Chain persistency in single-stranded DNA.

Anirban Sain; Bae-Yeun Ha; Heng-Kwong Tsao; Jeff Z Y Chen

doi:10.1103/physreve.69.061913

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Chain persistency in single-stranded DNA.

Anirban Sain·Bae-Yeun Ha·Heng-Kwong Tsao·Jeff Z Y Chen

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Abstract

We develop a theoretical approach to hairpin-loop formation of single-stranded (ss) DNA by treating the strand as a two-state system in which bases are either "stacked" or "unstacked." The looping kinetics of ssDNA is shown to be intrinsically different from that of a wormlike chain; it is mainly controlled by stacking-breakage probability, not by the mean curvature of loops, and highly sensitive to the composition of the loop as seen in recent experiments. Our estimate of a stacking energy for poly ( dA ), -3.9 kcal/mol, is consistent with known results.

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Base Sequence Computer Simulation DNA, Single-Stranded Models, Chemical Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Sequence Analysis, DNA Journal Article Research Support, Non-U.S. Gov't

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Anirban Sain, Bae-Yeun Ha, Heng-Kwong Tsao, Jeff Z Y Chen. 2004-06-15. Chain persistency in single-stranded DNA.. https://doi.org/10.1103/physreve.69.061913

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