Two-dimensional NMR investigation of a bent DNA fragment: Assignment of the proton resonances and preliminary structure analysis

Abstract

The resonances of all the non-exchangeable protons (except 5′H and 5″H) of d(CGAAAAATCGG)+d(CCGATTTTTCG), a putatively bent DNA duplex, have been assigned using 1H two-dimensional nuclear magnetic resonance methods. The nuclear Overhauser effect data indicate an overall B-form structure for this double-helical DNA undecamer. However, several features of the NMR data such as some unusually weak C8/C6 proton to C1′ proton NOE cross-peaks, the presence of relatively intense C2H to C1′H NOE cross-peaks, and unusual chemical shifts of some 2″, 2′, and 1′ protons suggest a substantial perturbation of the helix structure at the junctions and along the length of the tract of A residues. These structural deviations are considered in terms of models of DNA bending. © 1987 IRL Press Limited.