Synthesizing topological structures containing RNA

Di Liu, Yaming Shao, Gang Chen, Yuk-Ching Tse-Dinh, Joseph A. Piccirilli and Yossi Weizmann ()
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Di Liu: The University of Chicago
Yaming Shao: The University of Chicago
Gang Chen: The University of Chicago
Yuk-Ching Tse-Dinh: Biomolecular Sciences Institute, Florida International University
Joseph A. Piccirilli: The University of Chicago
Yossi Weizmann: The University of Chicago

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biological properties pertaining to RNA topology, and these properties in turn could facilitate identifying naturally occurring topologically nontrivial RNA molecules. Here we show that topological structures containing single-stranded RNA (ssRNA) free of strong base pairing interactions can be created either by configuring RNA–DNA hybrid four-way junctions or by template-directed synthesis with a single-stranded DNA (ssDNA) topological structure. By using a constructed ssRNA knot as a highly sensitive topological probe, we find that Escherichia coli DNA topoisomerase I has low RNA topoisomerase activity and that the R173A point mutation abolishes the unknotting activity for ssRNA, but not for ssDNA. Furthermore, we discover the topological inhibition of reverse transcription (RT) and obtain different RT–PCR patterns for an ssRNA knot and circle of the same sequence.

Date: 2017
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14936

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DOI: 10.1038/ncomms14936

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