Nanopore electric snapshots of an RNA tertiary folding pathway

Xinyue Zhang, Dong Zhang, Chenhan Zhao, Kai Tian, Ruicheng Shi, Xiao Du, Andrew J. Burcke, Jing Wang, Shi-Jie Chen () and Li-Qun Gu ()
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Xinyue Zhang: Department of Bioengineering, University of Missouri
Dong Zhang: Department of Physics, University of Missouri
Chenhan Zhao: Department of Physics, University of Missouri
Kai Tian: Department of Bioengineering, University of Missouri
Ruicheng Shi: Department of Bioengineering, University of Missouri
Xiao Du: Department of Bioengineering, University of Missouri
Andrew J. Burcke: Department of Bioengineering, University of Missouri
Jing Wang: Department of Bioengineering, University of Missouri
Shi-Jie Chen: Department of Physics, University of Missouri
Li-Qun Gu: Department of Bioengineering, University of Missouri

Nature Communications, 2017, vol. 8, issue 1, 1-11

Abstract: Abstract The chemical properties and biological mechanisms of RNAs are determined by their tertiary structures. Exploring the tertiary structure folding processes of RNA enables us to understand and control its biological functions. Here, we report a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master equation analysis to elucidate the folding of an RNA pseudoknot structure. In this approach, single RNA molecules captured by the nanopore can freely fold from the unstructured state without constraint and can be programmed to terminate their folding process at different intermediates. By identifying the nanopore signatures and measuring their time-dependent populations, we can “visualize” a series of kinetically important intermediates, track the kinetics of their inter-conversions, and derive the RNA pseudoknot folding pathway. This approach can potentially be developed into a single-molecule toolbox to investigate the biophysical mechanisms of RNA folding and unfolding, its interactions with ligands, and its functions.

Date: 2017
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DOI: 10.1038/s41467-017-01588-z

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