Nucleic Acids Research, Vol 25, Issue 13 2627-2634, Copyright © 1997 by Oxford University Press
MR Conte, GL Conn, T Brown and AN Lane
The thermodynamic stability of nine dodecamers (four DNA and five RNA) of
the same base composition has been compared by UV-melting. TheDeltaG of
stabilisation were in the order: r(GACUGAUCAGUC)2>r(CGCAAATTTGCG)2
approximately r(CGCAUAUAUGCG)2>d(CGCAAATTTGCG)2 approximately
r(CGCAAAUUUGCG)2>d(CGCATATATGCG)2 approximately
d(GACTGATCAGTC)2>r(CGCUUUAAAGCG)2 approximately d(CGCTTTAAAGCG)2.
Compared with the mixed sequences, both r(AAAUUU) and r(UUUAAA) are greatly
destablising in RNA, whereas in DNA, d(TTTAAA) is destabilising but
d(AAATTT) is stabilising, which has been attributed to the formation of a
special B'structure involving large propeller twists of the A-T base pairs.
The solution structure of the RNA dodecamer r(CGCAAAUUUGCG)2has been
determined using NMR and restrained molecular dynamics calculations to
assess the conformational reasons for its stability in comparison with
d(CGCAAATTTGCG)2. The structures refined to a mean pairwise r.m.s.d. of
0.89+/-0.29 A. The nucleotide conformations are typical of the A family of
structures. However, although the helix axis displacement is approximately
4.6 A into the major groove, the rise (3.0 A) and base inclination (
approximately 6 degrees ) are different from standard A form RNA. The
extensive base- stacking found in the AAATTT tract of the DNA homologue
that is largely responsible for the higher thermodynamic stability of the
DNA duplex is reduced in the RNA structure, which may account for its low
relative stability.
ARTICLES
Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2
Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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