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Journal articles

Overstretching and force-driven strand separation of double-helix DNA.

Abstract : We analyze whether the "overstretched," or "S" form of double-stranded DNA consists of essentially separated, or essentially interacting, polynucleotide strands. Comparison of force-extension data for S-DNA and single-stranded DNA shows S-DNA to be distinct from both double helix and single-stranded forms. We use a simple thermodynamical model for tension-melted double-stranded DNA, which indicates that the overstretching transition near 65 piconewtons cannot be explained in terms of conversion of double helix to noninteracting polynucleotide strands. However, the single-strand-like response observed in some experiments can be explained in terms of "unpeeling" of large regions of one strand, starting from nicks on the original double helix. We show that S-DNA becomes unstable to unpeeling at large forces, and that at low ionic strength, or for weakly base-paired sequences, unpeeling can preempt formation of S-DNA. We also analyze the kinetics of unpeeling including the effect of sequence-generated free energy inhomogeneity. We find that strongly base-paired regions generate large barriers that stabilize DNA against unpeeling. For long genomic sequences, these barriers to unpeeling cannot be kinetically crossed until force exceeds approximately 150 piconewtons.
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Contributor : Laurent Bourdieu Connect in order to contact the contributor
Submitted on : Thursday, May 10, 2007 - 2:27:50 PM
Last modification on : Wednesday, March 9, 2022 - 7:00:02 PM


  • HAL Id : hal-00145485, version 1



Simona Cocco, Jie Yan, Jean-Francois Léger, Didier Chatenay, John F Marko. Overstretching and force-driven strand separation of double-helix DNA.. Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, American Physical Society, 2004, 70 (1 Pt 1), pp.011910. ⟨hal-00145485⟩



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