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.
Cocco
Simona
S
Laboratoire de Dynamiques des Fluides Complexes, CNRS, 3 rue de l'Université, Strasbourg, France.
Yan
Jie
J
Léger
Jean-Francois
JF
Chatenay
Didier
D
Marko
John F
JF
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