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Structure and axis curvature in two dA 6 ·dT 6 DNA oligonucleotides: Comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy
Author(s) -
Dixit Surjit B.,
Pitici Felicia,
Beveridge D. L.
Publication year - 2004
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20157
Subject(s) - chemistry , oligonucleotide , nuclear magnetic resonance spectroscopy , crystallography , molecular dynamics , spectroscopy , curvature , dna , computational chemistry , stereochemistry , biochemistry , physics , geometry , mathematics , quantum mechanics
Molecular dynamics (MD) simulations have been performed on the A6 containing DNA dodecamers d(GGCCGG) solved by NMR and d(CGCGCG) solved by crystallography. The experimental structures differ in the direction of axis bending and in other small but important aspects relevant to the DNA curvature problem. Five nanosecond MD simulations of each sequence have been performed, beginning with both the NMR and crystal forms as well as canonical B‐form DNA. The results show that all simulations converge to a common form in close proximity to the observed NMR structure, indicating that the structure obtained in the crystal is likely a strained form due to packing effects. A‐tracts in the MD model are essentially straight. The origin of axis curvature is found at pyrimidine–purine steps in the flanking sequences. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004