Conformation of a bulge‐containing oligomer from a hot‐spot sequence by NMR and energy minimization

Sarah A. Woodson, Donald M. Crothers

Research output: Contribution to journalArticlepeer-review


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°.

Original languageEnglish (US)
Pages (from-to)1149-1177
Number of pages29
Issue number6
StatePublished - Jun 1989

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry


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