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Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies
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    Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies
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    Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden,
    School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
    Address correspondence to [email protected]
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    ACS Nano

    Cite this: ACS Nano 2011, 5, 9, 7565–7575
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    https://doi.org/10.1021/nn202568q
    Published August 10, 2011
    Copyright © 2011 American Chemical Society

    Abstract

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    We demonstrate the stepwise assembly of a fully addressable polycyclic DNA hexagon nanonetwork for the preparation of a four-ring system, one of the biggest networks yet constructed from tripodal building blocks. We find that the yield exhibits a distinct upper level <100%, a fundamental problem of thermodynamic DNA assembly that appears to have been overlooked in the DNA nanotechnology literature. A simplistic model based on a single step-yield parameter y can quantitatively describe the total yield of DNA assemblies in one-pot reactions as Y = yduplexn, with n the number of hybridization steps. Experimental errors introducing deviations from perfect stoichiometry and the thermodynamics of hybridization equilibria contribute to decreasing the value of yduplex (on average y = 0.96 for our 10 base pair hybridization). For the four-ring system (n = 31), the total yield is thus less than 30%, which is clearly unsatisfactory if bigger nanoconstructs of this class are to be designed. Therefore, we introduced site-specific click chemistry for making and purifying robust building blocks for future modular constructs of larger assemblies. Although the present yield of this robust module was only about 10%, it demonstrates a first step toward a general fabrication approach. Interestingly, we find that the click yields follow quantitatively a binomial distribution, the predictability of which indicates the usefulness of preparing pools of pure and robust building blocks in this way. The binomial behavior indicates that there is no interference between the six simultaneous click reactions but that step-yield limiting factors such as topological constraints and Cu(I) catalyst concentration are local and independent.

    Copyright © 2011 American Chemical Society

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    Supporting Information

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    DNA sequences of oligonucleotides; analysis of the binomial distributions, starting from templates of different sizes and yield error analysis. This material is available free of charge via the Internet at http://pubs.acs.org.

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    This article is cited by 20 publications.

    1. Nicolò Zuin Fantoni, Afaf H. El-Sagheer, Tom Brown. A Hitchhiker’s Guide to Click-Chemistry with Nucleic Acids. Chemical Reviews 2021, 121 (12) , 7122-7154. https://doi.org/10.1021/acs.chemrev.0c00928
    2. Yuhang Dong, Chi Yao, Yi Zhu, Lu Yang, Dan Luo, Dayong Yang. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chemical Reviews 2020, 120 (17) , 9420-9481. https://doi.org/10.1021/acs.chemrev.0c00294
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    8. Vinod K. Tiwari, Manoj K. Jaiswal, Sanchayita Rajkhowa, Sumit K. Singh. Click Chemistry in Nucleic Acids. 2024, 437-478. https://doi.org/10.1007/978-981-97-4596-8_14
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    10. Yumeng Liao, Jiaxi Gao, Yuxuan Zhang, Yaxi Zhou, Ruo Yuan, Wenju Xu. Proximity ligation-responsive catalytic hairpin assembly-guided DNA dendrimers for synergistically amplified electrochemical biosensing. Sensors and Actuators B: Chemical 2020, 322 , 128566. https://doi.org/10.1016/j.snb.2020.128566
    11. Alessio Ottaviani, Federico Iacovelli, Andrea Idili, Mattia Falconi, Francesco Ricci, Alessandro Desideri. Engineering a responsive DNA triple helix into an octahedral DNA nanostructure for a reversible opening/closing switching mechanism: a computational and experimental integrated study. Nucleic Acids Research 2018, 46 (19) , 9951-9959. https://doi.org/10.1093/nar/gky857
    12. G. Chatelain, G. Clavé, C. Saint-Pierre, D. Gasparutto, S. Campidelli. Self-assembly of porphyrin–DNA hybrids into large flat nanostructures. Organic & Biomolecular Chemistry 2017, 15 (29) , 6257-6263. https://doi.org/10.1039/C7OB01267E
    13. Anna I. Ponomarenko, Vladimir A. Brylev, Ksenia A. Sapozhnikova, Alexey V. Ustinov, Igor A. Prokhorenko, Timofei S. Zatsepin, Vladimir A. Korshun. Tetrahedral DNA conjugates from pentaerythritol-based polyazides. Tetrahedron 2016, 72 (19) , 2386-2391. https://doi.org/10.1016/j.tet.2016.03.051
    14. Anupamjeet Kaur, Sukhmani Mann, Bhupesh Goyal, Bhupender Pal, Deepti Goyal. CuO nanostructures of variable shapes as an efficient catalyst for [3 + 2] cycloaddition of azides with terminal alkyne. RSC Advances 2016, 6 (104) , 102733-102743. https://doi.org/10.1039/C6RA20725A
    15. Guillaume Clavé, Grégory Chatelain, Arianna Filoramo, Didier Gasparutto, Christine Saint-Pierre, Eric Le Cam, Olivier Piétrement, Vincent Guérineau, Stéphane Campidelli. Synthesis of a multibranched porphyrin–oligonucleotide scaffold for the construction of DNA-based nano-architectures. Org. Biomol. Chem. 2014, 12 (17) , 2778-2783. https://doi.org/10.1039/C4OB00202D
    16. Piotr Hanczyc, Marek Samoc, Bengt Norden. Multiphoton absorption in amyloid protein fibres. Nature Photonics 2013, 7 (12) , 969-972. https://doi.org/10.1038/nphoton.2013.282
    17. Jonas Hannestad. DNA: Molecular Recognition and Information Storage. 2013, 11-28. https://doi.org/10.1007/978-3-319-01068-7_3
    18. Niklas Bosaeus, Afaf H. El-Sagheer, Tom Brown, Steven B. Smith, Björn Åkerman, Carlos Bustamante, Bengt Nordén. Tension induces a base-paired overstretched DNA conformation. Proceedings of the National Academy of Sciences 2012, 109 (38) , 15179-15184. https://doi.org/10.1073/pnas.1213172109
    19. Johan R. Johansson, Bengt Nordén. Sniffing out early reaction intermediates. Proceedings of the National Academy of Sciences 2012, 109 (7) , 2186-2187. https://doi.org/10.1073/pnas.1120308109
    20. Christopher K. McLaughlin, Graham D. Hamblin, Hanadi F. Sleiman. Supramolecular DNA assembly. Chemical Society Reviews 2011, 40 (12) , 5647. https://doi.org/10.1039/c1cs15253j

    ACS Nano

    Cite this: ACS Nano 2011, 5, 9, 7565–7575
    Click to copy citationCitation copied!
    https://doi.org/10.1021/nn202568q
    Published August 10, 2011
    Copyright © 2011 American Chemical Society

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