Synthesizing topological structures containing RNA

• Published in: Nature communications Vol. 8; no. 1; p. 14936
• Main Authors: Liu, Di, Shao, Yaming, Chen, Gang, Tse-Dinh, Yuk-Ching, Piccirilli, Joseph A., Weizmann, Yossi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 31.03.2017; Nature Publishing Group; Nature Portfolio
• Subjects: 38/22; 38/77; 38/88; 38/90; 45/29; 639/638/541/964; 639/638/92/500; Base Sequence; Biochemistry; Biology; DNA - chemistry; DNA - metabolism; DNA Topoisomerases, Type I - metabolism; E coli; Humanities and Social Sciences; Kinases; multidisciplinary; Mutant Proteins - chemistry; Mutant Proteins - metabolism; Nucleic Acid Conformation; RNA - chemistry; Science; Science (multidisciplinary); Substrate Specificity - drug effects; Topoisomerase I Inhibitors - chemistry; Topoisomerase I Inhibitors - pharmacology; Chicago Illinois; Florida; United States > US; Illinois
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms14936

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. In vivo , complex topologies have been identified in proteins and DNA, while their existence in RNA is still unclear. Here, the authors design synthetic topological structures containing single stranded RNA, offering tools for investigating biologically relevant questions about RNA topology.