4.8 Article

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

期刊

NUCLEIC ACIDS RESEARCH
卷 48, 期 19, 页码 10726-10738

出版社

OXFORD UNIV PRESS
DOI: 10.1093/nar/gkaa854

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资金

  1. National Science Foundation [1931487]
  2. Arizona State University
  3. Office of Advanced Cyberinfrastructure (OAC)
  4. Direct For Computer & Info Scie & Enginr [1931487] Funding Source: National Science Foundation

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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 k(on) is increased by the crowding effect, while k(on) is changed only moderately. The increase in k(on) 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.

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