Nucleic Acids Research, Vol 24, Issue 6 1073-1079, Copyright © 1996 by Oxford University Press
JJ Dalluge, T Hashizume, AE Sopchik, JA McCloskey and DR Davis
In order to further understand the structural role of the modified
nucleoside dihydrouridine in RNA the solution conformations of Dp and ApDpA
were analyzed by one- and two-dimensional proton NRM spectroscopy and
compared with those of the related uridine-containing compounds. The
analyses indicate that dihydrouridine significantly destabilizes the
C3'-endo sugar conformation associated with base stacked, ordered, A-type
helical RNA. Equilibrium constants (Keq = [C2'-endo]/[C3'-endo]) for
C2'-endo-C3'-endo interconversion at 25 degrees C for Dp, the 5'- terminal
A of ApDpA and D in ApDpA are 2.08, 1.35 and 10.8 respectively.
Stabilization of the C2'-endo form was shown to be enhanced at low
temperature, indicating that C2'-endo is the thermodynamically favored
conformation for dihydrouridine. DeltaH values show that for Dp the
C2'-endo sugar conformation is stabilized by 1.5 kcal/mol compared with Up.
This effect is amplified for D in the oligonucleotide ApDpA and propagated
to the 5'-neighboring A, with stabilization of the C2'-endo form by 5.3
kcal/mol for D and 3.6 kcal/mol for the 5'-terminal A. Post-transcriptional
formation of dihydrouridine therefore represents a biological strategy
opposite in effect to ribose methylation, 2-thiolation or
pseudouridylation, all of which enhance regional stability through
stabilization of the C3'-endo conformer. Dihydrouridine effectively
promotes the C2'-endo sugar conformation, allowing for greater
conformational flexibility and dynamic motion in regions of RNA where
tertiary interactions and loop formation must be simultaneously
accommodated.
ARTICLES
Conformational flexibility in RNA: the role of dihydrouridine
Department of Biochemistry, University of Utah, Salt Lake City, 84112 USA.
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