Overstretching and force-driven strand separation of double-helix DNA.
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.
Laboratoire de Dynamiques des Fluides Complexes, CNRS, 3 rue de l'Université, Strasbourg, France.
Simona
S
Cocco
Jie
J
Yan
Jean-Francois
JF
Léger
Didier
D
Chatenay
John F
JF
Marko
D020029:Base Pairing; D001483:Base Sequence; D001826:Body Fluids / Q000737:chemistry; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D004548:Elasticity; D007700:Kinetics; D008846:Micromanipulation / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012965:Sodium Chloride / Q000737:chemistry*; D012996:Solutions; D013314:Stress, Mechanical
D012996:Solutions; D012965:Sodium Chloride; D004247:DNA