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.

中文翻译：

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纳米孔易位实验如何测量 RNA 的解折叠

生物分子通过固态纳米孔的电动易位代表了一种无标记的单分子技术，可用于测量生物分子结构和动力学。最近的研究试图根据相关的孔易位时间、离子电流噪声和阻塞电流来区分单个转移 RNA (tRNA) 种类。通过制造足够小的孔，每个 tRNA 都需要经过变形才能移位。因此，纳米孔易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”能量模型应用分子动力学模拟。计算不同 tRNA 物种的自由能景观涉及纳米孔易位期间末端 RNA 螺旋的瞬时展开。这为解释当前实验提供了结构和能量框架，可以帮助设计使用纳米孔识别大分子的方法。