Premium
Conformation of a bulge‐containing oligomer from a hot‐spot sequence by NMR and energy minimization
Author(s) -
Woodson Sarah A.,
Crothers Donald M.
Publication year - 1989
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360280608
Subject(s) - oligomer , two dimensional nuclear magnetic resonance spectroscopy , chemistry , nuclear overhauser effect , nuclear magnetic resonance spectroscopy , proton nmr , proton , crystallography , helix (gastropod) , nmr spectra database , spectral line , energy minimization , spectroscopy , molecule , stereochemistry , computational chemistry , physics , polymer chemistry , ecology , organic chemistry , quantum mechanics , astronomy , snail , biology
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°.