Xiao Shiyan, Liang Haojun, Wales David J
CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China.
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
J Phys Chem Lett. 2019 Sep 5;10(17):4829-4835. doi: 10.1021/acs.jpclett.9b01960. Epub 2019 Aug 12.
The mechanics of DNA bending is crucially related to many vital biological processes. Recent experiments reported anomalous flexibility for DNA on short length scales, calling into doubt the validity of the harmonic worm-like chain (WLC) model in this region. In the present work, we systematically probed the bending dynamics of DNA at different length scales. In contrast to the remarkable deviation from the WLC description for DNA duplexes of less than three helical turns, our atomistic studies indicate that the neutral "null isomer" behaves in accord with the ideal elastic WLC and exhibits a uniform decay for the directional correlation of local bending. The backbone neutralization weakens the anisotropy in the effective bending preference and the helical periodicity of bend correlation that have previously been observed for normal DNA. The contribution of electrostatic repulsion to stretching cooperativity and the mechanical properties of DNA strands is length-scale-dependent: the phosphate neutralization increases the stiffness of DNA below two helical turns, but it is decreased for longer strands. We find that DNA rigidity is largely determined by base pair stacking, with electrostatic interactions contributing only around 10% of the total persistence length.
DNA弯曲的力学机制与许多重要的生物过程密切相关。最近的实验报道了DNA在短长度尺度上具有异常的柔韧性，这使人们对该区域的谐波蠕虫状链（WLC）模型的有效性产生了怀疑。在本研究中，我们系统地探究了不同长度尺度下DNA的弯曲动力学。与对少于三个螺旋圈的DNA双链体的WLC描述存在显著偏差不同，我们的原子研究表明，中性的“零异构体”的行为符合理想弹性WLC，并且局部弯曲的方向相关性呈现均匀衰减。主链中和减弱了先前在正常DNA中观察到的有效弯曲偏好的各向异性以及弯曲相关性的螺旋周期性。静电排斥对拉伸协同性和DNA链机械性能的贡献取决于长度尺度：磷酸盐中和增加了少于两个螺旋圈的DNA的刚度，但对于更长的链则降低了刚度。我们发现，DNA的刚性在很大程度上由碱基对堆积决定，静电相互作用对总持久长度的贡献仅约为10%。
