MOLECULAR DYNAMICS SIMULATION OF DNA STRETCHING IS CONSISTENT WITH THE TENSION OBSERVED FOR EXTENSION AND STRAND SEPARATION AND PREDICTS A NOVEL LADDER STRUCTURE

摘要

Molecular dynamics simulations were used to model the response of several double-stranded dodecamers to gradually increasing tension applied to the opposing 3' ends of the two polynucleotide strands. At forces between 0.80 and 1.45 nN, depending on sequence, the strands separated completely. The separation force for one of the dodecamers studied has been measured and is close to that seen in the simulation. Before strand separation, at forces between 0.065 and 0.090 nN, again depending on sequence, there was an abrupt extension and transition to a novel ladder structure in which bases of one strand were stacked on those of the other strand. Sudden extensions have been observed in very long DNA molecules at forces similar to those seen in the simulations. After the abrupt extension but before strand separation, the ladder structure became more regular, and the phosphate backbones became more linear. Throughout the entire molecular extension, most hydrogen-bonded base pairs remained intact.