Assignment of the proton Nmr chemical shifts of the T-N3H and G-N1H proton resonances in isolated AT and GC Watson-Crick base pairs in double-stranded deoxy oligonucleotides in aqueous solution.

Abstract

AbstractThe 300‐MHz proton nmr spectra (between 11 and 14 ppm) of a series of double‐stranded deoxy oligonucleotides of known sequence have been recorded in H2O solution. These resonances have been assigned to the GN1H and TN3H protons of specific base pairs from an evaluation of the temperature dependence of the ring NH linewidths and from the selective ring NH chemical shift changes on actinomycin‐D binding. The deoxy oligonucleotides exist predominantly in the DNA‐B conformation as evaluated from antibiotic binding studies. Ring‐current calculations have been utilized to evaluate the up‐field shifts of the GN1H and TN3H protons in Watson‐Crick base pairs due to the ring currents from the pyrimidine and purine rings of nearest neighbor base pairs in regular DNA‐B‐ and RNA‐A‐type helices. The perturbations on these up‐field ring‐current contributions that arise from twisting and tilting a base pair adjacent to the ring NH under study have been evaluated and found to change the calculated chemical shift by ±0.6 ppm for twist and tilt distortions of <30°C in a single adjacent base pair. A knowledge of the experimentally assigned ring NH chemical shifts of specific base pairs in known sequences of double‐stranded deoxy oligonucleotides coupled with the ring‐current tables for the DNA‐B helical structure permit the assignment of 13.6 ± 0.1 ppm and 14.6 ± 0.2 ppm for the GN1H proton of an isolated GC base pair and the TN3H proton of an isolated AT base pair, respectively.