Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields.
Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure in a crystal environment. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field, and an "extra-point" force field (with additional charges on extranuclear sites). It is found that all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force field, however, provides the most accurate representation of the crystal structure and the sequence-dependent effects observed in the experiment. These results point out to the need of the inclusion of polarization for accurate descriptions of DNA.
Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA.
Jason
J
Baucom
Thomas
T
Transue
Miguel
M
Fuentes-Cabrera
J M
JM
Krahn
Thomas A
TA
Darden
Celeste
C
Sagui
D003198:Computer Simulation; D003460:Crystallization; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides