Open AccessConformational analysis of m42C-m42C-m42A: a chemically modified 3′-acceptor end of tRNA, studied by NMR and CD methods
Author(s) -
Johannes Doombos,
Harry P. M. de Leeuw,
Corndis S.M. Olsthoom,
Gerry WQle-Hazeleger,
Henk P. Westerinlc,
Jacques H. van Boom,
Cornelis Ahona
Publication year - 1983
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/11.21.7517
Subject(s) - crystallography , phosphodiester bond , dihedral angle , stereochemistry , coupling constant , spectral line , nmr spectra database , chemistry , physics , hydrogen bond , molecule , rna , biochemistry , organic chemistry , gene , particle physics , astronomy
A study on the conformation of the title compound, C-C-A, and on its constituent dinucleotides is presented. 1H-NMR spectra at 360 and 500 MHz were completely assigned by decoupling experiments. Computer simulation of the spectra yielded precise proton-proton and proton-phosphorus coupling constant values. The coupling constants are analyzed in terms of torsion angles and of N- and S-type sugar pucker. 31P-NMR spectra gave some information about P-O backbone torsion angles alpha and zeta. CD spectroscopy was used to obtain insight in the base-base interaction. The C(1) and C(2) unit in C-C-A show normal preference for N-type conformation of the sugar ring, whereas the A(3) residue appears rather biased towards the S-conformation. The zeta and alpha backbone torsion angles in the C-C phosphodiester linkage in C-C-A appear to assume normal g-, g- conformation, the zeta, alpha combination in the C-A linkage is proposed to have a g+, t conformation. In the C-C fragment in C-C-A a regular stack is indicated; it is suggested that the C-A part adopts an unusual antiparallel base stack.