Sequence-dependent elasticity and electrostatics of single-stranded DNA: signatures of base-stacking.

ABSTRACT: Base-stacking is a key factor in the energetics that determines nucleic acid structure. We measure the tensile response of single-stranded DNA as a function of sequence and monovalent salt concentration to examine the effects of base-stacking on the mechanical and thermodynamic properties of single-stranded DNA. By comparing the elastic response of highly stacked poly(dA) and that of a polypyrimidine sequence with minimal stacking, we find that base-stacking in poly(dA) significantly enhances the polymer's rigidity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than mean-field predictions. Further, we provide a model-independent estimate of the free energy differenc

SUBMITTER: McIntosh DB 

PROVIDER: S-EPMC3945002 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature