TBI-Preprint 04-02-003
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Titel:
Determination of Thermodynamic Parameters for HIV-1 DIS
Type Loop-Loop Kissing Complexes
Author(s):
Albert Weixlbaumer,
Andreas Werner,
Christoph Flamm,
Eric Westhof
and Renée Schroeder
Appeared in:
Nucl. Acids Res., 32, 5126-5133 (2004)
Abstract:
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