DNA Conformational Variations Induced by Stretching 3'5'-Termini Studied by Molecular Dynamics Simulations

Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction. The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA. We study the conformational variations of a 22-mer DNA caused by stretching both 3'− and 5'−termini by molecular dynamics simulations. It requires 250 kJ/mol to stretch the DNA molecule by 3'5'−termini for 3.5 nm and the force plateau is at 123.8 pN. The stretching 3'5'−termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair, the double helix untwists from 34° to 20° and the successive base pairs rolls to the side of the DNA major groove. The distances between successive base pairs increases from 3.2 Å to 5.6 Å.