Probing Hydrogen Bonding in a DNA Triple Helix Using Protium−Deuterium Fractionation Factors
- 10 May 2003
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 125 (22) , 6626-6627
- https://doi.org/10.1021/ja034223b
Abstract
In this communication we report protium-deuterium fractionation factors for the intramolecular triple helix formed by the DNA oligonucleotide 5'-d(AGAGAGAACCCCTTCTCTCTTTTTCTCTCTT)-3'. The fractionation factors of individual Watson-Crick and Hoogsteen hydrogen bonds in the structure are measured by NMR spectroscopy. The results show that, in contrast to proteins, the fractionation factors are all equal or lower than unity. On the average, the values of the fractionation factors are centered between 0.6 and 0.8, and no significant differences are observed between Hoogsteen and Watson-Crick hydrogen bonds. Deviations from the average are observed for the 5'-end region of the molecule where a base triad is absent and the structure is strained by the intramolecular folding of the DNA strand.Keywords
This publication has 13 references indexed in Scilit:
- Proton exchange and local stability in a DNA triple helix containing a G.TA triadNucleic Acids Research, 2001
- Escherichia coli Uracil DNA Glycosylase: NMR Characterization of the Short Hydrogen Bond from His187 to Uracil O2Biochemistry, 2000
- Hydrogen Bond Geometry and 2H/1H Fractionation in ProteinsJournal of the American Chemical Society, 2000
- Hydrogen Bonding and Equilibrium Protium−Deuterium Fractionation Factors in the Immunoglobulin G Binding Domain of Protein GBiochemistry, 1999
- Equilibrium Protium/Deuterium Fractionation of Backbone Amides in U−13C/15N Labeled Human Ubiquitin by Triple Resonance NMRJournal of the American Chemical Society, 1996
- Theoretical Studies of Protium/Deuterium Fractionation Factors and Cooperative Hydrogen Bonding in PeptidesJournal of the American Chemical Society, 1995
- Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplexJournal of Molecular Biology, 1992
- Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junctionBiochemistry, 1992
- Low-barrier hydrogen bonds and low fractionation factor bases in enzymic reactionsBiochemistry, 1992
- Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequencesJournal of the American Chemical Society, 1982