Meng W L, Zhang N H, Tang H S, Tan Z Q
Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai, 200072, China,
Biomech Model Mechanobiol. 2015 Oct;14(5):1157-65. doi: 10.1007/s10237-015-0661-5. Epub 2015 Mar 8.
Determining mechanical properties of single-stranded DNA film grafted on gold surface is critical for analysis and design of DNA-microcantilever biosensors. However, it remains an open issue to quantify the relations among the disordered packing patterns of DNA chains, the mechanical properties of DNA film and the resultant biodetection signals. In this paper, first, the bending experiment of microcantilever is carried out to provide the basic data for a refined multi-scale model of microcantilever deflection induced by ssDNA immobilization. In the model, the complicated interactions in DNA film (consisting of DNA, water molecules and salt ions) are simplified as effective interactions among coarse-grained soft cylinders, which can reveal the varieties of DNA structure in the circumstances of different lengths and salt concentrations; Ohshima's distribution of net charge density is employed to incorporate compositional variations of salt ions along the thickness direction into the Strey's mesoscopic empirical potential on molecular interactions in DNA solutions, and the related model parameters for ssDNA film on substrate are obtained from the curve fitting with our microcantilever bending experiment. Second, the effect of nanoscopic distribution of DNA chains on elastic modulus of ssDNA film is studied by a thought experiment of uniaxial compression, and the disordered patterns of DNA chains are generated by Monte Carlo method. Simulation results point out that nanoscale ssDNA film shows size effect, gradient and diversity in elastic modulus and can achieve maximum stiffness by preferring a disordered and energetically favorable packing pattern collectively induced by electrostatic force, hydration force and configurational entropy.
确定接枝在金表面的单链DNA薄膜的力学性能对于DNA微悬臂生物传感器的分析和设计至关重要。然而，量化DNA链的无序堆积模式、DNA薄膜的力学性能与所得生物检测信号之间的关系仍然是一个悬而未决的问题。本文首先进行了微悬臂梁的弯曲实验，为单链DNA固定诱导的微悬臂梁挠度的精细多尺度模型提供基础数据。在该模型中，DNA薄膜（由DNA、水分子和盐离子组成）中的复杂相互作用被简化为粗粒化软圆柱体之间的有效相互作用，这可以揭示不同长度和盐浓度情况下DNA结构的变化；采用大岛净电荷密度分布将盐离子沿厚度方向的组成变化纳入斯特雷关于DNA溶液中分子相互作用的介观经验势中，并通过与我们的微悬臂梁弯曲实验进行曲线拟合获得基底上单链DNA薄膜的相关模型参数。其次，通过单轴压缩的思想实验研究了DNA链纳米尺度分布对单链DNA薄膜弹性模量的影响，并用蒙特卡罗方法生成了DNA链的无序模式。模拟结果表明，纳米尺度的单链DNA薄膜在弹性模量上表现出尺寸效应、梯度和多样性，并且通过优先选择由静电力、水化力和构型熵共同诱导的无序且能量有利的堆积模式可以实现最大刚度。
