An interaction of DNA with lipids is of great interest because of their functions. As fatty acids and lipids can specifically bind to nucleic acids forming a code sequence of the genomic DNA, it is important to study the interaction of the oligonucleotide DNA (dA)20-(dT)20 with phosphatidylglycerol by the molecular dynamics method. Molecular docking has shown that these components form a stable complex with 5.8 kcal/mole binding energy, wherein the lipid is located in the DNA minor groove. This configuration marks 354 atom groups separated by a distance less than 3.4 Ǻ. The van der Waals and hydrophobic interactions play the leading part in the DNA-phospholipid complex stabilization along with hydrogen bonds.
Credit: Kazan Federal University
An interaction of DNA with lipids is of great interest because of their functions. As fatty acids and lipids can specifically bind to nucleic acids forming a code sequence of the genomic DNA, it is important to study the interaction of the oligonucleotide DNA (dA)20-(dT)20 with phosphatidylglycerol by the molecular dynamics method. Molecular docking has shown that these components form a stable complex with 5.8 kcal/mole binding energy, wherein the lipid is located in the DNA minor groove. This configuration marks 354 atom groups separated by a distance less than 3.4 Ǻ. The van der Waals and hydrophobic interactions play the leading part in the DNA-phospholipid complex stabilization along with hydrogen bonds.
For the first time, the interaction between a relatively long part of the DNA molecule and phosphatidylglycerol (as a ligand) along a minor groove of the DNA in aqueous solutions is shown. The structural parameters of the complex of phosphatidylglycerol with DNA are determined; the differences compared with DNA interaction with free fatty acid are explained.
The features of the phosphatidylglycerol molecule location in the double helix of DNA are shown based on the structural peculiarities of this molecule.
Journal
Biointerface Research in Applied Chemistry
DOI
10.33263/BRIAC123.32383246
Method of Research
Computational simulation/modeling
Subject of Research
Not applicable
Article Title
Interfacial Interactions of Phosphatidylglycerol with Oligonucleotide DNA Revealed by Molecular Dynamics Method
Article Publication Date
8-Aug-2021
COI Statement
The authors declare no conflict of interest.
