DNA structural changes under different stretching methods studied by molecular dynamics simulations.

We present a molecular dynamics simulation study of 22-mer DNA conformational variations obtained by stretching both 3'-termini and both 5'-termini. Stretching 3'-termini by 3.5 nm required 142 kJ mol(-1) and the force plateau was approximately 80 pN, whereas stretching 5'-termini by the same length required 190 kJ mol(-1) and the force plateau was approximately 100 pN. Stretching 3'-termini led to a larger untwisting of the double helix and the successive base pairs rolled to the side of the DNA minor groove, while stretching 5'-termini resulted in the base pairs rolling to the major groove side and reducing of the diameter of DNA molecule. The most distinctive difference between stretching 3'-termini and 5'-termini was that at the force plateau region stretching the 5'-termini resulted in breakage of the base pairs, which considerably disturbed the structure of the DNA double helix. All of the variations of base rotation and translation for both stretching methods took place when the relative length of DNA l was longer than 1.2, which was the point the force plateau appeared.