358. (Nature Portfolio)A review. DNA nanotechnol. has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biol. applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biol. applications is their susceptibility to attack by nucleases present in the physiol. environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biol. fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degrdn. and quantify stability.
- 25Schaffter, S. W.; Green, L. N.; Schneider, J.; Subramanian, H. K. K.; Schulman, R.; Franco, E. T7 RNA Polymerase Non-Specifically Transcribes and Induces Disassembly of DNA Nanostructures. Nucleic Acids Res. 2018, 46 (10), 5332– 5343, DOI: 10.1093/nar/gky283Google ScholarThere is no corresponding record for this reference.
- 26Rajendran, A.; Krishnamurthy, K.; Giridasappa, A.; Nakata, E.; Morii, T. Stabilization and Structural Changes of 2D DNA Origami by Enzymatic Ligation. Nucleic Acids Res. 2021, 49 (14), 7884– 7900, DOI: 10.1093/nar/gkab611Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXisVCqt7vK&md5=481bc4cdc8a3d43c5a61bb82d9d203f2Stabilization and structural changes of 2D DNA origami by enzymatic ligationRajendran, Arivazhagan; Krishnamurthy, Kirankumar; Giridasappa, Amulya; Nakata, Eiji; Morii, TakashiNucleic Acids Research (2021), 49 (14), 7884-7900CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In mol. biol., enzymic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnol., the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed anal. and optimization of the conditions for the enzymic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temp., and typically requires much higher concn. of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a max. ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concn.-dependent manner.
- 27Weizenmann, N.; Scheidgen-Kleyboldt, G.; Ye, J.; Krause, C. B.; Kauert, D.; Helmi, S.; Rouillon, C.; Seidel, R. Chemical Ligation of an Entire DNA Origami Nanostructure. Nanoscale 2021, 13 (41), 17556– 17565, DOI: 10.1039/D1NR04225DGoogle Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXitFaqtbbM&md5=839f87dd89c32e95d02ca0f24f2b9c9aChemical ligation of an entire DNA origami nanostructureWeizenmann, Nicole; Scheidgen-Kleyboldt, Gerda; Ye, Jingjing; Krause, Cordula B.; Kauert, Dominik; Helmi, Seham; Rouillon, Christophe; Seidel, RalfNanoscale (2021), 13 (41), 17556-17565CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)Within the field of DNA nanotechnol., numerous methods were developed to produce complex two- and three-dimensional DNA nanostructures for many different emerging applications. These structures typically suffer from a low tolerance against non-optimal environmental conditions including elevated temps. Here, we apply a chem. ligation method to covalently seal the nicks between adjacent 5 phosphorylated and 3 amine-modified strands within the DNA nanostructures. Using a cost-effective enzymic strand modification procedure, we are able to batch-modify all DNA strands even of large DNA objects, such as origami nanostructures. The covalent strand linkage increases the temp. stability of the structures by ~ 10 K. Generally, our method also allows a 'surgical' introduction of covalent strand linkages at preselected positions. It can also be used to map the strand ligation into chains throughout the whole nanostructure and identify assembly defects. We expect that our method can be applied to a large variety of DNA nanostructures, in particular when full control over the introduced covalent linkages and the absence of side adducts and DNA damages are required.
- 28Cassinelli, V.; Oberleitner, B.; Sobotta, J.; Nickels, P.; Grossi, G.; Kempter, S.; Frischmuth, T.; Liedl, T.; Manetto, A. One-Step Formation of “Chain-Armor”-Stabilized DNA Nanostructures. Angew. Chem., Int. Ed. 2015, 54 (27), 7795– 7798, DOI: 10.1002/anie.201500561Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXosVGjsbc%253D&md5=9cdc08d2063e1316ee00ca29cefa9ef8One-Step Formation of "Chain-Armor"-Stabilized DNA NanostructuresCassinelli, Valentina; Oberleitner, Birgit; Sobotta, Jessica; Nickels, Philipp; Grossi, Guido; Kempter, Susanne; Frischmuth, Thomas; Liedl, Tim; Manetto, AntonioAngewandte Chemie, International Edition (2015), 54 (27), 7795-7798CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)DNA-based self-assembled nanostructures are widely used to position org. and inorg. objects with nanoscale precision. A particular promising application of DNA structures is their usage as programmable carrier systems for targeted drug delivery. To provide DNA-based templates that are robust against degrdn. at elevated temps., low ion concns., adverse pH conditions, and DNases, we built 6-helix DNA tile tubes consisting of 24 oligonucleotides carrying alkyne groups on their 3'-ends and azides on their 5'-ends. By a mild click reaction, the two ends of selected oligonucleotides were covalently connected to form rings and interlocked DNA single strands, so-called DNA catenanes. Strikingly, the structures stayed topol. intact in pure water and even after pptn. from EtOH. The structures even withstood a temp. of 95 °C when all of the 24 strands were chem. interlocked.
- 29Gerling, T.; Kube, M.; Kick, B.; Dietz, H. Sequence-Programmable Covalent Bonding of Designed DNA Assemblies. Sci. Adv. 2018, 4 (8), eaau1157 DOI: 10.1126/sciadv.aau1157Google ScholarThere is no corresponding record for this reference.
- 30Engelhardt, F. A. S.; Praetorius, F.; Wachauf, C. H.; Brüggenthies, G.; Kohler, F.; Kick, B.; Kadletz, K. L.; Pham, P. N.; Behler, K. L.; Gerling, T.et al. Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds. ACS Nano 2019, 13 (5), 5015– 5027, DOI: 10.1021/acsnano.9b01025Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXnsV2ktbo%253D&md5=2fb7ea8b75471e18715911c299deeeb9Custom-Size, Functional, and Durable DNA Origami with Design-Specific ScaffoldsEngelhardt, Floris A. S.; Praetorius, Florian; Wachauf, Christian H.; Brueggenthies, Gereon; Kohler, Fabian; Kick, Benjamin; Kadletz, Karoline L.; Pham, Phuong Nhi; Behler, Karl L.; Gerling, Thomas; Dietz, HendrikACS Nano (2019), 13 (5), 5015-5027CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA origami nano-objects are usually designed around generic single-stranded "scaffolds". Many properties of the target object are detd. by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable prodn. methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence compn. on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent crosslinking of DNA origami via UV irradn., and we built DNAzyme-contg. scaffolds that allow postfolding DNA origami domain sepn.
- 31Chen, H.; Li, R.; Li, S.; Andréasson, J.; Choi, J. H. Conformational Effects of UV Light on DNA Origami. J. Am. Chem. Soc. 2017, 139 (4), 1380– 1383, DOI: 10.1021/jacs.6b10821Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtVKhsro%253D&md5=1d9fa46fb2d7d2fe2b2458cea89ea58cConformational Effects of UV Light on DNA OrigamiChen, Haorong; Li, Ruixin; Li, Shiming; Andreasson, Joakim; Choi, Jong HyunJournal of the American Chemical Society (2017), 139 (4), 1380-1383CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The responses of DNA origami conformation to UV radiation of different wavelengths and doses are investigated. Short and medium wavelength UV light can cause photolesions in DNA origami. At moderate doses, the lesions do not cause any visible defects in the origami, nor do they significantly affect the hybridization capability. Instead, they help relieve the internal stress in the origami structure and restore it to the designed conformation. At high doses, staple dissocn. increases and causes structural disintegration. Long wavelength UV does not show any effect on origami conformation by itself. We show that this UV range can be used in conjunction with photoactive mols. for photoreconfiguration, while avoiding any damage to the DNA structures.
- 32Moser, H. E.; Dervan, P. B. Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation. Science 1987, 238 (4827), 645– 650, DOI: 10.1126/science.3118463Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXltVKitA%253D%253D&md5=15690e4871f93135460d2ea26516ab38Sequence-specific cleavage of double helical DNA by triple helix formationMoser, Heinz E.; Dervan, Peter B.Science (Washington, DC, United States) (1987), 238 (4827), 645-50CODEN: SCIEAS; ISSN:0036-8075.Homopyrimidine oligodeoxyribonucleotides with EDTA-Fe attached at a single position bind the corresponding homopyrimidine-homopurine tracts within large double-stranded DNA by triple helix formation and cleave at that site. Oligonucleotides with EDTA-Fe at the 5' end cause a sequence specific double strand break. The location and asymmetry of the cleavage pattern reveal that the homopyrimidine-EDTA probes bind in the major groove parallel to the homopurine strand of Watson-Crick double helical DNA. The sequence-specific recognition of double helical DNA by homopyrimidine probes is sensitive to single base mismatches. Homopyrimidine probes equipped with DNA cleaving moieties could be useful tools for mapping chromosomes.
- 33Dalla Pozza, M.; Abdullrahman, A.; Cardin, C. J.; Gasser, G.; Hall, J. P. Three’s a Crowd – Stabilisation, Structure, and Applications of DNA Triplexes. Chem. Sci. 2022, 13 (35), 10193– 10215, DOI: 10.1039/D2SC01793HGoogle ScholarThere is no corresponding record for this reference.
- 34Chandrasekaran, A. R.; Rusling, D. A. Triplex-Forming Oligonucleotides: A Third Strand for DNA Nanotechnology. Nucleic Acids Res. 2018, 46 (3), 1021– 1037, DOI: 10.1093/nar/gkx1230Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitlGisr%252FL&md5=c7e6d1549a0fabc2b0355b4740ca643dTriplex-forming oligonucleotides: a third strand for DNA nanotechnologyChandrasekaran, Arun Richard; Rusling, David A.Nucleic Acids Research (2018), 46 (3), 1021-1037CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)A review. DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.
- 35Hu, Y.; Cecconello, A.; Idili, A.; Ricci, F.; Willner, I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew. Chem., Int. Ed. 2017, 56 (48), 15210– 15233, DOI: 10.1002/anie.201701868Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslygsrzJ&md5=67320244b500dec9d4e96494f89a1e5bTriplex DNA Nanostructures: From Basic Properties to ApplicationsHu, Yuwei; Cecconello, Alessandro; Idili, Andrea; Ricci, Francesco; Willner, ItamarAngewandte Chemie, International Edition (2017), 56 (48), 15210-15233CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and mol. switches. Furthermore, the pH-induced, switchable assembly and dissocn. of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-org. frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-soln. transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
- 36Rusling, D. A.; Nandhakumar, I. S.; Brown, T.; Fox, K. R. Triplex-Directed Recognition of a DNA Nanostructure Assembled by Crossover Strand Exchange. ACS Nano 2012, 6 (4), 3604– 3613, DOI: 10.1021/nn300718zGoogle Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XksFWgsLs%253D&md5=2d238b3f015411a38517a7f9577d759dTriplex-Directed Recognition of a DNA Nanostructure Assembled by Crossover Strand ExchangeRusling, David A.; Nandhakumar, Iris S.; Brown, Tom; Fox, Keith R.ACS Nano (2012), 6 (4), 3604-3613CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA has been widely exploited for the self-assembly of nanosized objects and arrays that offer the potential to act as scaffolds for the spatial positioning of mol. components with nanometer precision. Methods that allow the targeting of components to specific locations within these structures are therefore highly sought after. Here the authors report that the triplex approach to DNA recognition, which relies on the specific binding of an oligonucleotide within the major groove of double-helical DNA, can be exploited to recognize specific loci within a DNA double-crossover tile and array, a nanostructure assembled by crossover strand exchange. The oligonucleotide can be targeted to both crossover and noncrossover strands and, surprisingly, across the region spanning the crossover junction itself. Moreover, by attaching biotin to the end of the oligonucleotide, the authors show that streptavidin mols. can be recruited to precise locations within a DX array, with an av. spacing of 31.9 (±1.3) nm. This is a promising approach that could be exploited to introduce other components compatible with oligonucleotide synthesis into the wide variety of DNA nanostructures assembled by crossover strand exchange, such as those generated by DNA origami.
- 37Rusling, D. A.; Chandrasekaran, A. R.; Ohayon, Y. P.; Brown, T.; Fox, K. R.; Sha, R.; Mao, C.; Seeman, N. C. Functionalizing Designer DNA Crystals with a Triple-Helical Veneer. Angew. Chem., Int. Ed. 2014, 53 (15), 3979– 3982, DOI: 10.1002/anie.201309914Google ScholarThere is no corresponding record for this reference.
- 38Zhao, Y.; Chandrasekaran, A. R.; Rusling, D. A.; Woloszyn, K.; Hao, Y.; Hernandez, C.; Vecchioni, S.; Ohayon, Y. P.; Mao, C.; Seeman, N. C.et al. The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals. J. Am. Chem. Soc. 2023, 145 (6), 3599– 3605, DOI: 10.1021/jacs.2c12667Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXitlamtr0%253D&md5=4a6231a9066dbe1a5909455f3cc2b794The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA CrystalsZhao, Yue; Chandrasekaran, Arun Richard; Rusling, David A.; Woloszyn, Karol; Hao, Yudong; Hernandez, Carina; Vecchioni, Simon; Ohayon, Yoel P.; Mao, Chengde; Seeman, Nadrian C.; Sha, RuojieJournal of the American Chemical Society (2023), 145 (6), 3599-3605CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnol. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addn. of the Watson-Crick complement to a TFO contg. a short toehold, and (c) the addn. of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.
- 39Takasugi, M.; Guendouz, A.; Chassignol, M.; Decout, J. L.; Lhomme, J.; Thuong, N. T.; Hélène, C. Sequence-Specific Photo-Induced Cross-Linking of the Two Strands of Double-Helical DNA by a Psoralen Covalently Linked to a Triple Helix-Forming Oligonucleotide. Proc. Natl. Acad. Sci. U. S. A. 1991, 88 (13), 5602– 5606, DOI: 10.1073/pnas.88.13.5602Google ScholarThere is no corresponding record for this reference.
- 40Abdallah, H. O.; Ohayon, Y. P.; Chandrasekaran, A. R.; Sha, R.; Fox, K. R.; Brown, T.; Rusling, D. A.; Mao, C.; Seeman, N. C. Stabilisation of Self-Assembled DNA Crystals by Triplex-Directed Photo-Cross-Linking. Chem. Commun. 2016, 52 (51), 8014– 8017, DOI: 10.1039/C6CC03695CGoogle Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xptl2rs7g%253D&md5=ebd58f07b1601808ee11c72c1fc90d75Stabilization of self-assembled DNA crystals by triplex-directed photocrosslinkingAbdallah, Hatem O.; Ohayon, Yoel P.; Chandrasekaran, Arun Richard; Sha, Ruojie; Fox, Keith R.; Brown, Tom; Rusling, David A.; Mao, Chengde; Seeman, Nadrian C.Chemical Communications (Cambridge, United Kingdom) (2016), 52 (51), 8014-8017CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)The tensegrity triangle is a robust DNA motif that can self-assemble to generate macroscopic 3-dimensional crystals. However, the stability of these crystals is dependent on the high ionic conditions used for crystal growth. Here, the authors demonstrate that a triplex-forming oligonucleotide can be used to direct the specific intercalation, and subsequent photocrosslinking, of 4,5',8-trimethylpsoralen to single or multiple loci within or between the tiles of the crystal. Crosslinking between the tiles of the crystal improves their thermostability. Such an approach is likely to facilitate the removal of crystals from their mother liquor and may prove useful for applications that require greater crystal stability.
- 41Rusling, D. A.; Nandhakumar, I. S.; Brown, T.; Fox, K. R. Triplex-Directed Covalent Cross-Linking of a DNA Nanostructure. Chem. Commun. 2012, 48 (77), 9592, DOI: 10.1039/c2cc35407aGoogle Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xht12qsrrF&md5=b87508de0cf0ee210a955035a14cad7fTriplex-directed covalent cross-linking of a DNA nanostructureRusling, David A.; Nandhakumar, Iris S.; Brown, Tom; Fox, Keith R.Chemical Communications (Cambridge, United Kingdom) (2012), 48 (77), 9592-9594CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)The triplex approach to DNA recognition is exploited to direct covalent inter-strand crosslinks to unique locations within a pre-assembled DNA nanostructure. This approach can be used to improve the stability of DNA nanostructures and demonstrates the feasibility of directing other reactive groups to unique locations within these complexes.
- 42Lin, C.; Perrault, S. D.; Kwak, M.; Graf, F.; Shih, W. M. Purification of DNA-Origami Nanostructures by Rate-Zonal Centrifugation. Nucleic Acids Res. 2013, 41 (2), e40–e40 DOI: 10.1093/nar/gks1070Google ScholarThere is no corresponding record for this reference.
- 43Suma, A.; Stopar, A.; Nicholson, A. W.; Castronovo, M.; Carnevale, V. Global and Local Mechanical Properties Control Endonuclease Reactivity of a DNA Origami Nanostructure. Nucleic Acids Res. 2020, 48 (9), 4672– 4680, DOI: 10.1093/nar/gkaa080Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisVKltbbI&md5=7ed9978d7d2126dbaeefaf14a1b5cdb9Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructureSuma, Antonio; Stopar, Alex; Nicholson, Allen W.; Castronovo, Matteo; Carnevale, VincenzoNucleic Acids Research (2020), 48 (9), 4672-4680CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)We used coarse-grained mol. dynamics simulations to characterize the global and local mech. properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations sepd. by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the exptl. data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40 nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.
- 44Mallik, L.; Dhakal, S.; Nichols, J.; Mahoney, J.; Dosey, A. M.; Jiang, S.; Sunahara, R. K.; Skiniotis, G.; Walter, N. G. Electron microscopic visualisation of protein assemblies on flattened DNA origami. ACS Nano 2015, 9 (7), 7133– 7141, DOI: 10.1021/acsnano.5b01841Google Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFWqtrjI&md5=97318b99c98d1742021acc5f4f327f95Electron Microscopic Visualization of Protein Assemblies on Flattened DNA OrigamiMallik, Leena; Dhakal, Soma; Nichols, Joseph; Mahoney, Jacob; Dosey, Anne M.; Jiang, Shuoxing; Sunahara, Roger K.; Skiniotis, Georgios; Walter, Nils G.ACS Nano (2015), 9 (7), 7133-7141CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small mols. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concn. of DMSO, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest mol. assemblies for biochem. and nanotechnol. applications.
- 45Bates, P. J.; Macaulay, V. M.; McLean, M. J.; Jenkins, T. C.; Reszka, A. P.; Laughton, C. J.; Neidle, S. Characteristics of triplex-directed photoadduct formation by psoralen-linked oligodeoxynucleotides. Nucleic Acids Res. 1995, 23 (21), 4283– 4289, DOI: 10.1093/nar/23.21.4283Google ScholarThere is no corresponding record for this reference.
- 46Rusling, D. A. Triplex-Forming Properties and Enzymatic Incorporation of a Base-Modified Nucleotide Capable of Duplex DNA Recognition at Neutral PH. Nucleic Acids Res. 2021, 49 (13), 7256– 7266, DOI: 10.1093/nar/gkab572Google ScholarThere is no corresponding record for this reference.
- 47Zhang, Z.; Park, S.; Pertsinidis, A.; Revyakin, A. Cloud-Point PEG Glass Surfaces for Imaging of Immobilized Single Molecules by Total-Internal-Reflection Microscopy. BIO-Protoc. 2016, 6 (7), e1784--e1784 DOI: 10.21769/BioProtoc.1784Google ScholarThere is no corresponding record for this reference.
- 48Katz, B. A. Binding of Biotin to Streptavidin Stabilizes Intersubunit Salt Bridges between Asp61 and His87 at Low PH. J. Mol. Biol. 1997, 274 (5), 776– 800, DOI: 10.1006/jmbi.1997.1444Google ScholarThere is no corresponding record for this reference.
- 49Wei, X.; Nangreave, J.; Jiang, S.; Yan, H.; Liu, Y. Mapping the Thermal Behavior of DNA Origami Nanostructures. J. Am. Chem. Soc. 2013, 135 (16), 6165– 6176, DOI: 10.1021/ja4000728Google Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXkslahs74%253D&md5=4f272f89d8cd7d75d282e146f6631297Mapping the Thermal Behavior of DNA Origami NanostructuresWei, Xixi; Nangreave, Jeanette; Jiang, Shuoxing; Yan, Hao; Liu, YanJournal of the American Chemical Society (2013), 135 (16), 6165-6176CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Understanding the thermodn. properties of complex DNA nanostructures, including rationally designed two- and three-dimensional (2D and 3D, resp.) DNA origami, facilitates more accurate spatiotemporal control and effective functionalization of the structures by other elements. In this work fluorescein and tetramethylrhodamine (TAMRA), a Foerster resonance energy transfer (FRET) dye pair, were incorporated into selected staples within various 2D and 3D DNA origami structures. We monitored the temp.-dependent changes in FRET efficiency that occurred as the dye-labeled structures were annealed and melted and subsequently extd. information about the associative and dissociative behavior of the origami. In particular, we examd. the effects of local and long-range structural defects (omitted staple strands) on the thermal stability of common DNA origami structures. The results revealed a significant decrease in thermal stability of the structures in the vicinity of the defects, in contrast to the negligible long-range effects that were obsd. Furthermore, we probed the global assembly and disassembly processes by comparing the thermal behavior of the FRET pair at several different positions. We demonstrated that the staple strands located in different areas of the structure all exhibit highly cooperative hybridization but have distinguishable melting temps. depending on their positions. This work underscores the importance of understanding fundamental aspects of the self-assembly of DNA nanostructures and can be used to guide the design of more complicated DNA nanostructures, to optimize annealing protocol and manipulate functionalized DNA nanostructures.
- 50Patrick, M.; Dennis, P. P.; Ehrenberg, M.; Bremer, H. Free RNA Polymerase in Escherichia Coli. Biochimie 2015, 119, 80– 91, DOI: 10.1016/j.biochi.2015.10.015Google ScholarThere is no corresponding record for this reference.
- 51Jackson, D. A.; Pombo, A.; Iborra, F. The Balance Sheet for Transcription: An Analysis of Nuclear RNA Metabolism in Mammalian Cells. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 2000, 14 (2), 242– 254, DOI: 10.1096/fasebj.14.2.242Google ScholarThere is no corresponding record for this reference.
- 52Lan, Y.; Leemis, L. M. The logistic-exponential survival distribution. Nav. Res. Logistics 2008, 55 (3), 252– 264, DOI: 10.1002/nav.20279Google ScholarThere is no corresponding record for this reference.
- 53Smith, S. I.; Brodbelt, J. S. Rapid Characterization of Cross-Links, Mono-Adducts, and Non-Covalent Binding of Psoralens to Deoxyoligonucleotides by LC-UV/ESI-MS and IRMPD Mass Spectrometry. Analyst 2010, 135 (5), 943, DOI: 10.1039/b924023cGoogle ScholarThere is no corresponding record for this reference.
- 54Li, H.; Broughton-Head, V. J.; Peng, G.; Powers, V. E. C.; Ovens, M. J.; Fox, K. R.; Brown, T. Triplex Staples: DNA Double-Strand Cross-Linking at Internal and Terminal Sites Using Psoralen-Containing Triplex-Forming Oligonucleotides. Bioconjugate Chem. 2006, 17 (6), 1561– 1567, DOI: 10.1021/bc0601875Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1WqtLbF&md5=74c3364df912fc5a85507a9453cd7928Triplex Staples: DNA Double-Strand Cross-Linking at Internal and Terminal Sites Using Psoralen-Containing Triplex-Forming OligonucleotidesLi, Hong; Broughton-Head, Victoria J.; Peng, Guomei; Powers, Vicki E. C.; Ovens, Matthew J.; Fox, Keith R.; Brown, TomBioconjugate Chemistry (2006), 17 (6), 1561-1567CODEN: BCCHES; ISSN:1043-1802. (American Chemical Society)A method has been developed to attach 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen to the 5 position of thymine bases during solid-phase oligonucleotide synthesis. UV irradn. of triplex-forming oligonucleotides (TFOs) contg. internally attached psoralens produces photoadducts at TpA steps within target duplexes, thus relaxing the constraints on selection of psoralen target sequences. Photoreaction of TFOs contg. two psoralens, located at the 5'- and 3'-ends, has been used to create double-strand cross-links (triplex staples) at both termini of the TFO. Such complexes have no free single-stranded ends. TFOs contg. 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen, 3-methyl-2-aminopyridine, and 5-(3-aminoprop-2-ynyl)deoxyuridine formed photoadducts with target duplexes under near-physiol. conditions.
- 55Walsh, S.; El-Sagheer, A. H.; Brown, T. Fluorogenic Thiazole Orange TOTFO Probes Stabilise Parallel DNA Triplexes at PH 7 and Above. Chem. Sci. 2018, 9 (39), 7681– 7687, DOI: 10.1039/C8SC02418AGoogle ScholarThere is no corresponding record for this reference.
- 56Sachenbacher, K.; Khoshouei, A.; Honemann, M. N.; Engelen, W.; Feigl, E.; Dietz, H. Triple-Stranded DNA As a Structural Element in DNA Origami. ACS Nano 2023, 17 (10), 9014– 9024, DOI: 10.1021/acsnano.2c11402Google Scholar56https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXpsFWmsb0%253D&md5=24a28642b7f5e44398888a96effa5ed3Triple-Stranded DNA As a Structural Element in DNA OrigamiSachenbacher, Ken; Khoshouei, Ali; Honemann, Maximilian Nicolas; Engelen, Wouter; Feigl, Elija; Dietz, HendrikACS Nano (2023), 17 (10), 9014-9024CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)Mol. self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional objects. To expand the palette of structural motifs in DNA origami, here we describe hybrid duplex-triplex DNA motifs as pH-dependent building blocks in DNA origami. We investigate design rules for incorporating triplex forming oligonucleotides and noncanonical duplex-triplex crossovers in multilayer DNA origami objects. We use single-particle cryoelectron microscopy to elucidate the structural basis of triplex domains and of duplex-triplex crossovers. We find that duplex-triplex crossovers can complement and fully replace the canonical duplex-duplex crossovers within DNA origami objects, for example, to increase the crossover d. for potentially greater rigidity and reduced interhelical spacing, and to create connections at sites where conventional crossovers may be undesirable. We also show the pH-induced formation of a DNA origami object stabilized entirely by triplex-mediated strand crossovers.
- 57Ng, C.; Samanta, A.; Mandrup, O. A.; Tsang, E.; Youssef, S.; Klausen, L. H.; Dong, M.; Nijenhuis, M. A. D.; Gothelf, K. V. Folding Double-Stranded DNA into Designed Shapes with Triplex-Forming Oligonucleotides. Adv. Mater. 2023, 35, 2302497, DOI: 10.1002/adma.202302497Google ScholarThere is no corresponding record for this reference.
- 58Dynan, W. S.; Burgess, R. R. In Vitro Transcription by Wheat Germ RNA Polymerase II. Initiation of RNA Synthesis on Relaxed, Closed Circular Template. J. Biol. Chem. 1981, 256 (11), 5866– 5873, DOI: 10.1016/S0021-9258(19)69288-4Google ScholarThere is no corresponding record for this reference.
- 59Dreyer, C.; Hausen, P. On the Initiation of Mammalian RNA Polymerase at Single-Strand Breaks in DNA. Eur. J. Biochem. 1976, 70 (1), 63– 74, DOI: 10.1111/j.1432-1033.1976.tb10956.xGoogle ScholarThere is no corresponding record for this reference.
- 60Chandler, D. W.; Gralla, J. The Interaction of RNA Polymerase II with Non-Promoter DNA Sites. Nucleic Acids Res. 1981, 9 (22), 6031– 6046, DOI: 10.1093/nar/9.22.6031Google ScholarThere is no corresponding record for this reference.
- 61Vogt, V. Breaks in DNA Stimulate Transcription by Core RNA Polymerase. Nature 1969, 223 (5208), 854– 855, DOI: 10.1038/223854a0Google ScholarThere is no corresponding record for this reference.
- 62Ishihama, A.; Murakami, S.; Fukuda, R.; Matsukage, A.; Kameyama, T. The Nature of Initiation Sites on DNA for the Core RNA Polymerase. Mol. Gen. Genet. 1971, 111 (1), 66– 76, DOI: 10.1007/BF00286555Google ScholarThere is no corresponding record for this reference.
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- 1Seeman, N. C.; Sleiman, H. F. DNA Nanotechnology. Nat. Rev. Mater. 2018, 3 (1), 17068, DOI: 10.1038/natrevmats.2017.681https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslOntLbM&md5=a8683cd5a65e013464f37bb6383853b4DNA nanotechnologySeeman, Nadrian C.; Sleiman, Hanadi F.Nature Reviews Materials (2018), 3 (1), 17068CODEN: NRMADL; ISSN:2058-8437. (Nature Research)DNA is the mol. that stores and transmits genetic information in biol. systems. The field of DNA nanotechnol. takes this mol. out of its biol. context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnol., and has been revolutionary in our ability to control mol. self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomol. structure detn., drug delivery and synthetic biol. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.
- 2Dey, S.; Fan, C.; Gothelf, K. V.; Li, J.; Lin, C.; Liu, L.; Liu, N.; Nijenhuis, M. A. D.; Saccà, B.; Simmel, F. C.et al. DNA Origami. Nat. Rev. Methods Primer 2021, 1 (1), 13, DOI: 10.1038/s43586-020-00009-8There is no corresponding record for this reference.
- 3Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440 (7082), 297– 302, DOI: 10.1038/nature045863https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XitlKgu7g%253D&md5=583caefdda9b1deb5d3f2ef78d9e6ecbFolding DNA to create nanoscale shapes and patternsRothemund, Paul W. K.Nature (London, United Kingdom) (2006), 440 (7082), 297-302CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)'Bottom-up fabrication', which exploits the intrinsic properties of atoms and mols. to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA mols. provides an attractive route towards this goal. Here the author describe a simple method for folding long, single-stranded DNA mols. into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diam. and approx. desired shapes such as squares, disks and five-pointed stars with a spatial resoln. of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton mol. complex).
- 4Douglas, S. M.; Marblestone, A. H.; Teerapittayanon, S.; Vazquez, A.; Church, G. M.; Shih, W. M. Rapid Prototyping of 3D DNA-Origami Shapes with CaDNAno. Nucleic Acids Res. 2009, 37 (15), 5001– 5006, DOI: 10.1093/nar/gkp4364https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtVKntbzE&md5=aa99732c1666373a70e9b7b4de6e6d5dRapid prototyping of 3D DNA-origami shapes with caDNAnoDouglas, Shawn M.; Marblestone, Adam H.; Teerapittayanon, Surat; Vazquez, Alejandro; Church, George M.; Shih, William M.Nucleic Acids Research (2009), 37 (15), 5001-5006CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)DNA nanotechnol. exploits the programmable specificity afforded by base-pairing to produce self-assembling macromol. objects of custom shape. For building megadalton-scale DNA nanostructures, a long scaffold' strand can be employed to template the assembly of hundreds of oligonucleotide staple' strands into a planar antiparallel array of cross-linked helixes. The authors recently adapted this scaffolded DNA origami' method to producing 3-dimensional shapes formed as pleated layers of double helixes constrained to a honeycomb lattice. However, completing the required design steps can be cumbersome and time-consuming. Here the authors present caDNAno, an open-source software package with a graphical user interface that aids in the design of DNA sequences for folding 3-dimensional honeycomb-pleated shapes rectangular-block motifs were designed, assembled, and analyzed to identify a well-behaved motif that could serve as a building block for future studies. The use of caDNAno significantly reduces the effort required to design 3-dimensional DNA-origami structures. The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.
- 5Knappe, G. A.; Wamhoff, E.-C.; Bathe, M. Functionalizing DNA Origami to Investigate and Interact with Biological Systems. Nat. Rev. Mater. 2023, 8 (2), 123– 138, DOI: 10.1038/s41578-022-00517-x5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XjtF2gsrvP&md5=6769af788ee460c1b00f9246194f148aFunctionalizing DNA origami to investigate and interact with biological systemsKnappe, Grant A.; Wamhoff, Eike-Christian; Bathe, MarkNature Reviews Materials (2023), 8 (2), 123-138CODEN: NRMADL; ISSN:2058-8437. (Nature Portfolio)A review. Abstr. DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophys. studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromol. cargos. Here, we review methods developed to functionalize, purify and characterize DNA origami nanostructures. We identify remaining challenges such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
- 6Oktay, E.; Alem, F.; Hernandez, K.; Girgis, M.; Green, C.; Mathur, D.; Medintz, I. L.; Narayanan, A.; Veneziano, R. DNA Origami Presenting the Receptor Binding Domain of SARS-CoV-2 Elicit Robust Protective Immune Response. Commun. Biol. 2023, 6 (1), 308, DOI: 10.1038/s42003-023-04689-2There is no corresponding record for this reference.
- 7Ke, G.; Liu, M.; Jiang, S.; Qi, X.; Yang, Y. R.; Wootten, S.; Zhang, F.; Zhu, Z.; Liu, Y.; Yang, C. J.et al. Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold. Angew. Chem., Int. Ed. 2016, 55 (26), 7483– 7486, DOI: 10.1002/anie.201603183There is no corresponding record for this reference.
- 8Ramezani, H.; Dietz, H. Building Machines with DNA Molecules. Nat. Rev. Genet. 2020, 21 (1), 5– 26, DOI: 10.1038/s41576-019-0175-68https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvF2ru7%252FN&md5=3d18110085ea649fbd537c4db681b0b5Building machines with DNA moleculesRamezani, Hamid; Dietz, HendrikNature Reviews Genetics (2020), 21 (1), 5-26CODEN: NRGAAM; ISSN:1471-0056. (Nature Research)A review. In nature, DNA mols. carry the hereditary information. But DNA has phys. and chem. properties that make it attractive for uses beyond heredity. In this Review, we discuss the potential of DNA for creating machines that are both encoded by and built from DNA mols. We review the main methods of DNA nanostructure assembly, describe recent advances in building increasingly complex mol. structures and discuss strategies for creating machine-like nanostructures that can be actuated and move. We highlight opportunities for applications of custom DNA nanostructures as scientific tools to address challenges across biol., chem. and engineering.
- 9Zhang, Q.; Jiang, Q.; Li, N.; Dai, L.; Liu, Q.; Song, L.; Wang, J.; Li, Y.; Tian, J.; Ding, B.et al. DNA Origami as an In Vivo Drug Delivery Vehicle for Cancer Therapy. ACS Nano 2014, 8 (7), 6633– 6643, DOI: 10.1021/nn502058j9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVCru7bL&md5=3e6a85ec691c013ac04041221c67a87fDNA origami as an in vivo drug delivery vehicle for cancer therapyZhang, Qian; Jiang, Qiao; Li, Na; Dai, Luru; Liu, Qing; Song, Linlin; Wang, Jinye; Li, Yaqian; Tian, Jie; Ding, Baoquan; Du, YangACS Nano (2014), 8 (7), 6633-6643CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)Many chemotherapeutics used for cancer treatments encounter issues during delivery to tumors in vivo and may have high levels of systemic toxicity due to their nonspecific distribution. Various materials have been explored to fabricate nanoparticles as drug carriers to improve delivery efficiency. However, most of these materials suffer from multiple drawbacks, such as limited biocompatibility and inability to engineer spatially addressable surfaces that can be utilized for multifunctional activity. Here, we demonstrate that DNA origami possessed enhanced tumor passive targeting and long-lasting properties at the tumor region. Particularly, the triangle-shaped DNA origami exhibits optimal tumor passive targeting accumulation. The delivery of the known anticancer drug doxorubicin into tumors by self-assembled DNA origami nanostructures was performed, and this approach showed prominent therapeutic efficacy in vivo. The DNA origami carriers were prepd. through the self-assembly of M13mp18 phage DNA and hundreds of complementary DNA helper strands; the doxorubicin was subsequently noncovalently intercalated into these nanostructures. After conducting fluorescence imaging and safety evaluation, the doxorubicin-contg. DNA origami exhibited remarkable antitumor efficacy without observable systemic toxicity in nude mice bearing orthotopic breast tumors labeled with green fluorescent protein. Our results demonstrated the potential of DNA origami nanostructures as innovative platforms for the efficient and safe drug delivery of cancer therapeutics in vivo.
- 10Steinhauer, C.; Jungmann, R.; Sobey, T.; Simmel, F.; Tinnefeld, P. DNA Origami as a Nanoscopic Ruler for Super-Resolution Microscopy. Angew. Chem., Int. Ed. 2009, 48 (47), 8870– 8873, DOI: 10.1002/anie.20090330810https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtl2rs7bF&md5=1393182cb421cb86eb2a6acd2965f861DNA Origami as a Nanoscopic Ruler for Super-Resolution MicroscopySteinhauer, Christian; Jungmann, Ralf; Sobey, Thomas L.; Simmel, Friedrich C.; Tinnefeld, PhilipAngewandte Chemie, International Edition (2009), 48 (47), 8870-8873, S8870/1-S8870/6CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Resolving the distances: Rectangular DNA origami labeled with fluorophores at specific positions has been used as a nanoscopic ruler. Super-resoln. microscopy based on the subsequent localization of single mols. enables two fluorophores at a distance of about 90 nm to be optically resolved. This combination of subdiffraction imaging and DNA nanotechnol. opens up new avenues for studying nanostructures and their dynamics.
- 11Martin, T. G.; Bharat, T. A. M.; Joerger, A. C.; Bai, X.; Praetorius, F.; Fersht, A. R.; Dietz, H.; Scheres, S. H. W. Design of a Molecular Support for Cryo-EM Structure Determination. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 47, DOI: 10.1073/pnas.1612720113There is no corresponding record for this reference.
- 12Kramm, K.; Schröder, T.; Gouge, J.; Vera, A. M.; Gupta, K.; Heiss, F. B.; Liedl, T.; Engel, C.; Berger, I.; Vannini, A.et al. DNA Origami-Based Single-Molecule Force Spectroscopy Elucidates RNA Polymerase III Pre-Initiation Complex Stability. Nat. Commun. 2020, 11 (1), 2828, DOI: 10.1038/s41467-020-16702-x12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtFahsb%252FI&md5=356bf10ead928725a76a074b250d3e07DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stabilityKramm, Kevin; Schroeder, Tim; Gouge, Jerome; Vera, Andres Manuel; Gupta, Kapil; Heiss, Florian B.; Liedl, Tim; Engel, Christoph; Berger, Imre; Vannini, Alessandro; Tinnefeld, Philip; Grohmann, DinaNature Communications (2020), 11 (1), 2828CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Abstr.: The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the addnl. initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-mol. level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilize TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.
- 13Kretzmann, J. A.; Liedl, A.; Monferrer, A.; Mykhailiuk, V.; Beerkens, S.; Dietz, H. Gene- encoding DNA origami for mammalian cell expression. Nat. Commun. 2023, 14 (1), 1017, DOI: 10.1038/s41467-023-36601-1There is no corresponding record for this reference.
- 14Shen, W.; Zhong, H.; Neff, D.; Norton, M. L. NTA Directed Protein Nanopatterning on DNA Origami Nanoconstructs. J. Am. Chem. Soc. 2009, 131 (19), 6660– 6661, DOI: 10.1021/ja901407j14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXltFemsbs%253D&md5=e54508dad59565401422d1c46ea0422eNTA Directed Protein Nanopatterning on DNA Origami NanoconstructsShen, Wanqiu; Zhong, Hong; Neff, David; Norton, Michael L.Journal of the American Chemical Society (2009), 131 (19), 6660-6661CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Precisely patterning proteins and other mols. at the nanoscale is crucial to future biosensing and optoelectronic applications. One- and two-dimensional DNA nanoconstructs have proven to be useful scaffolds for nanopatterning. This paper demonstrates the application of nitrilotriacetic acid (NTA) forming chelate complexes to localize histidine (His) tagged proteins via Ni2+ ions onto DNA based structures. Particularly, enhanced green fluorescent protein (EGFP) was directed to sp. surface locations on a designed DNA Origami nanoconstruct, and the resulting EGFP nanopattern was visualized using at. force microscopy (AFM).
- 15Voigt, N. V.; To̷rring, T.; Rotaru, A.; Jacobsen, M. F.; Ravnsbæk, J. B.; Subramani, R.; Mamdouh, W.; Kjems, J.; Mokhir, A.; Besenbacher, F.et al. Single-Molecule Chemical Reactions on DNA Origami. Nat. Nanotechnol. 2010, 5 (3), 200– 203, DOI: 10.1038/nnano.2010.515https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXislais78%253D&md5=5ae93254bf59d7cd04b18ce8e48724eeSingle-molecule chemical reactions on DNA origamiVoigt, Niels V.; Torring, Thomas; Rotaru, Alexandru; Jacobsen, Mikkel F.; Ravnsbaek, Jens B.; Subramani, Ramesh; Mamdouh, Wael; Kjems, Jorgen; Mokhir, Andriy; Besenbacher, Flemming; Gothelf, Kurt VesteragerNature Nanotechnology (2010), 5 (3), 200-203CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)DNA nanotechnol. and particularly DNA origami, in which long, single-stranded DNA mols. are folded into predetd. shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chem., optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomols. can also be integrated into DNA nanostructures and imaged. Here, we show that chem. reactions with single mols. can be performed and imaged at a local position on a DNA origami scaffold by at. force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions obsd. in these expts. demonstrate the feasibility of post-assembly chem. modification of DNA nanostructures and their potential use as locally addressable solid supports.
- 16Kuzuya, A.; Kimura, M.; Numajiri, K.; Koshi, N.; Ohnishi, T.; Okada, F.; Komiyama, M. Precisely Programmed and Robust 2D Streptavidin Nanoarrays by Using Periodical Nanometer-Scale Wells Embedded in DNA Origami Assembly. ChemBiochem 2009, 10 (11), 1811– 1815, DOI: 10.1002/cbic.200900229There is no corresponding record for this reference.
- 17Chhabra, R.; Sharma, J.; Ke, Y.; Liu, Y.; Rinker, S.; Lindsay, S.; Yan, H. Spatially Addressable Multiprotein Nanoarrays Templated by Aptamer-Tagged DNA Nanoarchitectures. J. Am. Chem. Soc. 2007, 129 (34), 10304– 10305, DOI: 10.1021/ja072410u17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXos1Sksbs%253D&md5=16c7e974dcc65bae02b3d40a479478ccSpatially Addressable Multiprotein Nanoarrays Templated by Aptamer-Tagged DNA NanoarchitecturesChhabra, Rahul; Sharma, Jaswinder; Ke, Yonggang; Liu, Yan; Rinker, Sherri; Lindsay, Stuart; Yan, HaoJournal of the American Chemical Society (2007), 129 (34), 10304-10305CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Here the authors generalize a highly programmable strategy to self-assemble multiprotein nanoarrays with deterministic positional addressability. These protein nanoarrays were templated by aptamer-tagged DNA nanoarchitectures. Arrays of proteins with precisely controlled positions and interprotein spacings offer great potential in proteomics, tissue engineering, and medical diagnostics.
- 18Nakata, E.; Liew, F. F.; Uwatoko, C.; Kiyonaka, S.; Mori, Y.; Katsuda, Y.; Endo, M.; Sugiyama, H.; Morii, T. Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures. Angew. Chem., Int. Ed. 2012, 51 (10), 2421– 2424, DOI: 10.1002/anie.201108199There is no corresponding record for this reference.
- 19Linko, V.; Keller, A. Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions. Small 2023, 19, 2301935, DOI: 10.1002/smll.20230193519https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXosVKks7s%253D&md5=5f0c2287247b9a22089da60e3befe444Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular InteractionsLinko, Veikko; Keller, AdrianSmall (2023), 19 (34), 2301935CODEN: SMALBC; ISSN:1613-6810. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. Programmable, custom-shaped, and nanometer-precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnol. and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiol. conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct mol.-level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Addnl., specific issues demanding further investigation are identified. This review - through its specific viewpoint - may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiol. media.
- 20Rajendran, A.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-Assembly. J. Am. Chem. Soc. 2011, 133 (37), 14488– 14491, DOI: 10.1021/ja204546h20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtV2isbfO&md5=1e105ad880f0f23a80749ac9733b4e83Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-AssemblyRajendran, Arivazhagan; Endo, Masayuki; Katsuda, Yousuke; Hidaka, Kumi; Sugiyama, HiroshiJournal of the American Chemical Society (2011), 133 (37), 14488-14491CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Heat tolerance of DNA origami structures has been improved about 30 °C by photo-crosslinking of 8-methoxypsoralen. To demonstrate one of its applications, the crosslinked origami were used for higher-temp. self-assembly, which markedly increased the yield of the assembled product when compared to the self-assembly of non-crosslinked origami at lower-temp. By contrast, at higher-temp. annealing, native non-crosslinked tiles did not self-assemble to yield the desired product; however, they formed a non-specific broken structure.
- 21Ramakrishnan, S.; Krainer, G.; Grundmeier, G.; Schlierf, M.; Keller, A. Structural Stability of DNA Origami Nanostructures in the Presence of Chaotropic Agents. Nanoscale 2016, 8 (19), 10398– 10405, DOI: 10.1039/C6NR00835F21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xms1Wju74%253D&md5=71250697b13ab6e2b46195da7beb959fStructural stability of DNA origami nanostructures in the presence of chaotropic agentsRamakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, AdrianNanoscale (2016), 8 (19), 10398-10405CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)DNA origami represent powerful platforms for single-mol. investigations of biomol. processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concn. and temp. At room temp., the DNA origami triangles are stable up to at least 24 h in both denaturants at concns. as high as 6 M. At elevated temps., however, structural stability is governed by variations in the melting temp. of the individual staple strands. Therefore, the global melting temp. of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temp., its attack results in less structural damage than obsd. for urea under equiv. conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual exptl. requirements. Overall, their high stability renders DNA origami promising platforms for biomol. studies in the presence of chaotropic agents, including single-mol. protein folding or structural switching.
- 22Martin, T. G.; Dietz, H. Magnesium-Free Self-Assembly of Multi-Layer DNA Objects. Nat. Commun. 2012, 3 (1), 1103, DOI: 10.1038/ncomms209522https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3s%252FitF2guw%253D%253D&md5=25e8a9da6130f0460adad1d8ddb557b5Magnesium-free self-assembly of multi-layer DNA objectsMartin Thomas G; Dietz HendrikNature communications (2012), 3 (), 1103 ISSN:.Molecular self-assembly with DNA offers a route for building user-defined nanoscale objects, but an apparent requirement for magnesium in solution has limited the range of conditions for which practical utility of such objects may be achieved. Here we report conditions for assembling templated multi-layer DNA objects in the presence of monovalent ions, showing that neither divalent cations in general or magnesium in particular are essential ingredients for the successful assembly of such objects. The percentage of DNA strands in an object that do not form thermally stable double-helical DNA domains (T(m)>45 °C) with the template molecule correlated with the sodium requirements for obtaining folded objects. Minimizing the fraction of such weakly binding strands by rational design choices enhanced the yield of folding. The results support the view that DNA-based nanodevices may be designed and produced for a variety of target environments.
- 23Kim, H.; Surwade, S. P.; Powell, A.; O’Donnell, C.; Liu, H. Stability of DNA Origami Nanostructure under Diverse Chemical Environments. Chem. Mater. 2014, 26 (18), 5265– 5273, DOI: 10.1021/cm501966323https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVSrtb%252FI&md5=b676d6d7c7e79549f9fe5adb5137a1d4Stability of DNA Origami Nanostructure under Diverse Chemical EnvironmentsKim, Hyojeong; Surwade, Sumedh P.; Powell, Anna; O'Donnell, Christina; Liu, HaitaoChemistry of Materials (2014), 26 (18), 5265-5273CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)The authors report the effect of chem. and phys. treatments on the structural stability of DNA origami nanostructures. The DNA nanostructure maintains its shape under harsh processing conditions, including thermal annealing up to 200°C for 10 min, immersing in a wide range of org. solvents for up to 24 h, brief exposure to alk. aq. solns., and 5 min exposure to UV/O3. These results suggest that the application window of DNA nanostructure is significantly wider than previously believed.
- 24Chandrasekaran, A. R. Nuclease Resistance of DNA Nanostructures. Nat. Rev. Chem. 2021, 5 (4), 225– 239, DOI: 10.1038/s41570-021-00251-y24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXosFers70%253D&md5=699982fbddaa5e245fee0d6091d45a65Nuclease resistance of DNA nanostructuresChandrasekaran, Arun RichardNature Reviews Chemistry (2021), 5 (4), 225-239CODEN: NRCAF7; ISSN:2397-3358. (Nature Portfolio)A review. DNA nanotechnol. has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biol. applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biol. applications is their susceptibility to attack by nucleases present in the physiol. environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biol. fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degrdn. and quantify stability.
- 25Schaffter, S. W.; Green, L. N.; Schneider, J.; Subramanian, H. K. K.; Schulman, R.; Franco, E. T7 RNA Polymerase Non-Specifically Transcribes and Induces Disassembly of DNA Nanostructures. Nucleic Acids Res. 2018, 46 (10), 5332– 5343, DOI: 10.1093/nar/gky283There is no corresponding record for this reference.
- 26Rajendran, A.; Krishnamurthy, K.; Giridasappa, A.; Nakata, E.; Morii, T. Stabilization and Structural Changes of 2D DNA Origami by Enzymatic Ligation. Nucleic Acids Res. 2021, 49 (14), 7884– 7900, DOI: 10.1093/nar/gkab61126https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXisVCqt7vK&md5=481bc4cdc8a3d43c5a61bb82d9d203f2Stabilization and structural changes of 2D DNA origami by enzymatic ligationRajendran, Arivazhagan; Krishnamurthy, Kirankumar; Giridasappa, Amulya; Nakata, Eiji; Morii, TakashiNucleic Acids Research (2021), 49 (14), 7884-7900CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In mol. biol., enzymic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnol., the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed anal. and optimization of the conditions for the enzymic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temp., and typically requires much higher concn. of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a max. ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concn.-dependent manner.
- 27Weizenmann, N.; Scheidgen-Kleyboldt, G.; Ye, J.; Krause, C. B.; Kauert, D.; Helmi, S.; Rouillon, C.; Seidel, R. Chemical Ligation of an Entire DNA Origami Nanostructure. Nanoscale 2021, 13 (41), 17556– 17565, DOI: 10.1039/D1NR04225D27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXitFaqtbbM&md5=839f87dd89c32e95d02ca0f24f2b9c9aChemical ligation of an entire DNA origami nanostructureWeizenmann, Nicole; Scheidgen-Kleyboldt, Gerda; Ye, Jingjing; Krause, Cordula B.; Kauert, Dominik; Helmi, Seham; Rouillon, Christophe; Seidel, RalfNanoscale (2021), 13 (41), 17556-17565CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)Within the field of DNA nanotechnol., numerous methods were developed to produce complex two- and three-dimensional DNA nanostructures for many different emerging applications. These structures typically suffer from a low tolerance against non-optimal environmental conditions including elevated temps. Here, we apply a chem. ligation method to covalently seal the nicks between adjacent 5 phosphorylated and 3 amine-modified strands within the DNA nanostructures. Using a cost-effective enzymic strand modification procedure, we are able to batch-modify all DNA strands even of large DNA objects, such as origami nanostructures. The covalent strand linkage increases the temp. stability of the structures by ~ 10 K. Generally, our method also allows a 'surgical' introduction of covalent strand linkages at preselected positions. It can also be used to map the strand ligation into chains throughout the whole nanostructure and identify assembly defects. We expect that our method can be applied to a large variety of DNA nanostructures, in particular when full control over the introduced covalent linkages and the absence of side adducts and DNA damages are required.
- 28Cassinelli, V.; Oberleitner, B.; Sobotta, J.; Nickels, P.; Grossi, G.; Kempter, S.; Frischmuth, T.; Liedl, T.; Manetto, A. One-Step Formation of “Chain-Armor”-Stabilized DNA Nanostructures. Angew. Chem., Int. Ed. 2015, 54 (27), 7795– 7798, DOI: 10.1002/anie.20150056128https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXosVGjsbc%253D&md5=9cdc08d2063e1316ee00ca29cefa9ef8One-Step Formation of "Chain-Armor"-Stabilized DNA NanostructuresCassinelli, Valentina; Oberleitner, Birgit; Sobotta, Jessica; Nickels, Philipp; Grossi, Guido; Kempter, Susanne; Frischmuth, Thomas; Liedl, Tim; Manetto, AntonioAngewandte Chemie, International Edition (2015), 54 (27), 7795-7798CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)DNA-based self-assembled nanostructures are widely used to position org. and inorg. objects with nanoscale precision. A particular promising application of DNA structures is their usage as programmable carrier systems for targeted drug delivery. To provide DNA-based templates that are robust against degrdn. at elevated temps., low ion concns., adverse pH conditions, and DNases, we built 6-helix DNA tile tubes consisting of 24 oligonucleotides carrying alkyne groups on their 3'-ends and azides on their 5'-ends. By a mild click reaction, the two ends of selected oligonucleotides were covalently connected to form rings and interlocked DNA single strands, so-called DNA catenanes. Strikingly, the structures stayed topol. intact in pure water and even after pptn. from EtOH. The structures even withstood a temp. of 95 °C when all of the 24 strands were chem. interlocked.
- 29Gerling, T.; Kube, M.; Kick, B.; Dietz, H. Sequence-Programmable Covalent Bonding of Designed DNA Assemblies. Sci. Adv. 2018, 4 (8), eaau1157 DOI: 10.1126/sciadv.aau1157There is no corresponding record for this reference.
- 30Engelhardt, F. A. S.; Praetorius, F.; Wachauf, C. H.; Brüggenthies, G.; Kohler, F.; Kick, B.; Kadletz, K. L.; Pham, P. N.; Behler, K. L.; Gerling, T.et al. Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds. ACS Nano 2019, 13 (5), 5015– 5027, DOI: 10.1021/acsnano.9b0102530https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXnsV2ktbo%253D&md5=2fb7ea8b75471e18715911c299deeeb9Custom-Size, Functional, and Durable DNA Origami with Design-Specific ScaffoldsEngelhardt, Floris A. S.; Praetorius, Florian; Wachauf, Christian H.; Brueggenthies, Gereon; Kohler, Fabian; Kick, Benjamin; Kadletz, Karoline L.; Pham, Phuong Nhi; Behler, Karl L.; Gerling, Thomas; Dietz, HendrikACS Nano (2019), 13 (5), 5015-5027CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA origami nano-objects are usually designed around generic single-stranded "scaffolds". Many properties of the target object are detd. by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable prodn. methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence compn. on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent crosslinking of DNA origami via UV irradn., and we built DNAzyme-contg. scaffolds that allow postfolding DNA origami domain sepn.
- 31Chen, H.; Li, R.; Li, S.; Andréasson, J.; Choi, J. H. Conformational Effects of UV Light on DNA Origami. J. Am. Chem. Soc. 2017, 139 (4), 1380– 1383, DOI: 10.1021/jacs.6b1082131https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtVKhsro%253D&md5=1d9fa46fb2d7d2fe2b2458cea89ea58cConformational Effects of UV Light on DNA OrigamiChen, Haorong; Li, Ruixin; Li, Shiming; Andreasson, Joakim; Choi, Jong HyunJournal of the American Chemical Society (2017), 139 (4), 1380-1383CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The responses of DNA origami conformation to UV radiation of different wavelengths and doses are investigated. Short and medium wavelength UV light can cause photolesions in DNA origami. At moderate doses, the lesions do not cause any visible defects in the origami, nor do they significantly affect the hybridization capability. Instead, they help relieve the internal stress in the origami structure and restore it to the designed conformation. At high doses, staple dissocn. increases and causes structural disintegration. Long wavelength UV does not show any effect on origami conformation by itself. We show that this UV range can be used in conjunction with photoactive mols. for photoreconfiguration, while avoiding any damage to the DNA structures.
- 32Moser, H. E.; Dervan, P. B. Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation. Science 1987, 238 (4827), 645– 650, DOI: 10.1126/science.311846332https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXltVKitA%253D%253D&md5=15690e4871f93135460d2ea26516ab38Sequence-specific cleavage of double helical DNA by triple helix formationMoser, Heinz E.; Dervan, Peter B.Science (Washington, DC, United States) (1987), 238 (4827), 645-50CODEN: SCIEAS; ISSN:0036-8075.Homopyrimidine oligodeoxyribonucleotides with EDTA-Fe attached at a single position bind the corresponding homopyrimidine-homopurine tracts within large double-stranded DNA by triple helix formation and cleave at that site. Oligonucleotides with EDTA-Fe at the 5' end cause a sequence specific double strand break. The location and asymmetry of the cleavage pattern reveal that the homopyrimidine-EDTA probes bind in the major groove parallel to the homopurine strand of Watson-Crick double helical DNA. The sequence-specific recognition of double helical DNA by homopyrimidine probes is sensitive to single base mismatches. Homopyrimidine probes equipped with DNA cleaving moieties could be useful tools for mapping chromosomes.
- 33Dalla Pozza, M.; Abdullrahman, A.; Cardin, C. J.; Gasser, G.; Hall, J. P. Three’s a Crowd – Stabilisation, Structure, and Applications of DNA Triplexes. Chem. Sci. 2022, 13 (35), 10193– 10215, DOI: 10.1039/D2SC01793HThere is no corresponding record for this reference.
- 34Chandrasekaran, A. R.; Rusling, D. A. Triplex-Forming Oligonucleotides: A Third Strand for DNA Nanotechnology. Nucleic Acids Res. 2018, 46 (3), 1021– 1037, DOI: 10.1093/nar/gkx123034https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXitlGisr%252FL&md5=c7e6d1549a0fabc2b0355b4740ca643dTriplex-forming oligonucleotides: a third strand for DNA nanotechnologyChandrasekaran, Arun Richard; Rusling, David A.Nucleic Acids Research (2018), 46 (3), 1021-1037CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)A review. DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.
- 35Hu, Y.; Cecconello, A.; Idili, A.; Ricci, F.; Willner, I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew. Chem., Int. Ed. 2017, 56 (48), 15210– 15233, DOI: 10.1002/anie.20170186835https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslygsrzJ&md5=67320244b500dec9d4e96494f89a1e5bTriplex DNA Nanostructures: From Basic Properties to ApplicationsHu, Yuwei; Cecconello, Alessandro; Idili, Andrea; Ricci, Francesco; Willner, ItamarAngewandte Chemie, International Edition (2017), 56 (48), 15210-15233CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and mol. switches. Furthermore, the pH-induced, switchable assembly and dissocn. of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-org. frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-soln. transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
- 36Rusling, D. A.; Nandhakumar, I. S.; Brown, T.; Fox, K. R. Triplex-Directed Recognition of a DNA Nanostructure Assembled by Crossover Strand Exchange. ACS Nano 2012, 6 (4), 3604– 3613, DOI: 10.1021/nn300718z36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XksFWgsLs%253D&md5=2d238b3f015411a38517a7f9577d759dTriplex-Directed Recognition of a DNA Nanostructure Assembled by Crossover Strand ExchangeRusling, David A.; Nandhakumar, Iris S.; Brown, Tom; Fox, Keith R.ACS Nano (2012), 6 (4), 3604-3613CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA has been widely exploited for the self-assembly of nanosized objects and arrays that offer the potential to act as scaffolds for the spatial positioning of mol. components with nanometer precision. Methods that allow the targeting of components to specific locations within these structures are therefore highly sought after. Here the authors report that the triplex approach to DNA recognition, which relies on the specific binding of an oligonucleotide within the major groove of double-helical DNA, can be exploited to recognize specific loci within a DNA double-crossover tile and array, a nanostructure assembled by crossover strand exchange. The oligonucleotide can be targeted to both crossover and noncrossover strands and, surprisingly, across the region spanning the crossover junction itself. Moreover, by attaching biotin to the end of the oligonucleotide, the authors show that streptavidin mols. can be recruited to precise locations within a DX array, with an av. spacing of 31.9 (±1.3) nm. This is a promising approach that could be exploited to introduce other components compatible with oligonucleotide synthesis into the wide variety of DNA nanostructures assembled by crossover strand exchange, such as those generated by DNA origami.
- 37Rusling, D. A.; Chandrasekaran, A. R.; Ohayon, Y. P.; Brown, T.; Fox, K. R.; Sha, R.; Mao, C.; Seeman, N. C. Functionalizing Designer DNA Crystals with a Triple-Helical Veneer. Angew. Chem., Int. Ed. 2014, 53 (15), 3979– 3982, DOI: 10.1002/anie.201309914There is no corresponding record for this reference.
- 38Zhao, Y.; Chandrasekaran, A. R.; Rusling, D. A.; Woloszyn, K.; Hao, Y.; Hernandez, C.; Vecchioni, S.; Ohayon, Y. P.; Mao, C.; Seeman, N. C.et al. The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals. J. Am. Chem. Soc. 2023, 145 (6), 3599– 3605, DOI: 10.1021/jacs.2c1266738https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXitlamtr0%253D&md5=4a6231a9066dbe1a5909455f3cc2b794The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA CrystalsZhao, Yue; Chandrasekaran, Arun Richard; Rusling, David A.; Woloszyn, Karol; Hao, Yudong; Hernandez, Carina; Vecchioni, Simon; Ohayon, Yoel P.; Mao, Chengde; Seeman, Nadrian C.; Sha, RuojieJournal of the American Chemical Society (2023), 145 (6), 3599-3605CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnol. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addn. of the Watson-Crick complement to a TFO contg. a short toehold, and (c) the addn. of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.
- 39Takasugi, M.; Guendouz, A.; Chassignol, M.; Decout, J. L.; Lhomme, J.; Thuong, N. T.; Hélène, C. Sequence-Specific Photo-Induced Cross-Linking of the Two Strands of Double-Helical DNA by a Psoralen Covalently Linked to a Triple Helix-Forming Oligonucleotide. Proc. Natl. Acad. Sci. U. S. A. 1991, 88 (13), 5602– 5606, DOI: 10.1073/pnas.88.13.5602There is no corresponding record for this reference.
- 40Abdallah, H. O.; Ohayon, Y. P.; Chandrasekaran, A. R.; Sha, R.; Fox, K. R.; Brown, T.; Rusling, D. A.; Mao, C.; Seeman, N. C. Stabilisation of Self-Assembled DNA Crystals by Triplex-Directed Photo-Cross-Linking. Chem. Commun. 2016, 52 (51), 8014– 8017, DOI: 10.1039/C6CC03695C40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xptl2rs7g%253D&md5=ebd58f07b1601808ee11c72c1fc90d75Stabilization of self-assembled DNA crystals by triplex-directed photocrosslinkingAbdallah, Hatem O.; Ohayon, Yoel P.; Chandrasekaran, Arun Richard; Sha, Ruojie; Fox, Keith R.; Brown, Tom; Rusling, David A.; Mao, Chengde; Seeman, Nadrian C.Chemical Communications (Cambridge, United Kingdom) (2016), 52 (51), 8014-8017CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)The tensegrity triangle is a robust DNA motif that can self-assemble to generate macroscopic 3-dimensional crystals. However, the stability of these crystals is dependent on the high ionic conditions used for crystal growth. Here, the authors demonstrate that a triplex-forming oligonucleotide can be used to direct the specific intercalation, and subsequent photocrosslinking, of 4,5',8-trimethylpsoralen to single or multiple loci within or between the tiles of the crystal. Crosslinking between the tiles of the crystal improves their thermostability. Such an approach is likely to facilitate the removal of crystals from their mother liquor and may prove useful for applications that require greater crystal stability.
- 41Rusling, D. A.; Nandhakumar, I. S.; Brown, T.; Fox, K. R. Triplex-Directed Covalent Cross-Linking of a DNA Nanostructure. Chem. Commun. 2012, 48 (77), 9592, DOI: 10.1039/c2cc35407a41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xht12qsrrF&md5=b87508de0cf0ee210a955035a14cad7fTriplex-directed covalent cross-linking of a DNA nanostructureRusling, David A.; Nandhakumar, Iris S.; Brown, Tom; Fox, Keith R.Chemical Communications (Cambridge, United Kingdom) (2012), 48 (77), 9592-9594CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)The triplex approach to DNA recognition is exploited to direct covalent inter-strand crosslinks to unique locations within a pre-assembled DNA nanostructure. This approach can be used to improve the stability of DNA nanostructures and demonstrates the feasibility of directing other reactive groups to unique locations within these complexes.
- 42Lin, C.; Perrault, S. D.; Kwak, M.; Graf, F.; Shih, W. M. Purification of DNA-Origami Nanostructures by Rate-Zonal Centrifugation. Nucleic Acids Res. 2013, 41 (2), e40–e40 DOI: 10.1093/nar/gks1070There is no corresponding record for this reference.
- 43Suma, A.; Stopar, A.; Nicholson, A. W.; Castronovo, M.; Carnevale, V. Global and Local Mechanical Properties Control Endonuclease Reactivity of a DNA Origami Nanostructure. Nucleic Acids Res. 2020, 48 (9), 4672– 4680, DOI: 10.1093/nar/gkaa08043https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisVKltbbI&md5=7ed9978d7d2126dbaeefaf14a1b5cdb9Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructureSuma, Antonio; Stopar, Alex; Nicholson, Allen W.; Castronovo, Matteo; Carnevale, VincenzoNucleic Acids Research (2020), 48 (9), 4672-4680CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)We used coarse-grained mol. dynamics simulations to characterize the global and local mech. properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations sepd. by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the exptl. data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40 nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.
- 44Mallik, L.; Dhakal, S.; Nichols, J.; Mahoney, J.; Dosey, A. M.; Jiang, S.; Sunahara, R. K.; Skiniotis, G.; Walter, N. G. Electron microscopic visualisation of protein assemblies on flattened DNA origami. ACS Nano 2015, 9 (7), 7133– 7141, DOI: 10.1021/acsnano.5b0184144https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFWqtrjI&md5=97318b99c98d1742021acc5f4f327f95Electron Microscopic Visualization of Protein Assemblies on Flattened DNA OrigamiMallik, Leena; Dhakal, Soma; Nichols, Joseph; Mahoney, Jacob; Dosey, Anne M.; Jiang, Shuoxing; Sunahara, Roger K.; Skiniotis, Georgios; Walter, Nils G.ACS Nano (2015), 9 (7), 7133-7141CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small mols. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concn. of DMSO, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest mol. assemblies for biochem. and nanotechnol. applications.
- 45Bates, P. J.; Macaulay, V. M.; McLean, M. J.; Jenkins, T. C.; Reszka, A. P.; Laughton, C. J.; Neidle, S. Characteristics of triplex-directed photoadduct formation by psoralen-linked oligodeoxynucleotides. Nucleic Acids Res. 1995, 23 (21), 4283– 4289, DOI: 10.1093/nar/23.21.4283There is no corresponding record for this reference.
- 46Rusling, D. A. Triplex-Forming Properties and Enzymatic Incorporation of a Base-Modified Nucleotide Capable of Duplex DNA Recognition at Neutral PH. Nucleic Acids Res. 2021, 49 (13), 7256– 7266, DOI: 10.1093/nar/gkab572There is no corresponding record for this reference.
- 47Zhang, Z.; Park, S.; Pertsinidis, A.; Revyakin, A. Cloud-Point PEG Glass Surfaces for Imaging of Immobilized Single Molecules by Total-Internal-Reflection Microscopy. BIO-Protoc. 2016, 6 (7), e1784--e1784 DOI: 10.21769/BioProtoc.1784There is no corresponding record for this reference.
- 48Katz, B. A. Binding of Biotin to Streptavidin Stabilizes Intersubunit Salt Bridges between Asp61 and His87 at Low PH. J. Mol. Biol. 1997, 274 (5), 776– 800, DOI: 10.1006/jmbi.1997.1444There is no corresponding record for this reference.
- 49Wei, X.; Nangreave, J.; Jiang, S.; Yan, H.; Liu, Y. Mapping the Thermal Behavior of DNA Origami Nanostructures. J. Am. Chem. Soc. 2013, 135 (16), 6165– 6176, DOI: 10.1021/ja400072849https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXkslahs74%253D&md5=4f272f89d8cd7d75d282e146f6631297Mapping the Thermal Behavior of DNA Origami NanostructuresWei, Xixi; Nangreave, Jeanette; Jiang, Shuoxing; Yan, Hao; Liu, YanJournal of the American Chemical Society (2013), 135 (16), 6165-6176CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Understanding the thermodn. properties of complex DNA nanostructures, including rationally designed two- and three-dimensional (2D and 3D, resp.) DNA origami, facilitates more accurate spatiotemporal control and effective functionalization of the structures by other elements. In this work fluorescein and tetramethylrhodamine (TAMRA), a Foerster resonance energy transfer (FRET) dye pair, were incorporated into selected staples within various 2D and 3D DNA origami structures. We monitored the temp.-dependent changes in FRET efficiency that occurred as the dye-labeled structures were annealed and melted and subsequently extd. information about the associative and dissociative behavior of the origami. In particular, we examd. the effects of local and long-range structural defects (omitted staple strands) on the thermal stability of common DNA origami structures. The results revealed a significant decrease in thermal stability of the structures in the vicinity of the defects, in contrast to the negligible long-range effects that were obsd. Furthermore, we probed the global assembly and disassembly processes by comparing the thermal behavior of the FRET pair at several different positions. We demonstrated that the staple strands located in different areas of the structure all exhibit highly cooperative hybridization but have distinguishable melting temps. depending on their positions. This work underscores the importance of understanding fundamental aspects of the self-assembly of DNA nanostructures and can be used to guide the design of more complicated DNA nanostructures, to optimize annealing protocol and manipulate functionalized DNA nanostructures.
- 50Patrick, M.; Dennis, P. P.; Ehrenberg, M.; Bremer, H. Free RNA Polymerase in Escherichia Coli. Biochimie 2015, 119, 80– 91, DOI: 10.1016/j.biochi.2015.10.015There is no corresponding record for this reference.
- 51Jackson, D. A.; Pombo, A.; Iborra, F. The Balance Sheet for Transcription: An Analysis of Nuclear RNA Metabolism in Mammalian Cells. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 2000, 14 (2), 242– 254, DOI: 10.1096/fasebj.14.2.242There is no corresponding record for this reference.
- 52Lan, Y.; Leemis, L. M. The logistic-exponential survival distribution. Nav. Res. Logistics 2008, 55 (3), 252– 264, DOI: 10.1002/nav.20279There is no corresponding record for this reference.
- 53Smith, S. I.; Brodbelt, J. S. Rapid Characterization of Cross-Links, Mono-Adducts, and Non-Covalent Binding of Psoralens to Deoxyoligonucleotides by LC-UV/ESI-MS and IRMPD Mass Spectrometry. Analyst 2010, 135 (5), 943, DOI: 10.1039/b924023cThere is no corresponding record for this reference.
- 54Li, H.; Broughton-Head, V. J.; Peng, G.; Powers, V. E. C.; Ovens, M. J.; Fox, K. R.; Brown, T. Triplex Staples: DNA Double-Strand Cross-Linking at Internal and Terminal Sites Using Psoralen-Containing Triplex-Forming Oligonucleotides. Bioconjugate Chem. 2006, 17 (6), 1561– 1567, DOI: 10.1021/bc060187554https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1WqtLbF&md5=74c3364df912fc5a85507a9453cd7928Triplex Staples: DNA Double-Strand Cross-Linking at Internal and Terminal Sites Using Psoralen-Containing Triplex-Forming OligonucleotidesLi, Hong; Broughton-Head, Victoria J.; Peng, Guomei; Powers, Vicki E. C.; Ovens, Matthew J.; Fox, Keith R.; Brown, TomBioconjugate Chemistry (2006), 17 (6), 1561-1567CODEN: BCCHES; ISSN:1043-1802. (American Chemical Society)A method has been developed to attach 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen to the 5 position of thymine bases during solid-phase oligonucleotide synthesis. UV irradn. of triplex-forming oligonucleotides (TFOs) contg. internally attached psoralens produces photoadducts at TpA steps within target duplexes, thus relaxing the constraints on selection of psoralen target sequences. Photoreaction of TFOs contg. two psoralens, located at the 5'- and 3'-ends, has been used to create double-strand cross-links (triplex staples) at both termini of the TFO. Such complexes have no free single-stranded ends. TFOs contg. 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen, 3-methyl-2-aminopyridine, and 5-(3-aminoprop-2-ynyl)deoxyuridine formed photoadducts with target duplexes under near-physiol. conditions.
- 55Walsh, S.; El-Sagheer, A. H.; Brown, T. Fluorogenic Thiazole Orange TOTFO Probes Stabilise Parallel DNA Triplexes at PH 7 and Above. Chem. Sci. 2018, 9 (39), 7681– 7687, DOI: 10.1039/C8SC02418AThere is no corresponding record for this reference.
- 56Sachenbacher, K.; Khoshouei, A.; Honemann, M. N.; Engelen, W.; Feigl, E.; Dietz, H. Triple-Stranded DNA As a Structural Element in DNA Origami. ACS Nano 2023, 17 (10), 9014– 9024, DOI: 10.1021/acsnano.2c1140256https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXpsFWmsb0%253D&md5=24a28642b7f5e44398888a96effa5ed3Triple-Stranded DNA As a Structural Element in DNA OrigamiSachenbacher, Ken; Khoshouei, Ali; Honemann, Maximilian Nicolas; Engelen, Wouter; Feigl, Elija; Dietz, HendrikACS Nano (2023), 17 (10), 9014-9024CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)Mol. self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional objects. To expand the palette of structural motifs in DNA origami, here we describe hybrid duplex-triplex DNA motifs as pH-dependent building blocks in DNA origami. We investigate design rules for incorporating triplex forming oligonucleotides and noncanonical duplex-triplex crossovers in multilayer DNA origami objects. We use single-particle cryoelectron microscopy to elucidate the structural basis of triplex domains and of duplex-triplex crossovers. We find that duplex-triplex crossovers can complement and fully replace the canonical duplex-duplex crossovers within DNA origami objects, for example, to increase the crossover d. for potentially greater rigidity and reduced interhelical spacing, and to create connections at sites where conventional crossovers may be undesirable. We also show the pH-induced formation of a DNA origami object stabilized entirely by triplex-mediated strand crossovers.
- 57Ng, C.; Samanta, A.; Mandrup, O. A.; Tsang, E.; Youssef, S.; Klausen, L. H.; Dong, M.; Nijenhuis, M. A. D.; Gothelf, K. V. Folding Double-Stranded DNA into Designed Shapes with Triplex-Forming Oligonucleotides. Adv. Mater. 2023, 35, 2302497, DOI: 10.1002/adma.202302497There is no corresponding record for this reference.
- 58Dynan, W. S.; Burgess, R. R. In Vitro Transcription by Wheat Germ RNA Polymerase II. Initiation of RNA Synthesis on Relaxed, Closed Circular Template. J. Biol. Chem. 1981, 256 (11), 5866– 5873, DOI: 10.1016/S0021-9258(19)69288-4There is no corresponding record for this reference.
- 59Dreyer, C.; Hausen, P. On the Initiation of Mammalian RNA Polymerase at Single-Strand Breaks in DNA. Eur. J. Biochem. 1976, 70 (1), 63– 74, DOI: 10.1111/j.1432-1033.1976.tb10956.xThere is no corresponding record for this reference.
- 60Chandler, D. W.; Gralla, J. The Interaction of RNA Polymerase II with Non-Promoter DNA Sites. Nucleic Acids Res. 1981, 9 (22), 6031– 6046, DOI: 10.1093/nar/9.22.6031There is no corresponding record for this reference.
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Supporting Information
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.4c03413.
Contains experimental methods, oligonucleotide and staple sequences, and additional AGE, PAGE, TEM, and AFM data (PDF)
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