Denaturation of circular DNA: supercoil mechanism

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

Temperature REMD reveals how local chemical changes can result in markedly differing conformational landscapes for DNA and RNA hairpin loops.

Denaturation of circular DNA: supercoils and overtwist

The denaturation transition of circular DNA is studied within a Poland-Scheraga-type approach, generalized to account for the fact that the total linking number (LK), which measures the number of windings of one strand around the other, is conserved. In the model the LK conservation is maintained by invoking both overtwisting and writhing (supercoiling) mechanisms. This generalizes previous studies, which considered each mechanism separately. The phase diagram of the model is analyzed as a function of the temperature and the elastic constant κ associated with the overtwisting energy for any given loop entropy exponent c. As in the case where the two mechanisms apply separately, the model exhibits no denaturation transition for c ≤ 2. For c > 2 and κ = 0 we find that the model exhibits a first-order transition. The transition becomes of higher order for any κ > 0. We also calculate the contribution of the two mechanisms separately in maintaining the conservation of the linking number and find that it is weakly dependent on the loop exponent c.

Macroscopic loop formation in circular DNA denaturation

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.