title: Synthesizing topological structures containing RNA.
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.
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Di
authors.initials: D
authors.lastname: Liu
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Yaming
authors.initials: Y
authors.lastname: Shao
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Chen
authors.affiliation: Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, USA.
authors.forename: Yuk-Ching
authors.initials: YC
authors.lastname: Tse-Dinh
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.|Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Piccirilli
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Yossi
authors.initials: Y
authors.lastname: Weizmann
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004264:DNA Topoisomerases, Type I / Q000378:metabolism; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013379:Substrate Specificity / Q000187:drug effects; D059004:Topoisomerase I Inhibitors / Q000737:chemistry / Q000494:pharmacology
chemical_list: D050505:Mutant Proteins; D059004:Topoisomerase I Inhibitors; D012313:RNA; D004247:DNA; D004264:DNA Topoisomerases, Type I