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Assignment of the proton nmr chemical shifts of the TN 3 H and GN 1 H proton resonances in isolated AT and GC Watson‐Crick base pairs in double‐stranded deoxy oligonucleotides in aqueous solution
Author(s) -
Patel Dinshaw J.,
Tonelli Alan E.
Publication year - 1974
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1974.360131003
Subject(s) - chemistry , molecular structure of nucleic acids: a structure for deoxyribose nucleic acid , chemical shift , ring (chemistry) , crystallography , base pair , oligonucleotide , stereochemistry , proton , dna , base (topology) , proton nmr , pyrimidine , physics , biochemistry , organic chemistry , quantum mechanics , mathematical analysis , mathematics
The 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 H 2 O solution. These resonances have been assigned to the GN 1 H and TN 3 H 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 GN 1 H and TN 3 H 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 GN 1 H proton of an isolated GC base pair and the TN 3 H proton of an isolated AT base pair, respectively.