Premium
Sequence‐dependent structural variations in two right‐handed alternating pyrimidine‐purine DNA oligomers in solution determined by nuclear Overhauser enhancement measurements.
Author(s) -
Clore G.M.,
Gronenborn A.M.
Publication year - 1983
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1002/j.1460-2075.1983.tb01710.x
Subject(s) - nuclear overhauser effect , oligonucleotide , proton , pyrimidine , helix (gastropod) , dna , base pair , triple helix , biology , nuclear magnetic resonance , crystallography , physics , nuclear magnetic resonance spectroscopy , chemistry , biochemistry , quantum mechanics , ecology , snail
A 500 MHz 1H‐n.m.r. study on two right‐handed self‐complementary double‐stranded alternating pyrimidine‐purine oligodeoxyribonucleotides, 5′dCGTACG and 5′dACGCGCGT, is presented. Using the proton‐proton nuclear Overhauser effect, proton resonances are assigned by a sequential method and a large number of interproton distances, both intra‐ and internucleotide, are determined (113 for 5′dCGTACG and 79 for 5′dACGCGCGT). The general procedure required to solve the three‐dimensional solution structures of oligonucleotides from such distance data is outlined and applied to these two oligonucleotides. In the case of both oligonucleotides the overall solution structure is that of B DNA, namely a right‐handed helix with a helical rise of approximately 3.3 A, 10 bp per turn and the base pairs approximately perpendicular to the helix axis. In the case of 5′dCGTACG, subtle local structural variations associated with the pyrimidine and purine nucleotides are superimposed on the overall structure but the mononucleotide repeating unit is preserved. In contrast, 5′dACGCGCGT has a clear alternating structure with a dinucleotide repeat, alternation occurring in the local helical twist and the glycosidic bond, sugar pucker and phosphodiester backbone conformations.