Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution.

ABSTRACT: Understanding biological and physical processes involving nucleic acids, such as the binding of proteins to DNA and RNA, DNA condensation, and RNA folding, requires an understanding of the ion atmosphere that surrounds nucleic acids. We have used a simple model DNA system to determine how the ion atmosphere modulates interactions between duplexes in the absence of specific metal ion-binding sites and other complicated interactions. In particular, we have tested whether the Coulomb repulsion between nucleic acids can be reversed by counterions to give a net attraction, as has been proposed recently for the rapid collapse observed early in RNA folding. The conformation of two DNA duplexes tethered by a flexible neutral linker was determined in the presence of a series of cations by small ang

SUBMITTER: Bai Y 

PROVIDER: S-EPMC545826 | biostudies-literature | 2005 Jan

REPOSITORIES: biostudies-literature