Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG).
We have presented a detailed analysis for structure determinations for the DNA duplex d(CGCAAAAATGCG) obtained from X-ray crystallography, nuclear magnetic resonance, and molecular dynamics simulation. Each of the structures for the duplex deviates from the structure of the canonical form of B-DNA in a number of observable characteristics. Specifically, the three determinations all contain DNA axis deflections at the junctions of the A-tract with the flanking sequences. The analysis provided shows that the general characteristics of the structures obtained for d(CGCAAAAATGCG) from X-ray, NMR, and MD methods turn out to be quite similar. The extent to which this result can be generalized remains to be established by consideration of similar cross-comparisons on diverse oligonucleotide structures.
Young
M A
MA
Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459-0280, USA.
Srinivasan
J
J
Goljer
I
I
Kumar
S
S
Beveridge
D L
DL
Bolton
P H
PH
D001483:Base Sequence; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D012984:Software
D009838:Oligodeoxyribonucleotides; D004247:DNA