Molecular dynamics simulation of DNA duplex, analog of PPT (polypurine tract), its conformation and hydration: a theoretical study

Abstract

Molecular Dynamics Simulation Study of DNA duplex is reported here in this communication. The duplex is a decamer, which consists of two non-self complementary sequences 5′(CAAAGAAAAG) and 5′(CTTTTCTTTG). This decamer is a DNA analog of the portion of the polypurine tract, which is a RNA/DNA hybrid that serves as a primer for the synthesis of the non-digestible DNA strand by human immunodeficiency virus reverse transcriptase. The result obtained is compared with the crystal structure of this decamer duplex. The calculations described here using AMBER throw light on the effect of counter ions on the binding of water molecules, within the grooves of the duplex. This study may provide important implications for understanding the functional, energetic, and specificity of the interactions of DNA/RNA with regulatory proteins, pharmaceutical agents, and other ligands.