Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium.
Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium.
Phys Rev E. 2019 Aug;100(2-1):022402. doi: 10.1103/PhysRevE.100.022402.
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately 100 base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an imposed bending stress, as recently found in DNA minicircles and observed in nucleosomal DNA. These twist oscillations, here referred to as twist waves, are due to the coupling between twist and bending deformations, which in turn originates from the asymmetry between DNA major and minor grooves. We introduce a simple analytical variational shape that reproduces the exact loop energy up to the fourth significant digit and is in very good agreement with shapes obtained from coarse-grained simulations. We, finally, analyze the loop dynamics at room temperature, and show that the twist waves are robust against thermal fluctuations. They perform a normal diffusive motion, whose origin is briefly discussed.
通过结合分析和数值计算，我们研究了大约 100 个碱基对（bp）短 DNA 环的最小能量形状。我们表明，在这些环中，超螺旋密度会发生振荡，这是对施加的弯曲应力的响应，最近在 DNA 小环和核小体 DNA 中观察到了这种现象。这些扭转振荡，在这里被称为扭转波，是由于扭转和弯曲变形之间的耦合引起的，而这种耦合又源于 DNA 大沟和小沟之间的不对称性。我们引入了一种简单的分析变形势，它可以精确地再现环的能量，直到第四位有效数字，并且与粗粒化模拟得到的形状非常吻合。最后，我们分析了室温下的环动力学，并表明扭转波对热波动具有鲁棒性。它们表现出正常的扩散运动，其起源将简要讨论。
