Chain persistency in single-stranded DNA.
We develop a theoretical approach to hairpin-loop formation of single-stranded (ss) DNA by treating the strand as a two-state system in which bases are either "stacked" or "unstacked." The looping kinetics of ssDNA is shown to be intrinsically different from that of a wormlike chain; it is mainly controlled by stacking-breakage probability, not by the mean curvature of loops, and highly sensitive to the composition of the loop as seen in recent experiments. Our estimate of a stacking energy for poly ( dA ), -3.9 kcal/mol, is consistent with known results.
Sain
Anirban
A
Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.
Ha
Bae-Yeun
BY
Tsao
Heng-Kwong
HK
Chen
Jeff Z Y
JZ
D001483:Base Sequence; D003198:Computer Simulation; D004277:DNA, Single-Stranded / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods*
D004277:DNA, Single-Stranded