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Understanding DNA interactions in crowded environments with a coarse-grained model

View ORCID ProfileFan Hong, View ORCID ProfileJohn S. Schreck, View ORCID ProfilePetr Šulc
doi: https://doi.org/10.1101/2020.06.08.140434
Fan Hong
1School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
2Wyss Institute, Harvard University, Boston, MA 02115, USA
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John S. Schreck
1School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
3Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA
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Petr Šulc
1School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
4Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
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  • For correspondence: psulc@asu.edu
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Abstract

Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology.

Competing Interest Statement

The authors have declared no competing interest.

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Posted June 09, 2020.
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Understanding DNA interactions in crowded environments with a coarse-grained model
Fan Hong, John S. Schreck, Petr Šulc
bioRxiv 2020.06.08.140434; doi: https://doi.org/10.1101/2020.06.08.140434
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Understanding DNA interactions in crowded environments with a coarse-grained model
Fan Hong, John S. Schreck, Petr Šulc
bioRxiv 2020.06.08.140434; doi: https://doi.org/10.1101/2020.06.08.140434

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