Nuclear Overhauser effect as a tool for the complete assignment of nonexchangeable proton resonances in short deoxyribonucleic acid helices.

Abstract

A new strategy for the assignment of nonexchangeable proton resonances in oligonucleotide duplexes is presented and used to interpret the spectra of the oligonucleotide helix d(CpGpCpGpCpG) X d(CpGpCpGpCpG) in low salt (B form). This procedure is based on the use of sequential homodecoupling (1D) or COSY (2D) for the interconnection of the sugar resonances pertaining to the same residue and on the measurement of nuclear Overhauser effect (NOE) (1D or 2D) between critically located protons in order to establish the connectivity between the base protons and the sugar protons, as well as between consecutive base-sugar residues. The assignment performed by this method was found in perfect agreement with the one made previously by the incremental procedure [Cheng, D. M., Kan, L.-S., Frechet, D., Ts'o, P. O. P., Uesugi, S., Shida, T., & Ikehara, M. (1983) Biopolymers (in press)]. Also, this method is demonstrated to be applicable to DNA short helices containing A X T base pairs.