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PubMed · 17142263

Sequence-dependent twist-stretch coupling in DNA.

Timothée Lionnet·Filip Lankas
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Abstract

Recent single-molecule micromanipulation experiments on DNA subject to small distortion revealed positive coupling between DNA stretching and twisting--for instance, DNA elongates when overtwisted. Here we propose a method to calculate the twist-stretch coupling constant specific to a DNA fragment of a given sequence. The method employs a sequence-dependent dinucleotide force field and is based on constrained minimization of the fragment's deformation energy. Using a force field inferred from atomistic molecular dynamics simulations, we obtain the twist-stretch coupling for random sequence to be 0.30 nm/turn, close to experimental values. An exhaustive calculation for all oligomers of nine basepairs yields values between 0.14 and 0.45 nm/turn, positively correlated with the contents of pyrimidine-purine steps in the sequence. Our method is simple to use and allows one to explore the hypothesis that some sequences may be optimized for twist-stretch coupling.

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Base SequenceComputer SimulationDNAModels, ChemicalNucleic Acid ConformationJournal ArticleResearch Support, Non-U.S. Gov't

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Timothée Lionnet, Filip Lankas. 2006-12-01. Sequence-dependent twist-stretch coupling in DNA.. https://doi.org/10.1529/biophysj.106.099572

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