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.
Baucom
Jason
J
Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA.
Transue
Thomas
T
Fuentes-Cabrera
Miguel
M
Krahn
J M
JM
Darden
Thomas A
TA
Sagui
Celeste
C
D003198:Computer Simulation; D003460:Crystallization; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides