Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer.

ABSTRACT: A RNA aptamer (R06) raised against the trans- activation responsive (TAR) element of HIV-1 was previously shown to generate a loop-loop complex whose stability is strongly dependent on the selected G and A residues closing the aptamer loop. The rationally designed TAR* RNA hairpin with a loop sequence fully complementary to the TAR element, closed by U,A residues, also engages in a loop-loop association with TAR, but with a lower stability compared with the TAR-R06 complex. UV absorption monitored thermal denaturation showed that TAR-TAR*(GA), in which the U,A kissing residues were exchanged for G,A, is as stable as the selected TAR-R06 complex. Consequently, we used the TAR-TAR* structure deduced from NMR studies to model the TAR-R06 complex with either GA, CA or UA loop closing residues.

SUBMITTER: Beaurain F 

PROVIDER: S-EPMC165981 | biostudies-literature | 2003 Jul

REPOSITORIES: biostudies-literature