How Nanopore Translocation Experiments Can Measure RNA Unfolding
How Nanopore Translocation Experiments Can Measure RNA Unfolding
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DOI：
10.1016/j.bpj.2020.01.030
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发表时间：
2020-04-07
影响因子：
3.4
通讯作者：
Whitford, Paul C.
中科院分区：
文献类型：
--
作者：
Bandarkar, Prasad;Yang, Huan;Whitford, Paul C.
生物分子通过固态纳米孔的电动移位代表了可用于测量生物分子结构和动力学的无标记单分子技术。最近的研究试图区分个人的转移RNA（tRNA）物种的基础上相关的孔易位时间，离子电流噪声，和堵塞电流。通过制造足够小的孔，每个tRNA都需要经历变形才能移位。因此，纳米孔移位时间和分布的差异可用于推断单个tRNA分子的机械性质。为了弥合我们对tRNA结构动力学和纳米孔测量的理解，我们使用简化的“基于结构”的能量模型进行分子动力学模拟。计算不同tRNA种类的自由能景观暗示了纳米孔易位期间末端RNA螺旋的瞬时展开。这为解释当前的实验提供了结构和能量框架，这可以帮助设计使用纳米孔识别大分子的方法。
Electrokinetic translocation of biomolecules through solid-state nanopores represents a label-free single-molecule technique that may be used to measure biomolecular structure and dynamics. Recent investigations have attempted to distinguish individual transfer RNA (tRNA) species based on the associated pore translocation times, ion-current noise, and blockage currents. By manufacturing sufficiently smaller pores, each tRNA is required to undergo a deformation to translocate. Accordingly, differences in nanopore translocation times and distributions may be used to infer the mechanical properties of individual tRNA molecules. To bridge our understanding of tRNA structural dynamics and nanopore measurements, we apply molecular dynamics simulations using a simplified "structure-based" energetic model. Calculating the free-energy landscape for distinct tRNA species implicates transient unfolding of the terminal RNA helix during nanopore translocation. This provides a structural and energetic framework for interpreting current experiments, which can aid the design of methods for identifying macromolecules using nanopores.