Stretching of long double-stranded DNA and RNA described by the same model.

Afanasyev, A. Y.; Onufriev, A. V.

doi:10.1101/2022.03.09.483706

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bioRxiv · 10.1101/2022.03.09.483706

Stretching of long double-stranded DNA and RNA described by the same model.

Afanasyev, A. Y.·Onufriev, A. V.

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Abstract

We propose a bead-spring model that 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 non-convex energy function of the spring. We provide an algorithm for obtaining five required parameters of the model from experimental force-extension curves. 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.

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Afanasyev, A. Y., Onufriev, A. V.. 2022-03-11. Stretching of long double-stranded DNA and RNA described by the same model.. https://doi.org/10.1101/2022.03.09.483706

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