Correlating Divalent Ion Interactions with RNA Structure Changes in TAR RNA

Abstract

The HIV‐1 trans‐acting responsive (TAR) element plays an essential role in transcriptional activation through its interactions with the Tat protein. TAR RNA contains a trinucleotide bulge region that interacts with an arginine rich‐domain of the Tat protein. The presence of an asymmetric bulge in RNA distorts the helix and generates recognition sites for target molecules. Studies in our lab have shown that divalent ions bind to TAR RNA to stabilize the RNA and have demonstrated that calcium ions stabilize the TAR RNA more than magnesium ions. It was also determined that disruption of the bulge sequence (CCC‐TAR) significantly alters interactions with divalent ions. Several biochemical and biophysical studies of TAR RNA indicate that the observed thermodynamic stabilization could be a result of changes in RNA structure. In this study, we sought to determine if TAR RNA interactions with calcium and magnesium ions result in structural changes and if these changes were similar to those caused by interactions with arginine. Circular dichroism experiments were performed on wild TAR RNA containing the UCU bulge and repeated with a modified TAR RNA, which is not expected to bind to arginine. A comparison of structural studies with thermodynamic data will be presented. This work was funded by NSF MCB‐0621509 awarded to Neena Grover.