Molecular dynamics simulations of B-DNA: an analysis of the role of initial molecular configuration, randomly assigned velocity distribution, long integration times, and nonconstrained termini

Molecular dynamics simulations of three DNA sequences using the AMBER 3.0 force field were performed with implicit inclusion of water through a distance-dependent dielectric constant and solvated counterions. Simulations of the self-complementary DNA dodecamer D(CGCGAATTCGCG) were started from a reg...

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Bibliographic Details
Published inBiopolymers Vol. 33; no. 3; pp. 459 - 473
Main Authors Falsafi, S, Reich, N.O
Format Journal Article
LanguageEnglish
Published United States 01.03.1993
Subjects
Base Sequence
computer analysis
computer simulation
computer software
DNA
DNA - chemistry
DNA conformation
Molecular Sequence Data
Nucleic Acid Conformation
Oligodeoxyribonucleotides - chemistry
oligonucleotides
Polydeoxyribonucleotides - chemistry
simulation models
Thermodynamics
torsion
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Summary:Molecular dynamics simulations of three DNA sequences using the AMBER 3.0 force field were performed with implicit inclusion of water through a distance-dependent dielectric constant and solvated counterions. Simulations of the self-complementary DNA dodecamer D(CGCGAATTCGCG) were started from a regular B-DNA structure and the X-ray single crystal B-DNA structure. Although mean convergence during the 89-ps calculation was confirmed, localized differences in backbone torsionals and base-pair helicoidals were observed. A nanosecond simulation of the nonself-complementary 14 base-pair DNA d(GGCGGAATTGGCGG) indicates that most structural parameters stabilize within the first 100-200 ps, while isolated features show low-frequency oscillations throughout the calculation. The lack of harmonic constraints on the ends of the molecules was shown not to perturb the structural dynamics of the internal oligonucleotide beyond the external 2 base pairs. Comparison of three simulations of the nonself-complementary 14 base-pair DNA d(GGCGAAATTCGCGG), identical in all respects other than the assignment of initial Maxwellian atomic velocity distributions, revealed the inherent systematic variability. The three calculations result in nearly superimposable global structures, with localized variations in torsionals and helicoidals. Our results provide a basis for performing a comparative analysis of the effect of DNA sequence on localized structure.
ISSN:0006-3525
1097-0282
DOI:10.1002/bip.360330312