Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods.

ABSTRACT: To form secondary structure, nucleic acids (NAs) must overcome electrostatic strand-strand repulsion, which is moderated by the surrounding atmosphere of screening ions. The free energy of NA folding therefore depends on the interactions of this ion atmosphere with both the folded and unfolded states. We quantify such interactions using the preferential ion interaction coefficient or ion excess: the number of ions present near the NA in excess of the bulk concentration. The ion excess of the folded, double-helical state has been extensively studied; however, much less is known about the salt-dependent ion excess of the unfolded, single-stranded state. We measure this quantity using three complementary approaches: a direct approach of Donnan equilibrium dialysis read out by atomic emission

SUBMITTER: Jacobson DR 

PROVIDER: S-EPMC4856996 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature