Molecular Dynamics of Oligonucleotide DNA Complexes with Phosphatidylserine

Abstract

A formation of DNA-lipid complexes was studied by molec.docking and dynamics methods using the interaction of DNA with phosphatidylserine (PS). We have previously shown that some fatty acids and phosphatidylglycerol can specifically bind to oligonucleotide DNA (dA)20•(dT)20. It is shown that (dA)20•(dT)20 and phosphatidylserine formed a stable complex with a 6.3 kcal/mol binding energy and the PS molecule located in the minor groove of DNA. This complex contains 342 atom groups (interatomic distance ≤3.4 Å). The types of bonds in the PS-DNA(oligonucleotide) complex are suggested as hydrogen bonds, and hydrophobic and dipole-induced dipole interactions. In our previous study, a similar arrangement with close binding energy of 5.8 kcal/mol was shown for phosphatidylglycerol complex with the same oligonucleotide (complex contained 354 groups of atoms). The present study is of interest due to the importance of such complexes for applied biochemistry and biotechnology, genetics and molecular biology, cytology and pharmacology, nanotechnology, and self-assembly smart materials.