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arXiv · 0806.0505

Stretching chimeric DNA: a test for the putative S-form

Stephen Whitelam·Sander Pronk·Phillip L. Geissler
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Abstract

Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and technological application. Overstretching is thought by some to be a force-induced denaturation, and by others to consist of a transition to an elongated, hybridized state called S-DNA. Within a statistical mechanical model we consider the effect upon overstretching of extreme sequence heterogeneity. `Chimeric' sequences possessing halves of markedly different AT composition elongate under fixed external conditions via distinct, spatially segregated transitions. The corresponding force-extension data display two plateaux at forces whose difference varies with pulling rate in a manner that depends qualitatively upon whether the hybridized S-form is accessible. This observation implies a test for S-DNA that could be performed in experiment. Our results suggest that qualitatively different, spatially segregated conformational transitions can occur at a single thermodynamic state within single molecules of DNA.

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Stephen Whitelam, Sander Pronk, Phillip L. Geissler. 2008-06-03. Stretching chimeric DNA: a test for the putative S-form. https://doi.org/10.1063/1.3009266

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