Nucleic Acids Research, Vol 26, Issue 21 4925-4934, Copyright © 1998 by Oxford University Press
HT Allawi and J SantaLucia Jr
The three-dimensional solution structure of the self-complementary DNA
dodecamer lpile C G T G under A C G T T under A C G above up 21 G C A T
under T G C A G under T G C which contains the thermodynamically
destabilizing lpile T G under A above up 18 A T under T motif was
determined using two-dimensional NMR spectroscopy and simulated annealing
protocols. Relaxation matrix analysis methods were used to yield accurate
NOE derived distance restraints. Scalar coupling constants for the sugar
protons were determined by quantitative simulations of DQF-COSY cross-peaks
and used to determine sugar pucker populations. Twenty refined structures
starting from random geometries converged to an average pairwise root mean
square deviation of 0.49 A. Back calculated NOEs give Rc and Rx factors of
0.38 and 0.088, respectively. The final structure shows that each of the
single G@T mismatches form a wobble pair with two hydrogen bonds where the
guanine projects into the minor groove and the thymine projects into the
major groove. The incorporation of the destabilizing lpile T G under A
above up 18 A T under T motif has little effect on the backbone torsion
angles and helical parameters compared to standard B-form duplexes, which
may explain why G@T mismatches are among the most commonly observed in DNA.
The structure shows that perturbations caused by a G@T mismatch extend only
to its neighboring Watson-Crick base pair, thus providing a structural
basis for the applicability of the nearest- neighbor model to the
thermodynamics of internal G@T mismatches.
ARTICLES
NMR solution structure of a DNA dodecamer containing single G*T mismatches
Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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