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Robust nucleation control via crisscross polymerization of DNA slats

Dionis Minev, Christopher M. Wintersinger, Anastasia Ershova, William M. Shih
doi: https://doi.org/10.1101/2019.12.11.873349
Dionis Minev
John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USAWyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USADepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USADepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Christopher M. Wintersinger
John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USAWyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USADepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USADepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Anastasia Ershova
Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USADepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USADepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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William M. Shih
Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USADepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USADepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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  • For correspondence: William_Shih@dfci.harvard.edu
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Abstract

Natural biomolecular assemblies such as actin filaments or microtubules polymerize in a nucleation-limited fashion1,2. The barrier to nucleation arises in part from chelate cooperativity, where stable capture of incoming monomers requires straddling multiple subunits on a filament end3. For programmable self-assembly from building blocks such as synthetic DNA4–23, it is likewise desirable to be able to suppress spontaneous nucleation24–31. However, existing approaches that exploit just a low level of cooperativity can limit spontaneous nucleation only for slow growth, near-equilibrium conditions32. Here we introduce ultracooperative assembly of ribbons densely woven from single-stranded DNA slats. An inbound “crisscross” slat snakes over and under six or more previously captured slats on a growing ribbon end, forming weak but specific half-duplex interactions with each. We demonstrate growth of crisscross ribbons with distinct widths and twists to lengths representing many thousands of slat additions. Strictly seed-initiated extension is attainable over a broad range of temperatures, divalent-cation concentrations, and free-slat concentrations, without unseeded ribbons arising even after a hundred hours to the limit of agarose-gel detection. We envision that crisscross assembly will be broadly enabling for all-or-nothing formation of microstructures with nanoscale features, algorithmic self-assembly, and signal amplification in diagnostic applications requiring extreme sensitivity.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 12, 2019.
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Robust nucleation control via crisscross polymerization of DNA slats
Dionis Minev, Christopher M. Wintersinger, Anastasia Ershova, William M. Shih
bioRxiv 2019.12.11.873349; doi: https://doi.org/10.1101/2019.12.11.873349
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Robust nucleation control via crisscross polymerization of DNA slats
Dionis Minev, Christopher M. Wintersinger, Anastasia Ershova, William M. Shih
bioRxiv 2019.12.11.873349; doi: https://doi.org/10.1101/2019.12.11.873349

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