title: 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 difference between stacked poly(dA) and unstacked polypyrimidine, finding it to be ∼-0.25 kBT/base and nearly constant over three orders of magnitude in salt concentration.
authors: Physics Department, University of California-Santa Barbara, Santa Barbara, California.
authors: Dustin B
authors: DB
authors: McIntosh
authors: Physics Department, University of California-Santa Barbara, Santa Barbara, California.
authors: Gina
authors: G
authors: Duggan
authors: Physics Department, École Normale Supérieure, Paris, France.
authors: Quentin
authors: Q
authors: Gouil
authors: Materials Department and Biomolecular Science and Engineering Program, University of California-Santa Barbara, Santa Barbara, California. Electronic address: saleh@engineering.ucsb.edu.
authors: Omar A
authors: OA
authors: Saleh
mesh_terms: D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004548:Elasticity; D011061:Poly A / Q000737:chemistry; D055672:Static Electricity
chemical_list: D004277:DNA, Single-Stranded; D011061:Poly A; C015465:poly(dA)