TBI-Preprint 04-02-003


Determination of Thermodynamic Parameters for HIV-1 DIS Type Loop-Loop Kissing Complexes

Albert Weixlbaumer, Andreas Werner, Christoph Flamm, Eric Westhof and Renée Schroeder

Appeared in:
Nucl. Acids Res., 32, 5126-5133 (2004)

The HIV-1 type dimerization initiation signal (DIS) loop was used as a starting point for the analysis of the stability of WC base pairs in a tertiary structure context. We used UV melting to determine thermodynamic parameters for loop-loop interactions comparing them with regular 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 the stability of loop-loop interactions differs considerably from that of regular RNA helices. The stabilization by Na+ and Mg2+ is significantly greater if the helix is in the context of a loop-loop interaction. The dependence of the structural stability on salt concentration was defined via the slope of a Tm/log [ion] plot. Short RNA helices are stabilized by 8ºC/log [Mg2+] or 11ºC/log [Na+], whereas helices forming tertiary loop-loop interactions are stabilized by 16ºC/log [Mg2+] and 26ºC/log [Na+].

Keywords: RNA tertiary structure, loop-loop interactions, kissing loops, UV melting, HIV-1 DIS loop

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Last modified: 2004-04-19 12:24:14 xtof