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Biophys J, February 2000, p. 668-682, Vol. 78, No. 2
and
*Department of Biochemistry, Virginia Polytechnic Institute and
State University, Blacksburg, Virginia 24061, and
Laboratory of Structural Biology, National Institute of
Environmental Health Science, Research Triangle Park, North Carolina
27709 USA
Molecular dynamics (MD) simulations of the DNA duplex
d(CCAACGTTGG)2 were used to study the relationship between
DNA sequence and structure. Two crystal simulations were carried out;
one consisted of one unit cell containing two duplexes, and the other
of two unit cells containing four duplexes. Two solution simulations were also carried out, one starting from canonical B-DNA and the other
starting from the crystal structure. For many helicoidal parameters,
the results from the crystal and solution simulations were essentially
identical. However, for other parameters, in particular, 
, 
, 
,
(
), phase, and helical twist, differences between
crystal and solution simulations were apparent. Notably, during crystal
simulations, values of helical twist remained comparable to those in
the crystal structure, to include the sequence-dependent differences
among base steps, in which values ranged from 20° to 50° per base
step. However, in the solution simulations, not only did the average
values of helical twist decrease to ~30° per base step, but every
base step was ~30°, suggesting that the sequence-dependent
information may be lost. This study reveals that MD simulations of the
crystal environment complement solution simulations in validating the
applicability of MD to the analysis of DNA structure.
Biophys J, February 2000, p. 668-682, Vol. 78, No. 2
© 2000 by the Biophysical Society 0006-3495/00/02/668/15 $2.00
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