Macroscopic loop formation in circular DNA denaturation.

Alkan Kabakçıoğlu, Amir Bar, David Mukamel

Department of Physics, Koç University, Sarıyer 34450 İstanbul, Turkey.

Physical review. E, Statistical, nonlinear, and soft matter physics 2012 May

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The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T{c} and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T{c}, with a cusp at the critical point.

Citation

Alkan Kabakçıoğlu, Amir Bar, David Mukamel. Macroscopic loop formation in circular DNA denaturation. Physical review. E, Statistical, nonlinear, and soft matter physics. 2012 May;85(5 Pt 1):051919