Enzyme-Free Exponential Amplification via Growth and Scission of Crisscross Ribbons from Single-Stranded DNA ComponentsClick to copy article linkArticle link copied!
- Anastasia ErshovaAnastasia ErshovaDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United StatesWyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United StatesDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United StatesMore by Anastasia Ershova
- Dionis MinevDionis MinevDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United StatesWyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United StatesDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United StatesMore by Dionis Minev
- F. Eduardo Corea-DilbertF. Eduardo Corea-DilbertDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United StatesMore by F. Eduardo Corea-Dilbert
- Devon YuDevon YuDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United StatesMore by Devon Yu
- Jie DengJie DengDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United StatesWyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United StatesDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United StatesMore by Jie Deng
- Walter FontanaWalter FontanaDepartment of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United StatesMore by Walter Fontana
- William M. Shih*William M. Shih*Email: [email protected]Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United StatesWyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United StatesDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United StatesMore by William M. Shih
Abstract
The self-assembly of DNA-based monomers into higher-order structures has significant potential for realizing various biomimetic behaviors including algorithmic assembly, ultrasensitive detection, and self-replication. For these behaviors, it is desirable to implement high energetic barriers to undesired spurious nucleation, where such barriers can be bypassed via seed-initiated assembly. Joint-neighbor capture is a mechanism enabling the construction of such barriers while allowing for algorithmic behaviors, such as bit-copying. Cycles of polymerization with division could accordingly be used for implementing exponential growth in self-replicating materials. Previously, we demonstrated crisscross polymerization, a strategy that attains robust seed-dependent self-assembly of single-stranded DNA and DNA-origami monomers via joint-neighbor capture. Here, we expand the crisscross assembly to achieve autonomous, isothermal exponential amplification of ribbons through their concurrent growth and scission via toehold-mediated strand displacement. We demonstrate how this crisscross chain reaction, or 3CR, can be used as a detection strategy through coupling to single- and double-stranded nucleic acid targets and introduce a rule-based stochastic modeling approach for simulating molecular self-assembly behaviors such as crisscross-ribbon scission.
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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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Introduction
Results
Exponential Amplification via Ribbon Growth and Scission
Figure 1
Figure 1. Scission of a finite crisscross DNA structure through toehold-mediated displacement by a set of invader (i.e., cut) strands. (A) Principle of classical toehold-mediated strand displacement. An invader strand (green) engages a toehold domain on a substrate strand (light blue) and then proceeds to liberate a bound incumbent strand (dark blue) through branch migration. (B) Strand displacement where the substrate strand, including its toehold domain, is functionally replaced by a series of half-turn (5 or 6 bp) strand termini arranged on the face of a crisscross structure. (C) Fissure of a crisscross nanostructure through toehold-mediated recruitment of a set of invader strands followed by joint branch migration. (D) Analogous fissure of a crisscross ribbon fragment exhibiting xy growth (i.e., alternating staggered x and y slats). Light blue and gray boxes in B–D outline regions not involved in the strand displacement. See Figure 2 for how such a scission can be coupled with growth.
Figure 2
Figure 2. Principle of 3CR for exponential amplification of xy ribbons via isothermal growth and scission. (A) Schematic of the design for a v5 ribbon (detailed scadnano design in Supp. Figure 1C). Each intersection between a horizontal and vertical line represents a half-turn (5–6 base pairs) of dsDNA. Through linear growth, growth slats with single-stranded extensions are added to the ribbon in a specific order that allows cut slats to bind. Once bound, the cut slats compete with the growth slats via toehold-mediated strand displacement (see Supp. Movie 1 for a more in-depth view of ribbon scission via strand displacement). Once the cut slats had displaced the growth slats, the ribbon is severed into two fragments. Each of these fragments is capable of further growth and scission. (B) TEM image after ribbon growth without scission (mean length 409 nm, standard deviation 176 nm, based on 22 measurements). (C) TEM image after combined ribbon growth and scission (mean length of 44 nm, standard deviation of 19 nm, based on 226 measurements, corresponding to predominantly fully cut ribbons). Production of ribbons, long or short, is seed-dependent (see Figure 3). Note that linear ribbons appear twisted and irregular in width due to the use of 11 bp/turn and the presence of single-stranded extensions, which, when unbound, tend to cause aggregation. Scale bars: 200 nm. See “Assembly Reactions” for details of the conditions used. (D) Comparison of seeded and unseeded 3CR amplification at different slat concentrations with cy5-fluorophore 3′ labeling of the top x-slat from the repeat unit in A and Supp. Figure 1C (present at roughly 50% of the concentration of other growth slats). The red fluorescent signal (i.e., gel image captured with a red filter) is from this labeled x-slat, while the blue fluorescent signal (i.e., gel image captured with a blue filter) is from SYBR-Gold prestaining of the agarose gel. The fast-migrating bright species at the bottom of all agarose gels are unincorporated slats. See “Assembly Reactions” for details of conditions used.
Figure 3
Figure 3. Target-dependent nanoseed formation leading to the 3CR exponential growth of v5 ribbons. (A) Design of nanoseed formation from ssDNA or ssRNA, with coupling to v5 crisscross growth and scission (cut slats omitted from the cartoon for clarity). As in Figure 2A, one intersection between a horizontal and vertical line represents a half-turn (5–6 base pairs) of DNA. (B) Design of twinned-nanoseed formation from dsDNA. It is likely that nanoseed formation only proceeds efficiently for targets that are kinetically trapped in single-stranded states, e.g., through denaturation followed by incomplete renaturation, and that thereby are available for sequestration by the capture slats. (C) 3CR detection of different targets using a v5 design (p8064 ssDNA, JM109 E. coli dsDNA, MS2 RNA). The red fluorescent signal (i.e., gel image captured with a red filter) is from the top x-slat in Supp. Figure 1C labeled with a Cy5-fluorophore on its 3′ end, while the blue fluorescent signal (i.e., gel image captured with a blue filter) is from SYBR-Gold prestaining of the agarose gel. The fast-migrating bright species at the bottom of all agarose gels are the unincorporated slats. See “Assembly Reactions” for details of conditions used.
Detection of Nucleic Acid Targets
Stochastic Simulations of Ribbon Scission
Figure 4
Figure 4. Kappa simulations of scission of a two-repeat ribbon, in the absence of growth, for core slat length 10 (i.e., v5), extension length 5 (i.e., five-segment toeholds), and no wobbles. (A) Plot of 100 simulation trajectories tracking the number of slats in the ribbon. Scission breaks the ribbon into two complexes of comparable size. The four example graphs, depicted in pop-out squares, demonstrate a sequential maturation from the initial ribbon with two repeat-units and no cut-slats bound, followed by increases in complex size until all cut-slats are captured by the extensions, followed by scission. In the graphs, colored circles each represent a single slat, and edges are the bonds between them. (B) Simulations showing mean time to scission versus slat length, corresponding to the ribbon width, with 5-segment toeholds and no wobbles (trajectories for the core slat length 10 shown in (A)). Every data point (white circle) is a mean of 100 simulations, with individual simulations represented as transparent gray rectangles. Time to scission was determined as the sharp decrease in complex size shown in (A) Data-points are annotated with the mean time to scission normalized to that for the core slat length of 10. (C) Kappa simulations with prebound cut-slats (core slat length 10, extension length 5, wobble strength 2/3) showing effect of arrangement of 5 wobble-sites as represented by the different colors. Every data-point is a mean of 300 simulations.
Conclusions
Materials and Methods
Sequence Design
Denaturing Polyacrylamide Gel Electrophoresis (PAGE) Purification
Assembly Reactions
Agarose Gel Electrophoresis
Transmission Electron Microscopy
JM109 E. coli gDNA Preparation
Fluorophore Conjugation
Kappa Simulation Design
Kappa Simulation Implementation
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.3c08205.
Scadnano design schematics; additional agarose gel and negative-stain TEM data; and Kappa simulation constraints and simulated data (PDF)
Spreadsheet of all DNA sequences used in this work (XLSX)
Animation illustrating process of crisscross ribbon scission, with ribbon growth omitted for clarity. Slat types are colored as in Figure 2 (MP4)
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
The authors would like to thank James MacDonald and Christopher Wintersinger for fruitful discussions. A.E., D.M., and W.M.S. have filed a patent based on this work. The authors thank the following funding sources: Wyss Core Faculty Award, Wyss Molecular Robotics Initiative Award, ONR Award N00014-15-1- 0073, ONR Award N00014-18-1-2566, BMGF/Ragon Global Health Innovation Partnership Award, and BMGF Joint Stanford/Ragon Sentinel Award OPP112622, Alexander S. Onassis Scholarship for Hellenes to A.E.
References
This article references 36 other publications.
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- 3Evans, C. G.; Winfree, E. Physical Principles for DNA Tile Self-Assembly. Chem. Soc. Rev. 2017, 46 (12), 3808– 3829, DOI: 10.1039/C6CS00745GGoogle Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXns1Grtrc%253D&md5=8ea75912f1d14f0ac5cbaf5645b737d2Physical principles for DNA tile self-assemblyEvans, Constantine G.; Winfree, ErikChemical Society Reviews (2017), 46 (12), 3808-3829CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)DNA tiles provide a promising technique for assembling structures with nanoscale resoln. through self-assembly by basic interactions rather than top-down assembly of individual structures. Tile systems can be programmed to grow based on logical rules, allowing for a small no. of tile types to assemble large, complex assemblies that can retain nanoscale resoln. Such algorithmic systems can even assemble different structures using the same tiles, based on inputs that seed the growth. While programming and theor. anal. of tile self-assembly often makes use of abstr. logical models of growth, exptl. implemented systems are governed by nanoscale phys. processes that can lead to very different behavior, more accurately modeled by taking into account the thermodn. and kinetics of tile attachment and detachment in soln. This review discusses the relationships between more abstr. and more phys. realistic tile assembly models. A central concern is how consideration of model differences enables the design of tile systems that robustly exhibit the desired abstr. behavior in realistic phys. models and in exptl. implementations. Conversely, we identify situations where self-assembly in abstr. models can not be well-approximated by phys. realistic models, putting constraints on phys. relevance of the abstr. models. To facilitate the discussion, we introduce a unified model of tile self-assembly that clarifies the relationships between several well-studied models in the literature. Throughout, we highlight open questions regarding the phys. principles for DNA tile self-assembly.
- 4Mohammed, A. M.; Schulman, R. Directing Self-Assembly of DNA Nanotubes Using Programmable Seeds. Nano Lett. 2013, 13 (9), 4006– 4013, DOI: 10.1021/nl400881wGoogle Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1Wlt7rF&md5=de643802c3f8ae59e4da996a7bf355a3Directing Self-Assembly of DNA Nanotubes Using Programmable SeedsMohammed, Abdul M.; Schulman, RebeccaNano Letters (2013), 13 (9), 4006-4013CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)Control over when and where nanostructures arise is essential for the self-assembly of dynamic or multicomponent devices. We design and construct a DNA origami seed for the control of DAE-E tile DNA nanotube assembly. Seeds greatly accelerate nanotube nucleation and growth because they serve as nanotube nucleation templates. Seeds also control nanotube circumference. Simulations predict nanotube growth rates and suggest a small nucleation barrier remains when nanotubes grow from seeds.
- 5Zhang, Y.; Reinhardt, A.; Wang, P.; Song, J.; Ke, Y. Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand. Angew. Chem., Int. Ed. Engl. 2020, 59 (22), 8594– 8600, DOI: 10.1002/anie.201915063Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB387gs1Oksg%253D%253D&md5=463fd0ab38b57bc255f8b5f44e2e4101Programming the Nucleation of DNA Brick Self-Assembly with a Seeding StrandZhang Yingwei; Reinhardt Aleks; Wang Pengfei; Song Jie; Ke YonggangAngewandte Chemie (International ed. in English) (2020), 59 (22), 8594-8600 ISSN:.Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a "seed" strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4-7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.
- 6Dirks, R. M.; Pierce, N. A. Triggered Amplification by Hybridization Chain Reaction. Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (43), 15275– 15278, DOI: 10.1073/pnas.0407024101Google Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtVKhsbzI&md5=39c11ef0c74c78072ff30cf24b912932Triggered amplification by hybridization chain reactionDirks, Robert M.; Pierce, Niles A.Proceedings of the National Academy of Sciences of the United States of America (2004), 101 (43), 15275-15278CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the simplest version of this process, two stable species of DNA hairpins coexist in soln. until the introduction of initiator strands triggers a cascade of hybridization events that yields nicked double helixes analogous to alternating copolymers. The av. mol. wt. of the HCR products varies inversely with initiator concn. Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications.
- 7Ang, Y. S.; Yung, L.-Y. L. Rational Design of Hybridization Chain Reaction Monomers for Robust Signal Amplification. Chem. Commun. 2016, 52 (22), 4219– 4222, DOI: 10.1039/C5CC08907GGoogle Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xis1Cnur0%253D&md5=bc005ac3d79afc191c6c9b8727dc2157Rational design of hybridization chain reaction monomers for robust signal amplificationAng, Yan Shan; Yung, Lin-Yue LanryChemical Communications (Cambridge, United Kingdom) (2016), 52 (22), 4219-4222CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)We established four-point guidelines for the sequence design of hairpin monomers in hybridization chain reaction (HCR). This enabled greater flexibility to customize specific hairpin sequences for use with the readout platform of interest. Using shorter hairpin stem length, a one-pot signal amplification system was demonstrated by incorporating distance-sensitive Foddorster resonance energy transfer (FRET) readout.
- 8Barish, R. D.; Schulman, R.; Rothemund, P. W. K.; Winfree, E. An Information-Bearing Seed for Nucleating Algorithmic Self-Assembly. Proc. Natl. Acad. Sci. U. S. A. 2009, 106 (15), 6054– 6059, DOI: 10.1073/pnas.0808736106Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXlsFCrsb8%253D&md5=81b8b98a3e8ed88d0f6e177316bd4451An information-bearing seed for nucleating algorithmic self-assemblyBarish, Robert D.; Schulman, Rebecca; Rothemund, Paul W. K.; Winfree, ErikProceedings of the National Academy of Sciences of the United States of America (2009), 106 (15), 6054-6059CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Self-assembly creates natural mineral, chem., and biol. structures of great complexity. Often, the same starting materials have the potential to form an infinite variety of distinct structures; information in a seed mol. can det. which form is grown as well as where and when. These phenomena can be exploited to program the growth of complex supramol. structures, as demonstrated by the algorithmic self-assembly of DNA tiles. However, the lack of effective seeds has limited the reliability and yield of algorithmic crystals. Here, the authors present a programmable DNA origami seed that can display up to 32 distinct binding sites and demonstrate the use of seeds to nucleate three types of algorithmic crystals. In the simplest case, the starting materials are a set of tiles that can form cryst. ribbons of any width; the seed directs assembly of a chosen width with >90% yield. Increased structural diversity is obtained by using tiles that copy a binary string from layer to layer; the seed specifies the initial string and triggers growth under near-optimal conditions where the bit copying error rate is <0.2%. Increased structural complexity is achieved by using tiles that generate a binary counting pattern; the seed specifies the initial value for the counter. Self-assembly proceeds in a one-pot annealing reaction involving up to 300 DNA strands contg. >17 kb of sequence information. In sum, this work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication.
- 9Schulman, R.; Winfree, E. Programmable Control of Nucleation for Algorithmic Self-Assembly. SIAM Journal on Computing 2010, 39 (4), 1581– 1616, DOI: 10.1137/070680266Google ScholarThere is no corresponding record for this reference.
- 10Jacobs, W. M.; Reinhardt, A.; Frenkel, D. Rational Design of Self-Assembly Pathways for Complex Multicomponent Structures. Proc. Natl. Acad. Sci. U. S. A. 2015, 112 (20), 6313– 6318, DOI: 10.1073/pnas.1502210112Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXns1Olu74%253D&md5=a9770b10a0bc7fcc37c45f7a84373dfaRational design of self-assembly pathways for complex multicomponent structuresJacobs, William M.; Reinhardt, Aleks; Frenkel, DaanProceedings of the National Academy of Sciences of the United States of America (2015), 112 (20), 6313-6318CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The field of complex self-assembly is moving toward the design of multiparticle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such "addressable complexity," we need to understand the factors that optimize the yield and the kinetics of self-assembly. Here we use a simple theor. method to explain the key features responsible for the unexpected success of DNA-brick expts., which are currently the only demonstration of reliable self-assembly with such a large no. of components. Simulations confirm that our theory accurately predicts the narrow temp. window in which error-free assembly can occur. Even more strikingly, our theory predicts that correct assembly of the complete structure may require a time-dependent exptl. protocol. Furthermore, we predict that low coordination nos. result in nonclassical nucleation behavior, which we find to be essential for achieving optimal nucleation kinetics under mild growth conditions. We also show that, rather surprisingly, the use of heterogeneous bond energies improves the nucleation kinetics and in fact appears to be necessary for assembling certain intricate 3D structures. This observation makes it possible to sculpt nucleation pathways by tuning the distribution of interaction strengths. These insights not only suggest how to improve the design of structures based on DNA bricks, but also point the way toward the creation of a much wider class of chem. or colloidal structures with addressable complexity.
- 11Reinhardt, A.; Ho, C. P.; Frenkel, D. Effects of Co-Ordination Number on the Nucleation Behaviour in Many-Component Self-Assembly. Faraday Discuss. 2016, 186, 215– 228, DOI: 10.1039/C5FD00135HGoogle Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFamsbvN&md5=d5488cba461a6f2a9e9ae22f27d7d02eEffects of co-ordination number on the nucleation behaviour in many-component self-assemblyReinhardt, Aleks; Ho, Chon Pan; Frenkel, DaanFaraday Discussions (2016), 186 (Nanoparticle Assembly), 215-228CODEN: FDISE6; ISSN:1359-6640. (Royal Society of Chemistry)We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behavior, in the form of free-energy barriers to nucleation, changes significantly as the co-ordination no. of the building blocks is changed from 4 to 8 to 12. Unlike tetrahedral structures - which roughly correspond to DNA bricks that have been studied in expts. - the shapes of the free-energy barriers of higher co-ordination structures depend strongly on the supersatn., and such structures require a very significant driving force for structure growth before nucleation becomes thermally accessible. Although growth at high supersatn. results in more defects during self-assembly, we show that high co-ordination no. structures can still be assembled successfully in computer simulations and that they exhibit self-assembly behavior analogous to DNA bricks. In particular, the self-assembly remains modular, enabling in principle a wide variety of nanostructures to be assembled, with a greater spatial resoln. than is possible in low co-ordination structures.
- 12Winfree, E. Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments. J. Biomol. Struct. Dyn. 2000, 17 (Suppl 1), 263– 270, DOI: 10.1080/07391102.2000.10506630Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3s7ptlGruw%253D%253D&md5=e42edace138d22ba350a0849b3876182Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly ExperimentsWinfree EJournal of biomolecular structure & dynamics (2000), 17 Suppl 1 (), 263-70 ISSN:.Abstract Biology makes things far smaller and more complex than anything produced by human engineering. The biotechnology revolution has for the first time given us the tools necessary to consider engineering on the molecular level. Research in DNA computation, launched by Len Adleman, has opened the door for experimental study of programmable biochemical reactions. Here we focus on a single biochemical mechanism, the self-assembly of DNA structures, that is theoretically sufficient for Turing-universal computation. The theory combines Hao Wang's purely mathematical Tiling Problem with the branched DNA constructions of Ned Seeman. In the context of mathematical logic, Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. For a biochemical implementation, we will need molecular Wang tiles. DNA molecular structures and intermolecular interactions are particularly amenable to design and are sufficient for the creation of complex molecular objects. The structure of individual molecules can be designed by maximizing desired and minimizing undesired Watson-Crick complementarity. Intermolecular interactions are programmed by the design of sticky ends that determine which molecules associate, and how. The theory has been demonstrated experimentally using a system of synthetic DNA double-crossover molecules that self-assemble into two-dimensional crystals that have been visualized by atomic force microscopy. This experimental system provides an excellent platform for exploring the relationship between computation and molecular self-assembly, and thus represents a first step toward the ability to program molecular reactions and molecular structures.
- 13Woods, D.; Doty, D.; Myhrvold, C.; Hui, J.; Zhou, F.; Yin, P.; Winfree, E. Diverse and Robust Molecular Algorithms Using Reprogrammable DNA Self-Assembly. Nature 2019, 567 (7748), 366– 372, DOI: 10.1038/s41586-019-1014-9Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXotFansrg%253D&md5=aedf2cbf2295bd3597c79c6ec6d15019Diverse and robust molecular algorithms using reprogrammable DNA self-assemblyWoods, Damien; Doty, David; Myhrvold, Cameron; Hui, Joy; Zhou, Felix; Yin, Peng; Winfree, ErikNature (London, United Kingdom) (2019), 567 (7748), 366-372CODEN: NATUAS; ISSN:0028-0836. (Nature Research)Mol. biol. provides an inspiring proof-of-principle that chem. systems can store and process information to direct mol. activities such as the fabrication of complex structures from mol. components. To develop information-based chem. as a technol. for programming matter to function in ways not seen in biol. systems, it is necessary to understand how mol. interactions can encode and execute algorithms. The self-assembly of relatively simple units into complex products1 is particularly well suited for such investigations. Theory that combines math. tiling and statistical-mech. models of mol. crystn. has shown that algorithmic behavior can be embedded within mol. self-assembly processes2,3, and this has been exptl. demonstrated using DNA nanotechnol.4 with up to 22 tile types5-11. However, many information technologies exhibit a complexity threshold-such as the min. transistor count needed for a general-purpose computer-beyond which the power of a reprogrammable system increases qual., and it has been unclear whether the biophysics of DNA self-assembly allows that threshold to be exceeded. Here we report the design and exptl. validation of a DNA tile set that contains 355 single-stranded tiles and can, through simple tile selection, be reprogrammed to implement a wide variety of 6-bit algorithms. We use this set to construct 21 circuits that execute algorithms including copying, sorting, recognizing palindromes and multiples of 3, random walking, obtaining an unbiased choice from a biased random source, electing a leader, simulating cellular automata, generating deterministic and randomized patterns, and counting to 63, with an overall per-tile error rate of less than 1 in 3,000. These findings suggest that mol. self-assembly could be a reliable algorithmic component within programmable chem. systems. The development of mol. machines that are reprogrammable-at a high level of abstraction and thus without requiring knowledge of the underlying physics-will establish a creative space in which mol. programmers can flourish.
- 14Schulman, R.; Yurke, B.; Winfree, E. Robust Self-Replication of Combinatorial Information via Crystal Growth and Scission. Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (17), 6405– 6410, DOI: 10.1073/pnas.1117813109Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xmslyjtrg%253D&md5=d8842348d4bdb658a53cecf70a9cf399Robust self-replication of combinatorial information via crystal growth and scissionSchulman, Rebecca; Yurke, Bernard; Winfree, ErikProceedings of the National Academy of Sciences of the United States of America (2012), 109 (17), 6405-6410, S6405/1-S6405/55CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Understanding how a simple chem. system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary mol. design techniques. During biol. sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then sep. the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chem. sequences without enzymes. Crystal growth propagates a sequence of bits while mech.-induced scission creates new growth fronts. Together, these processes exponentially increase the no. of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% Of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and Darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chem. sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.
- 15He, X.; Sha, R.; Zhuo, R.; Mi, Y.; Chaikin, P. M.; Seeman, N. C. Exponential Growth and Selection in Self-Replicating Materials from DNA Origami Rafts. Nat. Mater. 2017, 16 (10), 993– 997, DOI: 10.1038/nmat4986Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFOju7bP&md5=2a6d8274bfcd1132ad849902620ef46dExponential growth and selection in self-replicating materials from DNA origami raftsHe, Xiaojin; Sha, Ruojie; Zhuo, Rebecca; Mi, Yongli; Chaikin, Paul M.; Seeman, Nadrian C.Nature Materials (2017), 16 (10), 993-997CODEN: NMAACR; ISSN:1476-1122. (Nature Research)Self-replication and evolution under selective pressure are inherent phenomena in life, but few artificial systems exhibit these phenomena. The authors have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temp. and UV illumination, producing >7 million copies in 24 cycles. The authors demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ∼1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8; similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.
- 16Minev, D.; Wintersinger, C. M.; Ershova, A.; Shih, W. M. Robust Nucleation Control via Crisscross Polymerization of Highly Coordinated DNA Slats. Nat. Commun. 2021, 12 (1), 1741, DOI: 10.1038/s41467-021-21755-7Google Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXmvFKrurc%253D&md5=74d7c88f24dfc06521c573263128de6dRobust nucleation control via crisscross polymerization of highly coordinated DNA slatsMinev, Dionis; Wintersinger, Christopher M.; Ershova, Anastasia; Shih, William M.Nature Communications (2021), 12 (1), 1741CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Natural biomol. assemblies such as actin filaments or microtubules can exhibit all-or-nothing polymn. in a kinetically controlled fashion. The kinetic barrier to spontaneous nucleation arises in part from pos. cooperativity deriving from joint-neighbor capture, where stable capture of incoming monomers requires straddling multiple subunits on a filament end. For programmable DNA self-assembly, it is likewise desirable to suppress spontaneous nucleation to enable powerful capabilities such as all-or-nothing assembly of nanostructures larger than a single DNA origami, ultrasensitive detection, and more robust algorithmic assembly. However, existing DNA assemblies use monomers with low coordination nos. that present an effective kinetic barrier only for slow, near-reversible growth conditions. Here we introduce crisscross polymn. of elongated slat monomers that engage beyond nearest neighbors which sustains the kinetic barrier under conditions that promote fast, irreversible growth. By implementing crisscross slats as single-stranded DNA, we attain strictly seed-initiated nucleation of crisscross ribbons with distinct widths and twists.
- 17Wintersinger, C. M.; Minev, D.; Ershova, A.; Sasaki, H. M.; Gowri, G.; Berengut, J. F.; Corea-Dilbert, F. E.; Yin, P.; Shih, W. M. Multi-Micron Crisscross Structures Grown from DNA-Origami Slats. Nat. Nanotechnol. 2023, 18, 281– 289, DOI: 10.1038/s41565-022-01283-1Google Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XjtFyms7vF&md5=89a134fd9f91a2a40d6764b6db373085Multi-micron crisscross structures grown from DNA-origami slatsWintersinger, Christopher M.; Minev, Dionis; Ershova, Anastasia; Sasaki, Hiroshi M.; Gowri, Gokul; Berengut, Jonathan F.; Corea-Dilbert, F. Eduardo; Yin, Peng; Shih, William M.Nature Nanotechnology (2023), 18 (3), 281-289CODEN: NNAABX; ISSN:1748-3387. (Nature Portfolio)Living systems achieve robust self-assembly across a wide range of length scales. In the synthetic realm, nanofabrication strategies such as DNA origami have enabled robust self-assembly of submicron-scale shapes from a multitude of single-stranded components. To achieve greater complexity, subsequent hierarchical joining of origami can be pursued. However, erroneous and missing linkages restrict the no. of unique origami that can be practically combined into a single design. Here we extend crisscross polymn., a strategy previously demonstrated with single-stranded components, to DNA-origami 'slats' for fabrication of custom multi-micron shapes with user-defined nanoscale surface patterning. Using a library of ∼2,000 strands that are combinatorially arranged to create unique DNA-origami slats, we realize finite structures composed of >1,000 uniquely addressable slats, with a mass exceeding 5 GDa, lateral dimensions of roughly 2μm and a multitude of periodic structures. Robust prodn. of target crisscross structures is enabled through strict control over initiation, rapid growth and minimal premature termination, and highly orthogonal binding specificities. Thus crisscross growth provides a route for prototyping and scalable prodn. of structures integrating thousands of unique components (i.e., origami slats) that each is sophisticated and molecularly precise.
- 18Zhang, D. Y.; Seelig, G. Dynamic DNA Nanotechnology Using Strand-Displacement Reactions. Nat. Chem. 2011, 3 (2), 103– 113, DOI: 10.1038/nchem.957Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXovVGhsg%253D%253D&md5=eab3b5fa59fa957ec01f89072dd2089cDynamic DNA nanotechnology using strand-displacement reactionsZhang, David Yu; Seelig, GeorgNature Chemistry (2011), 3 (2), 103-113CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)A review. The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnol. is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous mol. motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, the authors review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behavior.
- 19Srinivas, N.; Ouldridge, T. E.; Šulc, P.; Schaeffer, J. M.; Yurke, B.; Louis, A. A.; Doye, J. P. K.; Winfree, E. On the Biophysics and Kinetics of Toehold-Mediated DNA Strand Displacement. Nucleic Acids Res. 2013, 41 (22), 10641– 10658, DOI: 10.1093/nar/gkt801Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvV2lsbjP&md5=352336a395164bf796b4e6220e2edd04On the biophysics and kinetics of toehold-mediated DNA strand displacementSrinivas, Niranjan; Ouldridge, Thomas E.; Sulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, ErikNucleic Acids Research (2013), 41 (22), 10641-10658CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)Dynamic DNA nanotechnol. often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been exptl. characterized and phenomenol. modeled, detailed biophys. understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained mol. model that incorporates 3D geometric and steric effects. Further, we exptl. investigate the thermodn. of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the phys. process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodn. penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the addnl. overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophys. explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex mol. systems.
- 20Danos, V.; Feret, J.; Fontana, W.; Harmer, R.; Krivine, J. Rule-Based Modelling of Cellular Signalling. In CONCUR 2007 – Concurrency Theory; Caires, L., Vasconcelos, V. T., Eds.; Lecture Notes in Computer Science; Springer: Berlin, Heidelberg, 2007; pp 17– 41, DOI: 10.1007/978-3-540-74407-8_3 .Google ScholarThere is no corresponding record for this reference.
- 21Boutillier, P.; Maasha, M.; Li, X.; Medina-Abarca, H. F.; Krivine, J.; Feret, J.; Cristescu, I.; Forbes, A. G.; Fontana, W. The Kappa Platform for Rule-Based Modeling. Bioinformatics 2018, 34 (13), i583– i592, DOI: 10.1093/bioinformatics/bty272Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtV2gt7fO&md5=081755d2d99c58affbd2692eaf5dcd0cThe Kappa platform for rule-based modelingBoutillier, Pierre; Maasha, Mutaamba; Li, Xing; Medina-Abarca, Hector F.; Krivine, Jean; Feret, Jerome; Cristescu, Ioana; Forbes, Angus G.; Fontana, WalterBioinformatics (2018), 34 (13), i583-i592CODEN: BOINFP; ISSN:1367-4811. (Oxford University Press)Motivation: We present an overview of the Kappa platform, an integrated suite of anal. and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addn. to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biol. systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction. Results: We discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolns., the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymn., such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for early events in EGF signaling.
- 22Högberg, B.; Liedl, T.; Shih, W. M. Folding DNA Origami from a Double-Stranded Source of Scaffold. J. Am. Chem. Soc. 2009, 131 (26), 9154– 9155, DOI: 10.1021/ja902569xGoogle Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXnt1OnsbY%253D&md5=e903ecdad97e4061c58037c8019dd5b8Folding DNA Origami from a Double-Stranded Source of ScaffoldHogberg, Bjorn; Liedl, Tim; Shih, William M.Journal of the American Chemical Society (2009), 131 (26), 9154-9155CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Combined heat and chem. denaturation of double-stranded DNA scaffold strands in the presence of staple strands, followed by a sudden temp. drop and then stepwise dialysis to remove the chem. denaturant, leads to self-assembly of two distinct DNA-origami structures. We have shown that it is possible to fold the individual strands of a dsDNA mol. into two discrete nanoscale objects in a one-pot reaction contg. a mixt. of two sets of oligonucleotide staple strands. Even when only one set of staple strands is added the rapid temp. drop following denaturation enables formation of the DNA-origami kinetic product over reannealing of dsDNA. This method extends DNA origami by enabling access to a much broader range of scaffolds, including open circular DNA, linear plasmid DNA, and PCR products. This strategy also provides a means to sort the two strands of a dsDNA mol. based on programmable changes in size and gel mobility.
- 23Süß, B.; Flekna, G.; Wagner, M.; Hein, I. Studying the Effect of Single Mismatches in Primer and Probe Binding Regions on Amplification Curves and Quantification in Real-Time PCR. J. Microbiol. Methods 2009, 76 (3), 316– 319, DOI: 10.1016/j.mimet.2008.12.003Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhvFGqsbY%253D&md5=c8f77a3e5767c04d7bd5d571562c408bStudying the effect of single mismatches in primer and probe binding regions on amplification curves and quantification in real-time PCRSuess, Beate; Flekna, Gabriele; Wagner, Martin; Hein, IngeborgJournal of Microbiological Methods (2009), 76 (3), 316-319CODEN: JMIMDQ; ISSN:0167-7012. (Elsevier B.V.)Comparison of a broad range of characteristics of real-time PCR amplification curves yielded only slight alterations for low nos. of mismatches in the primer binding regions, resulting in a quantification error up to 63.12%. The effects were more pronounced for mismatches in the probe binding region and resulted in a quantification error up to 33%.
- 24Zimmermann, F.; Urban, M.; Krüger, C.; Walter, M.; Wölfel, R.; Zwirglmaier, K. In Vitro Evaluation of the Effect of Mutations in Primer Binding Sites on Detection of SARS-CoV-2 by RT-QPCR. Journal of Virological Methods 2022, 299, 114352 DOI: 10.1016/j.jviromet.2021.114352Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXisVyrsrjN&md5=72e6fc563ffc25e7459173854a3a878fIn vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCRZimmermann, Fee; Urban, Maria; Krueger, Christian; Walter, Mathias; Woelfel, Roman; Zwirglmaier, KatrinJournal of Virological Methods (2022), 299 (), 114352CODEN: JVMEDH; ISSN:0166-0934. (Elsevier B.V.)A no. of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous com. assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases - as seen with the B.1.1.7 variant - can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from -0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charite RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values obsd. with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.
- 25Nickels, P. C.; Ke, Y.; Jungmann, R.; Smith, D. M.; Leichsenring, M.; Shih, W. M.; Liedl, T.; Högberg, B. DNA Origami Structures Directly Assembled from Intact Bacteriophages. Small 2014, 10 (9), 1765– 1769, DOI: 10.1002/smll.201303442Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXisFWhtLk%253D&md5=21f5596b4b865047e2b8718f7c8e5c1cDNA Origami Structures Directly Assembled from Intact BacteriophagesNickels, Philipp C.; Ke, Yonggang; Jungmann, Ralf; Smith, David M.; Leichsenring, Marc; Shih, William M.; Liedl, Tim; Hoegberg, BjoernSmall (2014), 10 (9), 1765-1769CODEN: SMALBC; ISSN:1613-6810. (Wiley-VCH Verlag GmbH & Co. KGaA)A fast and versatile method for the direct employment of genomic nucleic acids from naturally occurring bacteriophages has been developed. Two bacteriophages (M13 and λ) were used as scaffold sources for the assembly of DNA origami constructs without further purifn. of the genomic DNA. A single DNA origami structure directly from the entire bacteriophage λ genome, although with low yields.
- 26Doty, D.; Lee, B. L.; Stérin, T. Scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26); Geary, C., Patitz, M. J., Eds.; Leibniz International Proceedings in Informatics (LIPIcs); Schloss Dagstuhl–Leibniz-Zentrum für Informatik: Dagstuhl, Germany, 2020; Vol. 174, p 9:1– 9:17, DOI: 10.4230/LIPIcs.DNA.2020.9 .Google ScholarThere is no corresponding record for this reference.
- 27Zadeh, J. N.; Steenberg, C. D.; Bois, J. S.; Wolfe, B. R.; Pierce, M. B.; Khan, A. R.; Dirks, R. M.; Pierce, N. A. NUPACK: Analysis and Design of Nucleic Acid Systems. J. Comput. Chem. 2011, 32 (1), 170– 173, DOI: 10.1002/jcc.21596Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsVCjsLzP&md5=9c60f0134ea55d9335301e2efe1602e8NUPACK: analysis and design of nucleic acid systemsZadeh, Joseph N.; Steenberg, Conrad D.; Bois, Justin S.; Wolfe, Brian R.; Pierce, Marshall B.; Khan, Asif R.; Dirks, Robert M.; Pierce, Niles A.Journal of Computational Chemistry (2011), 32 (1), 170-173CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)The Nucleic Acid Package (NUPACK) is a growing software suite for the anal. and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.
- 28Fornace, M. E.; Huang, J.; Newman, C. T.; Porubsky, N. J.; Pierce, M. B.; Pierce, N. A. NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems ChemRxiv 2022, DOI: 10.26434/chemrxiv-2022-xv98l , November 10 (accessed 2023–12–03).Google ScholarThere is no corresponding record for this reference.
- 29Schindelin, J.; Arganda-Carreras, I.; Frise, E.; Kaynig, V.; Longair, M.; Pietzsch, T.; Preibisch, S.; Rueden, C.; Saalfeld, S.; Schmid, B. Fiji: An Open-Source Platform for Biological-Image Analysis. Nat. Methods 2012, 9 (7), 676– 682, DOI: 10.1038/nmeth.2019Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVKnurbJ&md5=ad150521a33367d37a800bee853dd9dbFiji: an open-source platform for biological-image analysisSchindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, AlbertNature Methods (2012), 9 (7_part1), 676-682CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)Fiji is a distribution of the popular open-source software ImageJ focused on biol.-image anal. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biol. research communities.
- 30Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. Structural, Mechanical, and Thermodynamic Properties of a Coarse-Grained DNA Model. J. Chem. Phys. 2011, 134 (8), 085101 DOI: 10.1063/1.3552946Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXit1Kltbs%253D&md5=fe949636e1e4c02c0595c036e504b2eeStructural, mechanical, and thermodynamic properties of a coarse-grained DNA modelOuldridge, Thomas E.; Louis, Ard A.; Doye, Jonathan P. K.Journal of Chemical Physics (2011), 134 (8), 085101/1-085101/22CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We explore in detail the structural, mech., and thermodn. properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers. Effective interactions are used to represent chain connectivity, excluded vol., base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson-Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an "av. base" description of DNA. We quantify the relation to expt. of the thermodn. of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helixes. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodn. of the duplex formation transition. (c) 2011 American Institute of Physics.
- 31Šulc, P.; Romano, F.; Ouldridge, T. E.; Rovigatti, L.; Doye, J. P. K.; Louis, A. A. Sequence-Dependent Thermodynamics of a Coarse-Grained DNA Model. J. Chem. Phys. 2012, 137 (13), 135101, DOI: 10.1063/1.4754132Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsVejtr3L&md5=cda4715130b0234bd2cb2581df954e73Sequence-dependent thermodynamics of a coarse-grained DNA modelSulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Rovigatti, Lorenzo; Doye, Jonathan P. K.; Louis, Ard A.Journal of Chemical Physics (2012), 137 (13), 135101/1-135101/14CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We introduce a sequence-dependent parametrization for a coarse-grained DNA model originally designed to reproduce the properties of DNA mols. with av. sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temps. of short duplexes. By developing a histogram re-weighting technique, we are able to fit our parameters to the melting temps. of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its m.p., (c) the effects of stacking strength in the loop on the melting temp. of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with exptl. data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software. (c) 2012 American Institute of Physics.
- 32Poppleton, E.; Romero, R.; Mallya, A.; Rovigatti, L.; Šulc, P. OxDNA.Org: A Public Webserver for Coarse-Grained Simulations of DNA and RNA Nanostructures. Nucleic Acids Res. 2021, 49 (W1), W491– W498, DOI: 10.1093/nar/gkab324Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvV2isLfK&md5=a5ed15f30ec7da67deaa2d42e1650733OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructuresPoppleton, Erik; Romero, Roger; Mallya, Aatmik; Rovigatti, Lorenzo; Sulc, PetrNucleic Acids Research (2021), 49 (W1), W491-W498CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnol. community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA. org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA mol. dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-phys. states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and anal. interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user's specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the tech. aspects of mol. simulation. The webserver is freely available at oxdna.org.
- 33Maffeo, C.; Aksimentiev, A. MrDNA: A Multi-Resolution Model for Predicting the Structure and Dynamics of DNA Systems. Nucleic Acids Res. 2020, 48 (9), 5135– 5146, DOI: 10.1093/nar/gkaa200Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisVKlurfJ&md5=227f1d0a8a6cb7f01a56808bcdb4b652MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systemsMaffeo, Christopher; Aksimentiev, AlekseiNucleic Acids Research (2020), 48 (9), 5135-5146CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)Although the field of structural DNA nanotechnol. has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of exptl. characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resoln. simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resoln. structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equil. structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied elec. field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and mol. graphics tools.
- 34DNA Lab: Xgrow Tile Assembly Simulator. https://www.dna.caltech.edu/Xgrow/ (accessed Sep 14, 2023).Google ScholarThere is no corresponding record for this reference.
- 35Doty, D.; Fleming, H.; Hader, D.; Patitz, M. J.; Vaughan, L. A. Accelerating Self-Assembly of Crisscross Slat Systems. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29); Leibniz International Proceedings in Informatics (LIPIcs); 2023; Vol. 276, pp 7:1– 7:23, DOI: 10.4230/LIPIcs.DNA.29.7 .Google ScholarThere is no corresponding record for this reference.
- 36Page, M. I.; Jencks, W. P. Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect. Proc. Natl. Acad. Sci. U. S. A. 1971, 68 (8), 1678– 1683, DOI: 10.1073/pnas.68.8.1678Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE3MXltVGhtLw%253D&md5=f2190b0dde6c8b5ffdf43adec063265aEntropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effectPage, Michael I.; Jencks, William P.Proceedings of the National Academy of Sciences of the United States of America (1971), 68 (8), 1678-83CODEN: PNASA6; ISSN:0027-8424.Translational and (overall) rotational motions provide the important entropic driving force for enzymic and intramol. rate accelerations and the chelate effect; internal rotations and unusually severe orientational requirements are generally of secondary importance. The loss of translational and (overall) rotational entropy for 2 → 1 reactions in soln. is ordinarily on the order of 45 entropy units (e.u.) (std. state M, 25°); the translational entropy is much larger than 8 e.u. (corresponding to 55 M). Low-frequency motions in products and transition states, ∼17 e.u. for cyclopentadiene dimerization, partially compensate for this loss, but effective concns. on the order of 108 M may be accounted for without the introduction of new chem. concepts or terms.
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- Jie Deng, Dionis Minev, Anastasia Ershova, William M. Shih. Branching Crisscross Polymerization of Single-Stranded DNA Slats. Journal of the American Chemical Society 2024, 146
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Abstract
Figure 1
Figure 1. Scission of a finite crisscross DNA structure through toehold-mediated displacement by a set of invader (i.e., cut) strands. (A) Principle of classical toehold-mediated strand displacement. An invader strand (green) engages a toehold domain on a substrate strand (light blue) and then proceeds to liberate a bound incumbent strand (dark blue) through branch migration. (B) Strand displacement where the substrate strand, including its toehold domain, is functionally replaced by a series of half-turn (5 or 6 bp) strand termini arranged on the face of a crisscross structure. (C) Fissure of a crisscross nanostructure through toehold-mediated recruitment of a set of invader strands followed by joint branch migration. (D) Analogous fissure of a crisscross ribbon fragment exhibiting xy growth (i.e., alternating staggered x and y slats). Light blue and gray boxes in B–D outline regions not involved in the strand displacement. See Figure 2 for how such a scission can be coupled with growth.
Figure 2
Figure 2. Principle of 3CR for exponential amplification of xy ribbons via isothermal growth and scission. (A) Schematic of the design for a v5 ribbon (detailed scadnano design in Supp. Figure 1C). Each intersection between a horizontal and vertical line represents a half-turn (5–6 base pairs) of dsDNA. Through linear growth, growth slats with single-stranded extensions are added to the ribbon in a specific order that allows cut slats to bind. Once bound, the cut slats compete with the growth slats via toehold-mediated strand displacement (see Supp. Movie 1 for a more in-depth view of ribbon scission via strand displacement). Once the cut slats had displaced the growth slats, the ribbon is severed into two fragments. Each of these fragments is capable of further growth and scission. (B) TEM image after ribbon growth without scission (mean length 409 nm, standard deviation 176 nm, based on 22 measurements). (C) TEM image after combined ribbon growth and scission (mean length of 44 nm, standard deviation of 19 nm, based on 226 measurements, corresponding to predominantly fully cut ribbons). Production of ribbons, long or short, is seed-dependent (see Figure 3). Note that linear ribbons appear twisted and irregular in width due to the use of 11 bp/turn and the presence of single-stranded extensions, which, when unbound, tend to cause aggregation. Scale bars: 200 nm. See “Assembly Reactions” for details of the conditions used. (D) Comparison of seeded and unseeded 3CR amplification at different slat concentrations with cy5-fluorophore 3′ labeling of the top x-slat from the repeat unit in A and Supp. Figure 1C (present at roughly 50% of the concentration of other growth slats). The red fluorescent signal (i.e., gel image captured with a red filter) is from this labeled x-slat, while the blue fluorescent signal (i.e., gel image captured with a blue filter) is from SYBR-Gold prestaining of the agarose gel. The fast-migrating bright species at the bottom of all agarose gels are unincorporated slats. See “Assembly Reactions” for details of conditions used.
Figure 3
Figure 3. Target-dependent nanoseed formation leading to the 3CR exponential growth of v5 ribbons. (A) Design of nanoseed formation from ssDNA or ssRNA, with coupling to v5 crisscross growth and scission (cut slats omitted from the cartoon for clarity). As in Figure 2A, one intersection between a horizontal and vertical line represents a half-turn (5–6 base pairs) of DNA. (B) Design of twinned-nanoseed formation from dsDNA. It is likely that nanoseed formation only proceeds efficiently for targets that are kinetically trapped in single-stranded states, e.g., through denaturation followed by incomplete renaturation, and that thereby are available for sequestration by the capture slats. (C) 3CR detection of different targets using a v5 design (p8064 ssDNA, JM109 E. coli dsDNA, MS2 RNA). The red fluorescent signal (i.e., gel image captured with a red filter) is from the top x-slat in Supp. Figure 1C labeled with a Cy5-fluorophore on its 3′ end, while the blue fluorescent signal (i.e., gel image captured with a blue filter) is from SYBR-Gold prestaining of the agarose gel. The fast-migrating bright species at the bottom of all agarose gels are the unincorporated slats. See “Assembly Reactions” for details of conditions used.
Figure 4
Figure 4. Kappa simulations of scission of a two-repeat ribbon, in the absence of growth, for core slat length 10 (i.e., v5), extension length 5 (i.e., five-segment toeholds), and no wobbles. (A) Plot of 100 simulation trajectories tracking the number of slats in the ribbon. Scission breaks the ribbon into two complexes of comparable size. The four example graphs, depicted in pop-out squares, demonstrate a sequential maturation from the initial ribbon with two repeat-units and no cut-slats bound, followed by increases in complex size until all cut-slats are captured by the extensions, followed by scission. In the graphs, colored circles each represent a single slat, and edges are the bonds between them. (B) Simulations showing mean time to scission versus slat length, corresponding to the ribbon width, with 5-segment toeholds and no wobbles (trajectories for the core slat length 10 shown in (A)). Every data point (white circle) is a mean of 100 simulations, with individual simulations represented as transparent gray rectangles. Time to scission was determined as the sharp decrease in complex size shown in (A) Data-points are annotated with the mean time to scission normalized to that for the core slat length of 10. (C) Kappa simulations with prebound cut-slats (core slat length 10, extension length 5, wobble strength 2/3) showing effect of arrangement of 5 wobble-sites as represented by the different colors. Every data-point is a mean of 300 simulations.
References
This article references 36 other publications.
- 1Rothemund, P. W. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440 (7082), 297– 302, DOI: 10.1038/nature045861https://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).
- 2Douglas, S. M.; Dietz, H.; Liedl, T.; Hogberg, B.; Graf, F.; Shih, W. M. Self-Assembly of DNA into Nanoscale Three-Dimensional Shapes. Nature 2009, 459 (7245), 414– 418, DOI: 10.1038/nature080162https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXmtFKmtbs%253D&md5=9c6876c4b0358a9f31a0f4aaa5ba855aSelf-assembly of DNA into nanoscale three-dimensional shapesDouglas, Shawn M.; Dietz, Hendrik; Liedl, Tim; Hogberg, Bjorn; Graf, Franziska; Shih, William M.Nature (London, United Kingdom) (2009), 459 (7245), 414-418CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Mol. self-assembly offers a 'bottom-up' route to fabrication with subnanometre precision of complex structures from simple components. DNA has proved to be a versatile building block for programmable construction of such objects, including two-dimensional crystals, nanotubes, and three-dimensional wireframe nanopolyhedra. Templated self-assembly of DNA into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase scaffold strand' that is folded into a flat array of antiparallel helixes by interactions with hundreds of oligonucleotide 'staple strands'. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helixes constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes-monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross-with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concns. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manuf. of sophisticated devices bearing features on the nanometer scale.
- 3Evans, C. G.; Winfree, E. Physical Principles for DNA Tile Self-Assembly. Chem. Soc. Rev. 2017, 46 (12), 3808– 3829, DOI: 10.1039/C6CS00745G3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXns1Grtrc%253D&md5=8ea75912f1d14f0ac5cbaf5645b737d2Physical principles for DNA tile self-assemblyEvans, Constantine G.; Winfree, ErikChemical Society Reviews (2017), 46 (12), 3808-3829CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)DNA tiles provide a promising technique for assembling structures with nanoscale resoln. through self-assembly by basic interactions rather than top-down assembly of individual structures. Tile systems can be programmed to grow based on logical rules, allowing for a small no. of tile types to assemble large, complex assemblies that can retain nanoscale resoln. Such algorithmic systems can even assemble different structures using the same tiles, based on inputs that seed the growth. While programming and theor. anal. of tile self-assembly often makes use of abstr. logical models of growth, exptl. implemented systems are governed by nanoscale phys. processes that can lead to very different behavior, more accurately modeled by taking into account the thermodn. and kinetics of tile attachment and detachment in soln. This review discusses the relationships between more abstr. and more phys. realistic tile assembly models. A central concern is how consideration of model differences enables the design of tile systems that robustly exhibit the desired abstr. behavior in realistic phys. models and in exptl. implementations. Conversely, we identify situations where self-assembly in abstr. models can not be well-approximated by phys. realistic models, putting constraints on phys. relevance of the abstr. models. To facilitate the discussion, we introduce a unified model of tile self-assembly that clarifies the relationships between several well-studied models in the literature. Throughout, we highlight open questions regarding the phys. principles for DNA tile self-assembly.
- 4Mohammed, A. M.; Schulman, R. Directing Self-Assembly of DNA Nanotubes Using Programmable Seeds. Nano Lett. 2013, 13 (9), 4006– 4013, DOI: 10.1021/nl400881w4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1Wlt7rF&md5=de643802c3f8ae59e4da996a7bf355a3Directing Self-Assembly of DNA Nanotubes Using Programmable SeedsMohammed, Abdul M.; Schulman, RebeccaNano Letters (2013), 13 (9), 4006-4013CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)Control over when and where nanostructures arise is essential for the self-assembly of dynamic or multicomponent devices. We design and construct a DNA origami seed for the control of DAE-E tile DNA nanotube assembly. Seeds greatly accelerate nanotube nucleation and growth because they serve as nanotube nucleation templates. Seeds also control nanotube circumference. Simulations predict nanotube growth rates and suggest a small nucleation barrier remains when nanotubes grow from seeds.
- 5Zhang, Y.; Reinhardt, A.; Wang, P.; Song, J.; Ke, Y. Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand. Angew. Chem., Int. Ed. Engl. 2020, 59 (22), 8594– 8600, DOI: 10.1002/anie.2019150635https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BB387gs1Oksg%253D%253D&md5=463fd0ab38b57bc255f8b5f44e2e4101Programming the Nucleation of DNA Brick Self-Assembly with a Seeding StrandZhang Yingwei; Reinhardt Aleks; Wang Pengfei; Song Jie; Ke YonggangAngewandte Chemie (International ed. in English) (2020), 59 (22), 8594-8600 ISSN:.Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a "seed" strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4-7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.
- 6Dirks, R. M.; Pierce, N. A. Triggered Amplification by Hybridization Chain Reaction. Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (43), 15275– 15278, DOI: 10.1073/pnas.04070241016https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtVKhsbzI&md5=39c11ef0c74c78072ff30cf24b912932Triggered amplification by hybridization chain reactionDirks, Robert M.; Pierce, Niles A.Proceedings of the National Academy of Sciences of the United States of America (2004), 101 (43), 15275-15278CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the simplest version of this process, two stable species of DNA hairpins coexist in soln. until the introduction of initiator strands triggers a cascade of hybridization events that yields nicked double helixes analogous to alternating copolymers. The av. mol. wt. of the HCR products varies inversely with initiator concn. Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications.
- 7Ang, Y. S.; Yung, L.-Y. L. Rational Design of Hybridization Chain Reaction Monomers for Robust Signal Amplification. Chem. Commun. 2016, 52 (22), 4219– 4222, DOI: 10.1039/C5CC08907G7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xis1Cnur0%253D&md5=bc005ac3d79afc191c6c9b8727dc2157Rational design of hybridization chain reaction monomers for robust signal amplificationAng, Yan Shan; Yung, Lin-Yue LanryChemical Communications (Cambridge, United Kingdom) (2016), 52 (22), 4219-4222CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)We established four-point guidelines for the sequence design of hairpin monomers in hybridization chain reaction (HCR). This enabled greater flexibility to customize specific hairpin sequences for use with the readout platform of interest. Using shorter hairpin stem length, a one-pot signal amplification system was demonstrated by incorporating distance-sensitive Foddorster resonance energy transfer (FRET) readout.
- 8Barish, R. D.; Schulman, R.; Rothemund, P. W. K.; Winfree, E. An Information-Bearing Seed for Nucleating Algorithmic Self-Assembly. Proc. Natl. Acad. Sci. U. S. A. 2009, 106 (15), 6054– 6059, DOI: 10.1073/pnas.08087361068https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXlsFCrsb8%253D&md5=81b8b98a3e8ed88d0f6e177316bd4451An information-bearing seed for nucleating algorithmic self-assemblyBarish, Robert D.; Schulman, Rebecca; Rothemund, Paul W. K.; Winfree, ErikProceedings of the National Academy of Sciences of the United States of America (2009), 106 (15), 6054-6059CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Self-assembly creates natural mineral, chem., and biol. structures of great complexity. Often, the same starting materials have the potential to form an infinite variety of distinct structures; information in a seed mol. can det. which form is grown as well as where and when. These phenomena can be exploited to program the growth of complex supramol. structures, as demonstrated by the algorithmic self-assembly of DNA tiles. However, the lack of effective seeds has limited the reliability and yield of algorithmic crystals. Here, the authors present a programmable DNA origami seed that can display up to 32 distinct binding sites and demonstrate the use of seeds to nucleate three types of algorithmic crystals. In the simplest case, the starting materials are a set of tiles that can form cryst. ribbons of any width; the seed directs assembly of a chosen width with >90% yield. Increased structural diversity is obtained by using tiles that copy a binary string from layer to layer; the seed specifies the initial string and triggers growth under near-optimal conditions where the bit copying error rate is <0.2%. Increased structural complexity is achieved by using tiles that generate a binary counting pattern; the seed specifies the initial value for the counter. Self-assembly proceeds in a one-pot annealing reaction involving up to 300 DNA strands contg. >17 kb of sequence information. In sum, this work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication.
- 9Schulman, R.; Winfree, E. Programmable Control of Nucleation for Algorithmic Self-Assembly. SIAM Journal on Computing 2010, 39 (4), 1581– 1616, DOI: 10.1137/070680266There is no corresponding record for this reference.
- 10Jacobs, W. M.; Reinhardt, A.; Frenkel, D. Rational Design of Self-Assembly Pathways for Complex Multicomponent Structures. Proc. Natl. Acad. Sci. U. S. A. 2015, 112 (20), 6313– 6318, DOI: 10.1073/pnas.150221011210https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXns1Olu74%253D&md5=a9770b10a0bc7fcc37c45f7a84373dfaRational design of self-assembly pathways for complex multicomponent structuresJacobs, William M.; Reinhardt, Aleks; Frenkel, DaanProceedings of the National Academy of Sciences of the United States of America (2015), 112 (20), 6313-6318CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The field of complex self-assembly is moving toward the design of multiparticle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such "addressable complexity," we need to understand the factors that optimize the yield and the kinetics of self-assembly. Here we use a simple theor. method to explain the key features responsible for the unexpected success of DNA-brick expts., which are currently the only demonstration of reliable self-assembly with such a large no. of components. Simulations confirm that our theory accurately predicts the narrow temp. window in which error-free assembly can occur. Even more strikingly, our theory predicts that correct assembly of the complete structure may require a time-dependent exptl. protocol. Furthermore, we predict that low coordination nos. result in nonclassical nucleation behavior, which we find to be essential for achieving optimal nucleation kinetics under mild growth conditions. We also show that, rather surprisingly, the use of heterogeneous bond energies improves the nucleation kinetics and in fact appears to be necessary for assembling certain intricate 3D structures. This observation makes it possible to sculpt nucleation pathways by tuning the distribution of interaction strengths. These insights not only suggest how to improve the design of structures based on DNA bricks, but also point the way toward the creation of a much wider class of chem. or colloidal structures with addressable complexity.
- 11Reinhardt, A.; Ho, C. P.; Frenkel, D. Effects of Co-Ordination Number on the Nucleation Behaviour in Many-Component Self-Assembly. Faraday Discuss. 2016, 186, 215– 228, DOI: 10.1039/C5FD00135H11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFamsbvN&md5=d5488cba461a6f2a9e9ae22f27d7d02eEffects of co-ordination number on the nucleation behaviour in many-component self-assemblyReinhardt, Aleks; Ho, Chon Pan; Frenkel, DaanFaraday Discussions (2016), 186 (Nanoparticle Assembly), 215-228CODEN: FDISE6; ISSN:1359-6640. (Royal Society of Chemistry)We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behavior, in the form of free-energy barriers to nucleation, changes significantly as the co-ordination no. of the building blocks is changed from 4 to 8 to 12. Unlike tetrahedral structures - which roughly correspond to DNA bricks that have been studied in expts. - the shapes of the free-energy barriers of higher co-ordination structures depend strongly on the supersatn., and such structures require a very significant driving force for structure growth before nucleation becomes thermally accessible. Although growth at high supersatn. results in more defects during self-assembly, we show that high co-ordination no. structures can still be assembled successfully in computer simulations and that they exhibit self-assembly behavior analogous to DNA bricks. In particular, the self-assembly remains modular, enabling in principle a wide variety of nanostructures to be assembled, with a greater spatial resoln. than is possible in low co-ordination structures.
- 12Winfree, E. Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments. J. Biomol. Struct. Dyn. 2000, 17 (Suppl 1), 263– 270, DOI: 10.1080/07391102.2000.1050663012https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3s7ptlGruw%253D%253D&md5=e42edace138d22ba350a0849b3876182Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly ExperimentsWinfree EJournal of biomolecular structure & dynamics (2000), 17 Suppl 1 (), 263-70 ISSN:.Abstract Biology makes things far smaller and more complex than anything produced by human engineering. The biotechnology revolution has for the first time given us the tools necessary to consider engineering on the molecular level. Research in DNA computation, launched by Len Adleman, has opened the door for experimental study of programmable biochemical reactions. Here we focus on a single biochemical mechanism, the self-assembly of DNA structures, that is theoretically sufficient for Turing-universal computation. The theory combines Hao Wang's purely mathematical Tiling Problem with the branched DNA constructions of Ned Seeman. In the context of mathematical logic, Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. For a biochemical implementation, we will need molecular Wang tiles. DNA molecular structures and intermolecular interactions are particularly amenable to design and are sufficient for the creation of complex molecular objects. The structure of individual molecules can be designed by maximizing desired and minimizing undesired Watson-Crick complementarity. Intermolecular interactions are programmed by the design of sticky ends that determine which molecules associate, and how. The theory has been demonstrated experimentally using a system of synthetic DNA double-crossover molecules that self-assemble into two-dimensional crystals that have been visualized by atomic force microscopy. This experimental system provides an excellent platform for exploring the relationship between computation and molecular self-assembly, and thus represents a first step toward the ability to program molecular reactions and molecular structures.
- 13Woods, D.; Doty, D.; Myhrvold, C.; Hui, J.; Zhou, F.; Yin, P.; Winfree, E. Diverse and Robust Molecular Algorithms Using Reprogrammable DNA Self-Assembly. Nature 2019, 567 (7748), 366– 372, DOI: 10.1038/s41586-019-1014-913https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXotFansrg%253D&md5=aedf2cbf2295bd3597c79c6ec6d15019Diverse and robust molecular algorithms using reprogrammable DNA self-assemblyWoods, Damien; Doty, David; Myhrvold, Cameron; Hui, Joy; Zhou, Felix; Yin, Peng; Winfree, ErikNature (London, United Kingdom) (2019), 567 (7748), 366-372CODEN: NATUAS; ISSN:0028-0836. (Nature Research)Mol. biol. provides an inspiring proof-of-principle that chem. systems can store and process information to direct mol. activities such as the fabrication of complex structures from mol. components. To develop information-based chem. as a technol. for programming matter to function in ways not seen in biol. systems, it is necessary to understand how mol. interactions can encode and execute algorithms. The self-assembly of relatively simple units into complex products1 is particularly well suited for such investigations. Theory that combines math. tiling and statistical-mech. models of mol. crystn. has shown that algorithmic behavior can be embedded within mol. self-assembly processes2,3, and this has been exptl. demonstrated using DNA nanotechnol.4 with up to 22 tile types5-11. However, many information technologies exhibit a complexity threshold-such as the min. transistor count needed for a general-purpose computer-beyond which the power of a reprogrammable system increases qual., and it has been unclear whether the biophysics of DNA self-assembly allows that threshold to be exceeded. Here we report the design and exptl. validation of a DNA tile set that contains 355 single-stranded tiles and can, through simple tile selection, be reprogrammed to implement a wide variety of 6-bit algorithms. We use this set to construct 21 circuits that execute algorithms including copying, sorting, recognizing palindromes and multiples of 3, random walking, obtaining an unbiased choice from a biased random source, electing a leader, simulating cellular automata, generating deterministic and randomized patterns, and counting to 63, with an overall per-tile error rate of less than 1 in 3,000. These findings suggest that mol. self-assembly could be a reliable algorithmic component within programmable chem. systems. The development of mol. machines that are reprogrammable-at a high level of abstraction and thus without requiring knowledge of the underlying physics-will establish a creative space in which mol. programmers can flourish.
- 14Schulman, R.; Yurke, B.; Winfree, E. Robust Self-Replication of Combinatorial Information via Crystal Growth and Scission. Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (17), 6405– 6410, DOI: 10.1073/pnas.111781310914https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xmslyjtrg%253D&md5=d8842348d4bdb658a53cecf70a9cf399Robust self-replication of combinatorial information via crystal growth and scissionSchulman, Rebecca; Yurke, Bernard; Winfree, ErikProceedings of the National Academy of Sciences of the United States of America (2012), 109 (17), 6405-6410, S6405/1-S6405/55CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Understanding how a simple chem. system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary mol. design techniques. During biol. sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then sep. the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chem. sequences without enzymes. Crystal growth propagates a sequence of bits while mech.-induced scission creates new growth fronts. Together, these processes exponentially increase the no. of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% Of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and Darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chem. sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.
- 15He, X.; Sha, R.; Zhuo, R.; Mi, Y.; Chaikin, P. M.; Seeman, N. C. Exponential Growth and Selection in Self-Replicating Materials from DNA Origami Rafts. Nat. Mater. 2017, 16 (10), 993– 997, DOI: 10.1038/nmat498615https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFOju7bP&md5=2a6d8274bfcd1132ad849902620ef46dExponential growth and selection in self-replicating materials from DNA origami raftsHe, Xiaojin; Sha, Ruojie; Zhuo, Rebecca; Mi, Yongli; Chaikin, Paul M.; Seeman, Nadrian C.Nature Materials (2017), 16 (10), 993-997CODEN: NMAACR; ISSN:1476-1122. (Nature Research)Self-replication and evolution under selective pressure are inherent phenomena in life, but few artificial systems exhibit these phenomena. The authors have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temp. and UV illumination, producing >7 million copies in 24 cycles. The authors demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ∼1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8; similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.
- 16Minev, D.; Wintersinger, C. M.; Ershova, A.; Shih, W. M. Robust Nucleation Control via Crisscross Polymerization of Highly Coordinated DNA Slats. Nat. Commun. 2021, 12 (1), 1741, DOI: 10.1038/s41467-021-21755-716https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXmvFKrurc%253D&md5=74d7c88f24dfc06521c573263128de6dRobust nucleation control via crisscross polymerization of highly coordinated DNA slatsMinev, Dionis; Wintersinger, Christopher M.; Ershova, Anastasia; Shih, William M.Nature Communications (2021), 12 (1), 1741CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)Natural biomol. assemblies such as actin filaments or microtubules can exhibit all-or-nothing polymn. in a kinetically controlled fashion. The kinetic barrier to spontaneous nucleation arises in part from pos. cooperativity deriving from joint-neighbor capture, where stable capture of incoming monomers requires straddling multiple subunits on a filament end. For programmable DNA self-assembly, it is likewise desirable to suppress spontaneous nucleation to enable powerful capabilities such as all-or-nothing assembly of nanostructures larger than a single DNA origami, ultrasensitive detection, and more robust algorithmic assembly. However, existing DNA assemblies use monomers with low coordination nos. that present an effective kinetic barrier only for slow, near-reversible growth conditions. Here we introduce crisscross polymn. of elongated slat monomers that engage beyond nearest neighbors which sustains the kinetic barrier under conditions that promote fast, irreversible growth. By implementing crisscross slats as single-stranded DNA, we attain strictly seed-initiated nucleation of crisscross ribbons with distinct widths and twists.
- 17Wintersinger, C. M.; Minev, D.; Ershova, A.; Sasaki, H. M.; Gowri, G.; Berengut, J. F.; Corea-Dilbert, F. E.; Yin, P.; Shih, W. M. Multi-Micron Crisscross Structures Grown from DNA-Origami Slats. Nat. Nanotechnol. 2023, 18, 281– 289, DOI: 10.1038/s41565-022-01283-117https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XjtFyms7vF&md5=89a134fd9f91a2a40d6764b6db373085Multi-micron crisscross structures grown from DNA-origami slatsWintersinger, Christopher M.; Minev, Dionis; Ershova, Anastasia; Sasaki, Hiroshi M.; Gowri, Gokul; Berengut, Jonathan F.; Corea-Dilbert, F. Eduardo; Yin, Peng; Shih, William M.Nature Nanotechnology (2023), 18 (3), 281-289CODEN: NNAABX; ISSN:1748-3387. (Nature Portfolio)Living systems achieve robust self-assembly across a wide range of length scales. In the synthetic realm, nanofabrication strategies such as DNA origami have enabled robust self-assembly of submicron-scale shapes from a multitude of single-stranded components. To achieve greater complexity, subsequent hierarchical joining of origami can be pursued. However, erroneous and missing linkages restrict the no. of unique origami that can be practically combined into a single design. Here we extend crisscross polymn., a strategy previously demonstrated with single-stranded components, to DNA-origami 'slats' for fabrication of custom multi-micron shapes with user-defined nanoscale surface patterning. Using a library of ∼2,000 strands that are combinatorially arranged to create unique DNA-origami slats, we realize finite structures composed of >1,000 uniquely addressable slats, with a mass exceeding 5 GDa, lateral dimensions of roughly 2μm and a multitude of periodic structures. Robust prodn. of target crisscross structures is enabled through strict control over initiation, rapid growth and minimal premature termination, and highly orthogonal binding specificities. Thus crisscross growth provides a route for prototyping and scalable prodn. of structures integrating thousands of unique components (i.e., origami slats) that each is sophisticated and molecularly precise.
- 18Zhang, D. Y.; Seelig, G. Dynamic DNA Nanotechnology Using Strand-Displacement Reactions. Nat. Chem. 2011, 3 (2), 103– 113, DOI: 10.1038/nchem.95718https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXovVGhsg%253D%253D&md5=eab3b5fa59fa957ec01f89072dd2089cDynamic DNA nanotechnology using strand-displacement reactionsZhang, David Yu; Seelig, GeorgNature Chemistry (2011), 3 (2), 103-113CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)A review. The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnol. is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous mol. motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, the authors review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behavior.
- 19Srinivas, N.; Ouldridge, T. E.; Šulc, P.; Schaeffer, J. M.; Yurke, B.; Louis, A. A.; Doye, J. P. K.; Winfree, E. On the Biophysics and Kinetics of Toehold-Mediated DNA Strand Displacement. Nucleic Acids Res. 2013, 41 (22), 10641– 10658, DOI: 10.1093/nar/gkt80119https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvV2lsbjP&md5=352336a395164bf796b4e6220e2edd04On the biophysics and kinetics of toehold-mediated DNA strand displacementSrinivas, Niranjan; Ouldridge, Thomas E.; Sulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, ErikNucleic Acids Research (2013), 41 (22), 10641-10658CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)Dynamic DNA nanotechnol. often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been exptl. characterized and phenomenol. modeled, detailed biophys. understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained mol. model that incorporates 3D geometric and steric effects. Further, we exptl. investigate the thermodn. of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the phys. process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodn. penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the addnl. overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophys. explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex mol. systems.
- 20Danos, V.; Feret, J.; Fontana, W.; Harmer, R.; Krivine, J. Rule-Based Modelling of Cellular Signalling. In CONCUR 2007 – Concurrency Theory; Caires, L., Vasconcelos, V. T., Eds.; Lecture Notes in Computer Science; Springer: Berlin, Heidelberg, 2007; pp 17– 41, DOI: 10.1007/978-3-540-74407-8_3 .There is no corresponding record for this reference.
- 21Boutillier, P.; Maasha, M.; Li, X.; Medina-Abarca, H. F.; Krivine, J.; Feret, J.; Cristescu, I.; Forbes, A. G.; Fontana, W. The Kappa Platform for Rule-Based Modeling. Bioinformatics 2018, 34 (13), i583– i592, DOI: 10.1093/bioinformatics/bty27221https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtV2gt7fO&md5=081755d2d99c58affbd2692eaf5dcd0cThe Kappa platform for rule-based modelingBoutillier, Pierre; Maasha, Mutaamba; Li, Xing; Medina-Abarca, Hector F.; Krivine, Jean; Feret, Jerome; Cristescu, Ioana; Forbes, Angus G.; Fontana, WalterBioinformatics (2018), 34 (13), i583-i592CODEN: BOINFP; ISSN:1367-4811. (Oxford University Press)Motivation: We present an overview of the Kappa platform, an integrated suite of anal. and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addn. to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biol. systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction. Results: We discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolns., the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymn., such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for early events in EGF signaling.
- 22Högberg, B.; Liedl, T.; Shih, W. M. Folding DNA Origami from a Double-Stranded Source of Scaffold. J. Am. Chem. Soc. 2009, 131 (26), 9154– 9155, DOI: 10.1021/ja902569x22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXnt1OnsbY%253D&md5=e903ecdad97e4061c58037c8019dd5b8Folding DNA Origami from a Double-Stranded Source of ScaffoldHogberg, Bjorn; Liedl, Tim; Shih, William M.Journal of the American Chemical Society (2009), 131 (26), 9154-9155CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Combined heat and chem. denaturation of double-stranded DNA scaffold strands in the presence of staple strands, followed by a sudden temp. drop and then stepwise dialysis to remove the chem. denaturant, leads to self-assembly of two distinct DNA-origami structures. We have shown that it is possible to fold the individual strands of a dsDNA mol. into two discrete nanoscale objects in a one-pot reaction contg. a mixt. of two sets of oligonucleotide staple strands. Even when only one set of staple strands is added the rapid temp. drop following denaturation enables formation of the DNA-origami kinetic product over reannealing of dsDNA. This method extends DNA origami by enabling access to a much broader range of scaffolds, including open circular DNA, linear plasmid DNA, and PCR products. This strategy also provides a means to sort the two strands of a dsDNA mol. based on programmable changes in size and gel mobility.
- 23Süß, B.; Flekna, G.; Wagner, M.; Hein, I. Studying the Effect of Single Mismatches in Primer and Probe Binding Regions on Amplification Curves and Quantification in Real-Time PCR. J. Microbiol. Methods 2009, 76 (3), 316– 319, DOI: 10.1016/j.mimet.2008.12.00323https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhvFGqsbY%253D&md5=c8f77a3e5767c04d7bd5d571562c408bStudying the effect of single mismatches in primer and probe binding regions on amplification curves and quantification in real-time PCRSuess, Beate; Flekna, Gabriele; Wagner, Martin; Hein, IngeborgJournal of Microbiological Methods (2009), 76 (3), 316-319CODEN: JMIMDQ; ISSN:0167-7012. (Elsevier B.V.)Comparison of a broad range of characteristics of real-time PCR amplification curves yielded only slight alterations for low nos. of mismatches in the primer binding regions, resulting in a quantification error up to 63.12%. The effects were more pronounced for mismatches in the probe binding region and resulted in a quantification error up to 33%.
- 24Zimmermann, F.; Urban, M.; Krüger, C.; Walter, M.; Wölfel, R.; Zwirglmaier, K. In Vitro Evaluation of the Effect of Mutations in Primer Binding Sites on Detection of SARS-CoV-2 by RT-QPCR. Journal of Virological Methods 2022, 299, 114352 DOI: 10.1016/j.jviromet.2021.11435224https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXisVyrsrjN&md5=72e6fc563ffc25e7459173854a3a878fIn vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCRZimmermann, Fee; Urban, Maria; Krueger, Christian; Walter, Mathias; Woelfel, Roman; Zwirglmaier, KatrinJournal of Virological Methods (2022), 299 (), 114352CODEN: JVMEDH; ISSN:0166-0934. (Elsevier B.V.)A no. of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous com. assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases - as seen with the B.1.1.7 variant - can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from -0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charite RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values obsd. with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.
- 25Nickels, P. C.; Ke, Y.; Jungmann, R.; Smith, D. M.; Leichsenring, M.; Shih, W. M.; Liedl, T.; Högberg, B. DNA Origami Structures Directly Assembled from Intact Bacteriophages. Small 2014, 10 (9), 1765– 1769, DOI: 10.1002/smll.20130344225https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXisFWhtLk%253D&md5=21f5596b4b865047e2b8718f7c8e5c1cDNA Origami Structures Directly Assembled from Intact BacteriophagesNickels, Philipp C.; Ke, Yonggang; Jungmann, Ralf; Smith, David M.; Leichsenring, Marc; Shih, William M.; Liedl, Tim; Hoegberg, BjoernSmall (2014), 10 (9), 1765-1769CODEN: SMALBC; ISSN:1613-6810. (Wiley-VCH Verlag GmbH & Co. KGaA)A fast and versatile method for the direct employment of genomic nucleic acids from naturally occurring bacteriophages has been developed. Two bacteriophages (M13 and λ) were used as scaffold sources for the assembly of DNA origami constructs without further purifn. of the genomic DNA. A single DNA origami structure directly from the entire bacteriophage λ genome, although with low yields.
- 26Doty, D.; Lee, B. L.; Stérin, T. Scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26); Geary, C., Patitz, M. J., Eds.; Leibniz International Proceedings in Informatics (LIPIcs); Schloss Dagstuhl–Leibniz-Zentrum für Informatik: Dagstuhl, Germany, 2020; Vol. 174, p 9:1– 9:17, DOI: 10.4230/LIPIcs.DNA.2020.9 .There is no corresponding record for this reference.
- 27Zadeh, J. N.; Steenberg, C. D.; Bois, J. S.; Wolfe, B. R.; Pierce, M. B.; Khan, A. R.; Dirks, R. M.; Pierce, N. A. NUPACK: Analysis and Design of Nucleic Acid Systems. J. Comput. Chem. 2011, 32 (1), 170– 173, DOI: 10.1002/jcc.2159627https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsVCjsLzP&md5=9c60f0134ea55d9335301e2efe1602e8NUPACK: analysis and design of nucleic acid systemsZadeh, Joseph N.; Steenberg, Conrad D.; Bois, Justin S.; Wolfe, Brian R.; Pierce, Marshall B.; Khan, Asif R.; Dirks, Robert M.; Pierce, Niles A.Journal of Computational Chemistry (2011), 32 (1), 170-173CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)The Nucleic Acid Package (NUPACK) is a growing software suite for the anal. and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.
- 28Fornace, M. E.; Huang, J.; Newman, C. T.; Porubsky, N. J.; Pierce, M. B.; Pierce, N. A. NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems ChemRxiv 2022, DOI: 10.26434/chemrxiv-2022-xv98l , November 10 (accessed 2023–12–03).There is no corresponding record for this reference.
- 29Schindelin, J.; Arganda-Carreras, I.; Frise, E.; Kaynig, V.; Longair, M.; Pietzsch, T.; Preibisch, S.; Rueden, C.; Saalfeld, S.; Schmid, B. Fiji: An Open-Source Platform for Biological-Image Analysis. Nat. Methods 2012, 9 (7), 676– 682, DOI: 10.1038/nmeth.201929https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVKnurbJ&md5=ad150521a33367d37a800bee853dd9dbFiji: an open-source platform for biological-image analysisSchindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, AlbertNature Methods (2012), 9 (7_part1), 676-682CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)Fiji is a distribution of the popular open-source software ImageJ focused on biol.-image anal. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biol. research communities.
- 30Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. Structural, Mechanical, and Thermodynamic Properties of a Coarse-Grained DNA Model. J. Chem. Phys. 2011, 134 (8), 085101 DOI: 10.1063/1.355294630https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXit1Kltbs%253D&md5=fe949636e1e4c02c0595c036e504b2eeStructural, mechanical, and thermodynamic properties of a coarse-grained DNA modelOuldridge, Thomas E.; Louis, Ard A.; Doye, Jonathan P. K.Journal of Chemical Physics (2011), 134 (8), 085101/1-085101/22CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We explore in detail the structural, mech., and thermodn. properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers. Effective interactions are used to represent chain connectivity, excluded vol., base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson-Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an "av. base" description of DNA. We quantify the relation to expt. of the thermodn. of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helixes. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodn. of the duplex formation transition. (c) 2011 American Institute of Physics.
- 31Šulc, P.; Romano, F.; Ouldridge, T. E.; Rovigatti, L.; Doye, J. P. K.; Louis, A. A. Sequence-Dependent Thermodynamics of a Coarse-Grained DNA Model. J. Chem. Phys. 2012, 137 (13), 135101, DOI: 10.1063/1.475413231https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsVejtr3L&md5=cda4715130b0234bd2cb2581df954e73Sequence-dependent thermodynamics of a coarse-grained DNA modelSulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Rovigatti, Lorenzo; Doye, Jonathan P. K.; Louis, Ard A.Journal of Chemical Physics (2012), 137 (13), 135101/1-135101/14CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We introduce a sequence-dependent parametrization for a coarse-grained DNA model originally designed to reproduce the properties of DNA mols. with av. sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temps. of short duplexes. By developing a histogram re-weighting technique, we are able to fit our parameters to the melting temps. of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its m.p., (c) the effects of stacking strength in the loop on the melting temp. of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with exptl. data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software. (c) 2012 American Institute of Physics.
- 32Poppleton, E.; Romero, R.; Mallya, A.; Rovigatti, L.; Šulc, P. OxDNA.Org: A Public Webserver for Coarse-Grained Simulations of DNA and RNA Nanostructures. Nucleic Acids Res. 2021, 49 (W1), W491– W498, DOI: 10.1093/nar/gkab32432https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvV2isLfK&md5=a5ed15f30ec7da67deaa2d42e1650733OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructuresPoppleton, Erik; Romero, Roger; Mallya, Aatmik; Rovigatti, Lorenzo; Sulc, PetrNucleic Acids Research (2021), 49 (W1), W491-W498CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnol. community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA. org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA mol. dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-phys. states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and anal. interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user's specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the tech. aspects of mol. simulation. The webserver is freely available at oxdna.org.
- 33Maffeo, C.; Aksimentiev, A. MrDNA: A Multi-Resolution Model for Predicting the Structure and Dynamics of DNA Systems. Nucleic Acids Res. 2020, 48 (9), 5135– 5146, DOI: 10.1093/nar/gkaa20033https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisVKlurfJ&md5=227f1d0a8a6cb7f01a56808bcdb4b652MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systemsMaffeo, Christopher; Aksimentiev, AlekseiNucleic Acids Research (2020), 48 (9), 5135-5146CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)Although the field of structural DNA nanotechnol. has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of exptl. characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resoln. simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resoln. structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equil. structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied elec. field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and mol. graphics tools.
- 34DNA Lab: Xgrow Tile Assembly Simulator. https://www.dna.caltech.edu/Xgrow/ (accessed Sep 14, 2023).There is no corresponding record for this reference.
- 35Doty, D.; Fleming, H.; Hader, D.; Patitz, M. J.; Vaughan, L. A. Accelerating Self-Assembly of Crisscross Slat Systems. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29); Leibniz International Proceedings in Informatics (LIPIcs); 2023; Vol. 276, pp 7:1– 7:23, DOI: 10.4230/LIPIcs.DNA.29.7 .There is no corresponding record for this reference.
- 36Page, M. I.; Jencks, W. P. Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect. Proc. Natl. Acad. Sci. U. S. A. 1971, 68 (8), 1678– 1683, DOI: 10.1073/pnas.68.8.167836https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE3MXltVGhtLw%253D&md5=f2190b0dde6c8b5ffdf43adec063265aEntropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effectPage, Michael I.; Jencks, William P.Proceedings of the National Academy of Sciences of the United States of America (1971), 68 (8), 1678-83CODEN: PNASA6; ISSN:0027-8424.Translational and (overall) rotational motions provide the important entropic driving force for enzymic and intramol. rate accelerations and the chelate effect; internal rotations and unusually severe orientational requirements are generally of secondary importance. The loss of translational and (overall) rotational entropy for 2 → 1 reactions in soln. is ordinarily on the order of 45 entropy units (e.u.) (std. state M, 25°); the translational entropy is much larger than 8 e.u. (corresponding to 55 M). Low-frequency motions in products and transition states, ∼17 e.u. for cyclopentadiene dimerization, partially compensate for this loss, but effective concns. on the order of 108 M may be accounted for without the introduction of new chem. concepts or terms.
Supporting Information
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.3c08205.
Scadnano design schematics; additional agarose gel and negative-stain TEM data; and Kappa simulation constraints and simulated data (PDF)
Spreadsheet of all DNA sequences used in this work (XLSX)
Animation illustrating process of crisscross ribbon scission, with ribbon growth omitted for clarity. Slat types are colored as in Figure 2 (MP4)
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