Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes.

ABSTRACT: The HIV-1 type dimerization initiation signal (DIS) loop was used as a starting point for the analysis of the stability of Watson-Crick (WC) base pairs in a tertiary structure context. We used ultraviolet melting to determine thermodynamic parameters for loop-loop tertiary interactions and compared them with regular secondary structure RNA helices of the same sequences. In 1 M Na+ the loop-loop interaction of a HIV-1 DIS type pairing is 4 kcal/mol more stable than its sequence in an equivalent regular and isolated RNA helix. This difference is constant and sequence independent, suggesting that the rules governing the stability of WC base pairs in the secondary structure context are also valid for WC base pairs in the tertiary structure context. Moreover, the effect of ion concentration on

SUBMITTER: Weixlbaumer A 

PROVIDER: S-EPMC521654 | biostudies-literature | 2004

REPOSITORIES: biostudies-literature