A quantitative study of the flexibility contributed to RNA structures by nicks and single-stranded gaps.
Disulfide crosslinking via thiol-disulfide interchange was applied to quantitate the relative flexibility contributed by nicks and single-stranded gaps in an RNA structure. An RNA duplex comprised of three strands was constructed containing the disulfide crosslink precursors 1 and 2 at opposite ends of the duplex on opposite strands. The third strand was of varying length to yield a nick or single-stranded gaps of 1, 2, or 3 nt. Crosslinking rates Indicated relative flexibilities of the resulting two-helix junctions. Crosslinking in the nicked duplex occurred two orders of magnitude slower than in a duplex containing a 3-nt gap. Rates of crosslinking in duplexes with 3-and 2-nt gaps showed only modest dependence on the gap sequence. Many natural RNAs, including ribozymes, contain two-helix junctions related to the model system described here. The data suggest that two-helix junctions containing a nick in one strand will retain substantial rigidity, whereas one or more single-stranded nucleotides at a two-helix junction allow significant flexibility.
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Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA.
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D003432:Cross-Linking Reagents; D004220:Disulfides; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000138:chemical synthesis; D012313:RNA / Q000737:chemistry*; D012330:RNA, Double-Stranded / Q000737:chemistry
D003432:Cross-Linking Reagents; D004220:Disulfides; D009843:Oligoribonucleotides; D012330:RNA, Double-Stranded; D012313:RNA