A Study On The Influence Of Kink On The Topological Properties Of Kinked DNA Structures

Knot is a subject involving physics,chemistry,biology,mathematics and other disciplines.Knots are discovered in a wide variety of biophysical systems,such as DNA and proteins,a tightly knotted portion makes it a preferred substrate for binding and unknotting by type II DNA topoisomerases.Knotted portions in knotted DNA are tightened by supercoiling and become significantly more bent than the remaining portions.The bending angles are comparable with or larger than the sharp bending angle resulting in flexible defects and hence the reduction of bending rigidity,twist rigidity and the unwinding of DNA.Using Monte Carlo simulation,the roles of flexible defect in the interplay of supercoiling and knotting of circular DNA are predicted based on flexible defect excitations that resulted from local melting or unstacking of DNA base pairs.Effects of flexible defect on topological states of knotted DNA with a particular knot type are first looked at.Flexible defect obviously leads to fluctuation of linking number distribution of knotted DNA,and hence enhances its supercoiling.The decreasing excitation energy makes the knotted portion more compact.And then the reduction of twist rigidity and the unwinding of flexible defect areincorporated into the numerical simulations,so that the interplay of supercoiling and knotting of circular DNA can be studied under torsional conditions.The increasing unwinding angle not only results in a wider distribution,but also leads to the drift of linking number distribution to much lower values.At last,the dependence of knotting probability on flexible defect is detected further.The summation of equilibrium distributions for nontrivial knotted DNA with different counter length does not change with excitation energy monotonically and has a maximum at an intermediate value of excitation energy around5k_BT.The phase diagrams constructed in phase space of knot length and gyration radius of knotted DNA indicate that knot length does not anticorrelate with gyration radius of knotted DNA,which could attribute to the flexible defect in knot portion,which leads to the release of bending energy and inhibits the competition between entropy and bending energy.