Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations.
Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations.
复制标题
来自粗粒度分子动力学模拟的机械顺应性 DNA 纳米结构的构象动力学。
作者：
Ze Shi;C. Castro;G. Arya
结构DNA纳米技术，复杂而精确的几何形状的刚性3D结构的组装，最近已被用来设计动态的，机械顺应性的纳米结构与可调的平衡构象和构象分布。在这里，我们使用粗粒度的分子动力学模拟提供了一组机械顺应性的DNA纳米结构的构象动力学的见解-DNA铰链，使用单链DNA“弹簧”来调整的平衡构象的分层双链DNA“关节”连接两个刚性的“臂”从DNA螺旋束构建。模拟再现实验测量的平衡角铰链臂之间的铰链设计的范围。铰链被发现是结构稳定的，除了一些磨损的DNA螺旋的开放端组成的铰链臂和一些损失的碱基配对相互作用的关节区域重合的交叉路口，特别是在铰链设计表现出一个小的弯曲角度，表现出大的局部应力，导致在其关节强扭结。主成分分析表明，虽然铰链动力学的弯曲运动占主导地位，一些扭转和相对于彼此的铰链臂滑动也存在。铰链的强制变形揭示了具有较短的不可伸展弹簧的铰链与具有较长的可伸展弹簧的铰链的不同弯曲机制。最后，我们介绍了一种方法，用于快速预测平衡铰链角度从单个力变形行为的单链和双链DNA组件。综上所述，这些结果表明，粗粒度建模是一种很有前途的方法，用于设计，预测和研究顺应性DNA纳米结构的动力学，其中构象波动变得重要，存在多种变形机制，并且连续体方法可能不会产生准确的特性。
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles. The simulations reproduce the experimentally measured equilibrium angles between hinge arms for a range of hinge designs. The hinges are found to be structurally stable, except for some fraying of the open ends of the DNA helices comprising the hinge arms and some loss of base-pairing interactions in the joint regions coinciding with the crossover junctions, especially in hinges designed to exhibit a small bending angle that exhibit large local stresses resulting in strong kinks in their joints. Principal component analysis reveals that while the hinge dynamics are dominated by bending motion, some twisting and sliding of hinge arms relative to each other also exists. Forced deformation of the hinges reveals distinct bending mechanisms for hinges with short, inextensible springs versus those with longer, more extensible springs. Lastly, we introduce an approach for rapidly predicting equilibrium hinge angles from individual force-deformation behaviors of its single- and double-stranded DNA components. Taken together, these results demonstrate that coarse-grained modeling is a promising approach for designing, predicting, and studying the dynamics of compliant DNA nanostructures, where conformational fluctuations become important, multiple deformation mechanisms exist, and continuum approaches may not yield accurate properties.
影响因子：
6.8
作者：
Olson WK;Zhurkin VB
通讯作者：
Zhurkin VB
影响因子：
3.3
作者：
Doye, Jonathan P. K.;Ouldridge, Thomas E.;Smith, William P. J.
通讯作者：
Smith, William P. J.