Comparative13C and2H relaxation study of microsecond dynamics of the AT tract of selectively13C/2H double-labelled DNA duplexes

The microsecond dynamics of the sugar moiety of A and T residues in DNA duplexes, (1b) and (2b), containing 13C/2H double-labelled 2′(R/S),5′(R/S)-2H2-1′,2′,3′,4′,5′-13C5-2′-deoxyribofuranose moieties (all labelled A and T are shown in bold), were studied using 13C nuclear spin relaxation measurements. An exchange contribution was detected in the transverse relaxation rates (R1ρ) of 13C 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 2G·9C base pair in the former by a 2C·9G 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 2H nuclear magnetic spin relaxation (T1ρ) measurements of the same nucleotides show no dependence on the spin lock strength, it was concluded that the main mechanism of 2H T1ρ 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 13C relaxation (T1ρ) 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.