TAR RNA of HIV‐1 has a trinucleotide bulge region that interacts with the Tat protein of HIV‐1 to increase the rate of transcription. Two base pairs in upper and lower helices surrounding the bulge are conserved. Bulge nucleotides in a helix distort the RNA and hence create recognition sites for target molecules. Previous work in our laboratory has shown that divalent ions such as calcium and magnesium stabilize the RNA with calcium interactions being preferred for the wild type construct (UCU‐TAR). Here we examine the affect of altering the neighboring base pairs on RNA stability and ion preference of a trinuleotide bulge containing RNA. Thermal denaturation experiments were performed on an RNA construct in which the neighboring helix sequences above and below the bulge were altered. This altered RNA containing a UCU bulge was stabilized by ~1.43 kcal/mol in the presence of 9.5 mM magnesium as compared to 1 M KCl, and ~1.04 kcal/mol in the same concentration of calcium. Hence, a change in neighboring base pairs altered the preference and extent of stabilization by divalent ions. In this construct, the putative base triple between bulged U23 and the A27‐U38 is disrupted. Further examination of the role of base triple in RNA interactions with divalent ions is being examined. This work was funded by NSF MCB‐0621509 awarded to NG.
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