title: The trapping of a spontaneously "flipped-out" base from double helical nucleic acids by host-guest complexation with beta-cyclodextrin: the intrinsic base-flipping rate constant for DNA and RNA.
abstract: Beta-cyclodextrin, which forms stable host-guest complexes with purine bases, induces the melting of RNA and DNA duplexes below their normal melting temperatures. Alpha-cyclodextrin, which does not form stable complexes, has no effect on either RNA or DNA. Gamma-cyclodextrin, which forms weaker complexes, has no effect on RNA and a smaller effect than beta-cyclodextrin on DNA. The rate of melting is kinetically first-order in duplex and, above about 20 mM beta-cyclodextrin, is independent of the beta-cyclodextrin concentration with a first-order rate constant, common to both RNA and DNA, of (3.5 +/- 0.5) x 10(-3) s(-1) at 61 degrees C (DNA) and at 50 degrees C (RNA). This is taken to be the rate constant for spontaneous "flipping out" of a base from within the duplex structure of the nucleic acids, the exposed base being rapidly trapped by beta-cyclodextrin. Like beta-cyclodextrin, nucleic acid methyltransferases bind the target base for methylation in a site that requires it to have flipped out of its normal position in the duplex. The spontaneous flip-out rate constant of around 10(-3) s(-1) is near the value of k(cat) for the methyltransferases (ca. 10(-3) to 10(-1) s(-1)). In principle, the enzymes, therefore, need effect little or no catalysis of the flipping-out reaction. Nevertheless, the flip-out rate in enzyme/DNA complexes is much faster. This observation suggests that the in vivo circumstances may differ from in vitro models or that factors other than a simple drive toward higher catalytic power have been influential in the evolution of these enzymes.
authors.affiliation: Department of Molecular Biosciences, Higuchi Biosciences Center, University of Kansas, Lawrence, KS 66047, USA.
authors.forename: M Ashley
authors.initials: MA
authors.lastname: Spies
authors.forename: Richard L
authors.initials: RL
authors.lastname: Schowen
mesh_terms: D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003505:Cyclodextrins / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D012313:RNA / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D047391:alpha-Cyclodextrins; D047392:beta-Cyclodextrins; D047408:gamma-Cyclodextrins
chemical_list: D003505:Cyclodextrins; D047391:alpha-Cyclodextrins; D047392:beta-Cyclodextrins; D047408:gamma-Cyclodextrins; D012313:RNA; D004247:DNA; C031215:betadex; C023792:gamma-cyclodextrin; C032613:alpha-cyclodextrin