Microring Dna Micro-mechanics, Topological Properties Of The Dna Condensation Mechanism

This paper is mainly divided into three parts, investigating how the flexible hinge, protein binding on DNA affects the topological states of closed circular DNAand linear DNA, and the condensation mechanism of DNA molecule caused by multivalent conuterions. The first part is based on the flexible hinge model, the Monte Carlo simulation method is used to investigate the effects of flexible hinge on the topological states of DNA minicircle, namely the writhing number distribution, thetwist number distribution and the linking number distribution, at the same time, the effects of excited energy and the length of circular containing flexible hinge on the parameters mentioned above are taken into account. For a closed circular DNA molecule, linking number, twist number and writhing number satisfy the relation:â–³Tw + Wr =â–³Lk, based on this relation ,a semi-analytical method is set up to provide complete description of linking number distribution, especially for effects of excited energy on the variance of linking number distribution, which will show very important highlights into the electrophoresis of DNA minicircle. The flexible hinge plays an important role in solving the single molecule experiment difficulty done by Hari. shroff recently. In order to solve the difficulty, two simple models are built up based on the worm-like chain model and flexible hinge model, respectively; the model based on the worm-like chain model can be applied directly to investigate the Euler-bulking instability of linear DNA molecule, at the same time, the model based on the flexible hinge model not only gives a satisfactory explanation to the embarrassment meet by Shroff, but provide strong support on Widom's experiment result that short DNA circles appeared to form three orders of magnitude faster than predicted theoretically, the short DNA molecule is subjected to flexible hinge and become more flexible;In the second part, more attention are paid on explaining the single molecule experiment about the effects of protein binding on DNA, two models are introduced, which combine the protein concentration with chemical potential, by adjusting the parameters, such as chemical potential and bending angle, insights into the affects of protein concentration on the direct conformation, gyration radius and end-to-end distance will be shown, the comparison between the simulation results and experiment, which help us to understand the mechanism of nonspecific protein binding on DNA.In the third part, the mechanism of DNA condensation is discussed systematically based on the strong correlation of counterion condensed on DNA molecule, a coarse-grained but effective model is set up, which includes three parameters, interaction potential, interduplex distance and fluctuation strength, through which the effects of valence of counterion condensed on DNA can be represented reasonably. The model proposed by us not only includes elasticity energy but also considers the effects of bending manner, such as "kink" and flexible hinge, different from works done before, which only consider short, parallel DNA molecule, though it is convenient to strength the condensation mechanism, neglect the effects of DNA length. During the simulation process, the autocorrelation of segment is found as a useful method to describe the condensation states.