Abstract

The microsecond dynamics of the sugar moiety of A and T residues in DNA duplexes, d(5')((1)C(2)G(3)A(4)T(5)T(6)A(7)A(8)T(9)C(10)G)(2)(3') (1b) and d(5')((1)C(2)C(3)A(4)T(5)T(6)A(7)A(8)T(9)G(10)G)(2)(3') (2b), containing C-13/H-2 double-labelled 2'(R/S),5'(R/S)-H-2(2)-1',2',3',4',5'-C-13(5)-2'-deoxyribofuranose moieties (all labelled A and T are shown in bold), were studied using C-13 nuclear spin relaxation measurements. An exchange contribution was detected in the transverse relaxation rates (R-1 rho) of C-13 Of the labelled nucleotides. The comparison of the dynamics of various nucleotide residues of duplex 1b with those of the duplex 2b demonstrated that the replacement of the (2)G .C-9 base pair in the former by a C-2 .(9)G base pair in the latter alters the time-scale of motions in the AT tract. Moreover, the T residues show different microsecond dynamic behaviour to the A residues in the A-T base pairs. Since H-2 nuclear magnetic spin relaxation (T-1 rho) measurements of the same nucleotides show no dependence on the spin lock strength, it was concluded that the main mechanism of H-2 T-1 rho relaxation is quadrupolar. Although we observed a clear difference in the dynamic characteristics of the AT tract of the duplexes 1b and 2b [as evident from distinct differences in both spin lock dependent C-13 relaxation (T-1 rho) and in the amplitude of the exchange parameter amongst all deoxyadenosine nucleotide residues in both duplexes], we failed, however, to observe any difference in hydration behaviour in solution, thereby suggesting that there is no straightforward correlation in these two intrinsic dynamic properties of DNA duplex. It is noteworthy, however, that as the flexibility of the minor groove increases in both duplexes, we observe more long-lived water molecules around. Copyright (C) 2000 John Wiley & Sons, Ltd.

Keywords

NMR; C-13 NMR; H-2 NMR; relaxation; dynamics; AT tract; DNA duplexes

Published in

Magnetic Resonance in Chemistry
2000, Volume: 38, number: 6, pages: 403-414

UKÄ Subject classification

Physical Chemistry


Publication identifier

DOI: https://doi.org/10.1002/1097-458X(200006)38:6<403::AID-MRC659>3.0.CO;2-Q

Permanent link to this page (URI)

https://res.slu.se/id/publ/108055