Research Project: DNA molekülünün düşük çözünürlükte modellenmesi ve plazmid yapısının sıcaklığa bağlı değişiminin incelenmesi
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Contributors
Funders
ID
TB.00009
Authors
Sayar, Mehmet
Faculty Member
Publications
Supercoil formation in DNA denaturation
(American Physical Society (APS), 2009) Kabakçıoğlu, Alkan; Orlandini, E.; Mukamel, D.; Department of Physics; Yes; College of Sciences
We generalize the Poland-Scheraga model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional stress induced by denaturation enforces the formation of supercoils whose writhe absorbs the linking number expelled by the loops. Our model predicts that when the entropy parameter of a loop satisfies c <= 2, denaturation transition does not take place. On the other hand, for c>2, a first-order denaturation transition is consistent with our model and may take place in the actual system, as in the case with no supercoils. These results are in contrast with other treatments of circular DNA melting where denaturation is assumed to be accompanied by an increase in twist rather than writhe on the bound segments.
Twist-writhe partitioning in a coarse-grained DNA minicircle model
(American Physical Society (APS), 2010) Kabakçıoğlu, Alkan; Sayar, Mehmet; Avşaroğlu, Barış; Department of Mechanical Engineering; Department of Physics; Yes; College of Engineering; College of Sciences
Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.
