Conformation of a bulge-containing oligomer from a hot-spot sequence by NMR and energy minimization
- 1 June 1989
- journal article
- research article
- Published by Wiley in Biopolymers
- Vol. 28 (6), 1149-1177
- https://doi.org/10.1002/bip.360280608
Abstract
Two‐dimensional nmr data on a bulge‐containing oligodeoxyribonucleotide, 5′dGATGGGCAG · dCTGACCCATC, and a regular oligomer of similar sequence, 5′dGATGGCAG · dCTGCCATC, are presented. The nonexchangeable protons are assigned from sequential nuclear Overhauser effect spectroscopy (NOESY) connectivities. The two‐dimensional NOE (NOESY) and correlated (COSY) spectra of the bulge‐containing oligomer are compared to those of the perfect 8‐mer. Experimental proton‐proton distances are determined from NOESY spectra acquired with mixing times of 100, 150, and 200 ms, using comparable distances in the B‐DNA region of the molecule as a calibration. With this approach, measured distances do not depend systematically on mixing time. Energy minimization techniques are used to calculate a three‐dimensional structure for the bulge‐containing oligomer in agreement with the nmr data. The helix is of the B family, with the extra adenine stacked into the helix, and the helix axis is bent by 20°.This publication has 42 references indexed in Scilit:
- Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequenceBiochemistry, 1987
- Self-splicing of group II introns in vitro: Mapping of the branch point and mutational inhibition of lariat formationCell, 1986
- NMR evidence for dynamic secondary structure in helixes II and III of the 5S RNA of Escherichia coliBiochemistry, 1986
- Sequential resonance assignments in proton NMR spectra of oligonucleotides by two-dimensional NMR spectroscopyBiochemistry, 1984
- Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application.Proceedings of the National Academy of Sciences, 1984
- Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methodsJournal of Molecular Biology, 1983
- Genetic and sequence analysis of frameshift mutations induced by ICR-191Journal of Molecular Biology, 1981
- Molecular Basis of a Mutational Hot Spot in the Lysozyme Gene of Bacteriophage T4Nature, 1972
- Frameshift Mutations and the Genetic CodeCold Spring Harbor Symposia on Quantitative Biology, 1966
- THE STRUCTURE OF THE DNA-ACRIDINE COMPLEXProceedings of the National Academy of Sciences, 1963