Fosado Y A G, Michieletto D, Marenduzzo D
SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
Phys Rev Lett. 2017 Sep 15;119(11):118002. doi: 10.1103/PhysRevLett.119.118002. Epub 2017 Sep 12.
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular closed plasmids, is less abrupt than that of linear molecules. This finding points to an important role of topology in the physics of DNA denaturation, which is, however, poorly understood. Here, we shed light on this issue by combining large-scale Brownian dynamics simulations with an analytically solvable phenomenological Landau mean field theory. We find that the competition between melting and supercoiling leads to phase coexistence of denatured and intact phases at the single-molecule level. This coexistence occurs in a wide temperature range, thereby accounting for the broadening of the transition. Finally, our simulations show an intriguing topology-dependent scaling law governing the growth of denaturation bubbles in supercoiled plasmids, which can be understood within the proposed mean field theory.
长期以来的实验观察表明，拓扑受限的DNA（如环状闭合质粒）的解链比线性分子的解链更平缓。这一发现表明拓扑结构在DNA变性物理过程中起着重要作用，然而，人们对此了解甚少。在这里，我们通过将大规模布朗动力学模拟与可解析求解的唯象朗道平均场理论相结合，来阐明这个问题。我们发现解链和超螺旋之间的竞争导致了单分子水平上变性相和完整相的相共存。这种共存发生在很宽的温度范围内，从而解释了转变的展宽。最后，我们的模拟显示了一个有趣的拓扑依赖标度律，它控制着超螺旋质粒中变性泡的生长，这可以在所提出的平均场理论中得到理解。
