Journal article
The trapping of a spontaneously flipped-out base from double helical nucleic acids by host-guest complexation with β-cyclodextrin: The intrinsic base-flipping rate constant for DNA and RNA
Journal of the American Chemical Society, Vol.124(47), pp.14049-14053
2002
DOI: 10.1021/ja012272n
PMID: 12440903
Abstract
β-Cyclodextrin, which forms stable host-guest complexes with purine bases, induces the melting of RNA and DNA duplexes below their normal melting temperatures. α-Cyclodextrin, which does not form stable complexes, has no effect on either RNA or DNA. γ-Cyclodextrin, which forms weaker complexes, has no effect on RNA and a smaller effect than β-cyclodextrin on DNA. The rate of melting is kinetically first-order in duplex and, above about 20 mM β-cyclodextrin, is independent of the β-cyclodextrin concentration with a first-order rate constant, common to both RNA and DNA, of (3.5 ± 0.5) × 10-3 s-1 at 61 °C (DNA) and at 50 °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 β-cyclodextrin. Like β-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 kcat 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.
Details
- Title: Subtitle
- The trapping of a spontaneously flipped-out base from double helical nucleic acids by host-guest complexation with β-cyclodextrin: The intrinsic base-flipping rate constant for DNA and RNA
- Creators
- M. Ashley Spies - University of KansasRichard L Schowen - University of Kansas
- Resource Type
- Journal article
- Publication Details
- Journal of the American Chemical Society, Vol.124(47), pp.14049-14053
- Publisher
- American Chemical Society
- DOI
- 10.1021/ja012272n
- PMID
- 12440903
- ISSN
- 0002-7863
- eISSN
- 1520-5126
- Language
- English
- Date published
- 2002
- Academic Unit
- Pharmaceutical Sciences and Experimental Therapeutics; Biochemistry and Molecular Biology; Medicinal and Natural Products Chemistry
- Record Identifier
- 9984288733302771
Metrics
4 Record Views