Bandarkar Prasad, Yang Huan, Henley Robert Y, Wanunu Meni, Whitford Paul C
Department of Physics, Northeastern University, Boston, Massachusetts.
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California.
Biophys J. 2020 Apr 7;118(7):1612-1620. doi: 10.1016/j.bpj.2020.01.030. Epub 2020 Feb 4.
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.
生物分子通过固态纳米孔的电动转位代表了一种无标记单分子技术，可用于测量生物分子的结构和动力学。最近的研究试图根据相关的孔转位时间、离子电流噪声和阻断电流来区分单个转运RNA（tRNA）种类。通过制造足够小的孔，每个tRNA需要发生变形才能转位。因此，纳米孔转位时间和分布的差异可用于推断单个tRNA分子的机械特性。为了增进我们对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种类的自由能景观表明，在纳米孔转位过程中，末端RNA螺旋会发生瞬时解折叠。这为解释当前实验提供了一个结构和能量框架，有助于设计使用纳米孔识别大分子的方法。
