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Conformations of the alternating (C‐T) n sequence under neutral and low pH
Author(s) -
Jaishree T.N.,
Wang Andrew H.-J.
Publication year - 1994
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(94)80261-0
Subject(s) - antiparallel (mathematics) , chemistry , crystallography , base pair , molecule , chemical shift , nuclear magnetic resonance spectroscopy , stereochemistry , yield (engineering) , base (topology) , proton nmr , proton , dna , materials science , physics , biochemistry , metallurgy , mathematical analysis , mathematics , organic chemistry , quantum mechanics , magnetic field
The structures of the (C‐T) n sequence at two different pHs have been analyzed by 500 MHz 2D‐NMR using a modified DNA decamer d(CT[m 5 C]TCU[m 5 C]UCT) as a model system. The chemical modifications serve to perturb the monotonous C‐T repeat, and consequently to yield a better chemical shift dispersion. The results reinforce our earlier suggestion that there are three major pH‐depedent confonnational species: two antiparallel‐stranded (APS) duplexes at pH 7 and pH 3, and a different structure near pH 5. Structural refinement of the decamer duplexes at pH = 7.5 and pH = 2.9 using 2D‐NOE data suggests that the C : T or C + : T base pairs are continuously stacked. Exchangeable proton NMR spectra at pH 7.5 and pH 2.9 are consistent with C : T or C + : T base pairing schemes in which a water molecule bridges the two bases.