Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Molecular Dynamics Study of 3? Phosphoramidate Modified DNA Quadruplex in Solution: Conformation and Hydration

The structural impact on modified tetraplex was investigated by carrying out molecular dynamics simulation on a deoxyribose quadruplex and its phosphoramidate (replacing O3? by NH) analog using particle mesh Ewald electrostatics and the Cornoll et al force field. The N-H group can adopt different orientation ( characterized by the values of the C4¢-C3¢ -N3¢ -H angle in the range 40o to 80o ("NHin" ) and - 40o to - 80o ("NHout" ) . The exposure of the N-H to the water solvent plays a critical role on the observed conformational behavior of quadruplex during molecular dynamics simulations for NHin and NHout. The simulations were performed for both cases. These simulations were carried out for more than 1.6 ns, are consistent with the observed X-ray structure for the unmodified quadruplex. On the other hand, the phosphoramidate modified quadruplexes depend on the initial location of the N-H hydrogen. Due to the presence of phosphoramidate the conformational change in the quadruplex structure, the variation of the backbone torsion angles and helicoidal parameters have been examined.

R. P. Ojha

Biophysics Unit, Department of Physics, DDU Gorakhpur University, Gorakhpur - 273 009, India
Email: rp_ojha@yahoo.com