The differences in the T2 relaxation rates of the protons in the partially-deuteriated and fully protonated sugar residues in a large oligo-DNA (‘NMR-window’) gives complementary structural information

Agback, Peter; Maltseva, T.V.; Yamakage, S.-i.; Nilson, F.P.R.; Foldesi, A.; Chattopadhyaya, J.

doi:10.1093/nar/22.8.1404

Research article1994Peer reviewedOpen access

The differences in the T2 relaxation rates of the protons in the partially-deuteriated and fully protonated sugar residues in a large oligo-DNA (‘NMR-window’) gives complementary structural information

Agback, Peter; Maltseva, T.V.; Yamakage, S.-i.; Nilson, F.P.R.; Foldesi, A.; Chattopadhyaya, J.

Abstract

Selective incorporation of the stereospecifically deuteriated sugar moieties (>97 atom % H-2 enhancements at H2', H2'', H3' and H5'/5'' sites, similar to 85 atom % 2H enhancement at H4' and similar to 20 atom % H-2 enhancement at H1') in DNA and RNA by the 'NMR-window' approach has been shown to salve the problem of the resonance overlap [refs. 1, 2 & 3]. Such specific deuterium labelling gives much improved resolution and sensitivity of the residual sugar proton (i.e. H1' or H4') vicinal to the deuteriated centers (ref. 3). The T-2 relaxation time of the residual protons also increases considerably in the partially-deuteriated (shown by underline) sugar residues in dinucleotides [d(Cp ($) under bar G, d(Gp ($) under bar C, d(Ap ($) under bar T), d(Tp ($) under bar A], trinucleotide r(($) under bar A2'p5'A2'p5'($) under bar A) and 20-mer DNA duplex 5'd(($) under bar C-1 ($) under bar G(2) ($) under bar C-3-, ($) under bar G(4)C(5)G(6)C(7)G(8)A(9)A(10) T(11)T(12)C(13)G(14)C(15)G(16)($) under bar C-17($) under bar G(18) ($) under bar C-19;20)(2)3'. The protons with shorter Ta can be filtered away using a number of different NMR experiments such as ROESY, MINSY or HAL. The NOE intensity of the cross-peaks in these experiments includes only straight pathway from H1' to aromatic proton (i-i and i-i+1) without any spin-diffusion. The volumes of these NOE cross-peaks could be measured with high accuracy as their intensity is 3 to 4 times larger than the corresponding peaks in the fully protonated residues in the normal NOESY spectra. The structural informations thus obtainable from the residual protons in the partially-deuteriated part of the duplex and the fully protonated part in the 'NMR window' can indeed complement each other.

Published in

Nucleic Acids Research
1994, Volume: 22, number: 8, pages: 1404-1412
Publisher: OXFORD UNIV PRESS UNITED KINGDOM

UKÄ Subject classification

Structural Biology

Publication identifier

DOI: https://doi.org/10.1093/nar/22.8.1404

Permanent link to this page (URI)

https://res.slu.se/id/publ/83900