Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

J Chem Theory Comput. 2022 Jun 14;18(6):3911-3920. doi: 10.1021/acs.jctc.1c01221. Epub 2022 May 11.

Abstract

We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.

MeSH terms

  • DNA* / chemistry
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation
  • Polymers
  • RNA*

Substances

  • Polymers
  • RNA
  • DNA