Two- and three-dimensional 31P-driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides

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Abstract
Summary We describe a strategy for sequential assignment of 31P and deoxyribose 1H NMR resonances in oligodeoxyribonucleotides. The approach is based on 31P−1H J-cross-polarization (hetero TOCSY) experiments, recently demonstrated for the assignment of resonances in RNA [Kellogg, G.W. (1992) J. Magn. Reson., 98, 176; Kellogg, G.W. et al. (1992) J. Am. Chem. Soc., 114, 2727]. Two-dimensional hetero TOCSY and hetero TOCSY-NOESY experiments are used to connect proton spin systems from adjacent nucleotides in the dodecamer d(CGCGAATTCGCG)2 entirely on the basis of through-bond scalar connectivities. All phosphorus resonances of the dodecamer are assigned by this method, and many deoxyribose 1H resonances can be assigned as well. A new three-dimensional hetero TOCSY-NOESY experiment is used for backbone proton 4′, 5′ and 5″ resonance assignments, completing assignments begun on this molecule in 1983 [Hare, D.R. et al. (1983) J. Mol. Biol., 171, 319]. Numerical simulations of the time dependence of coherence transfer aid in the interpretation of hetero TOCSY spectra of oligonucleotides and address the dependence of hetero TOCSY and related spectra on structural features of nucleic acids. The possibility of a generalized backbone-driven 1H and 31P resonance-assignment strategy for oligonucleotides is discussed.