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

Simona Cocco, Jie Yan, Jean Francois Léger, Didier Chatenay, John F. Marko

Research output: Contribution to journalArticle

126 Scopus citations

Abstract

We analyze whether the “overstretched”, or “[Formula presented]” form of double-stranded DNA consists of essentially separated, or essentially interacting, polynucleotide strands. Comparison of force-extension data for [Formula presented]-DNA and single-stranded DNA shows [Formula presented]-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 [Formula presented]-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 [Formula presented]-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.

Original languageEnglish (US)
Number of pages1
JournalPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
Volume70
Issue number1
DOIs
StatePublished - Jan 1 2004

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Mathematical Physics
  • Condensed Matter Physics
  • Physics and Astronomy(all)

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