The conformation and dynamics of the deoxyribose rings of a (nogalamycin)2-d(5′-GCATGC)2 complex have been determined from an analysis of 1H-1H vicinal coupling constants and sums of coupling constants (J1′-2′,J1′-2″,epsilon 1′, epsilon 2′ and epsilon 2″) measured from one-dimensional n.m.r. spectra and from H-1′-H-2′ and H-1′-H-2″ cross-peaks in high-resolution phase-sensitive two-dimensional correlation spectroscopy (COSY) and double-quantum-filtered correlation spectroscopy (DQF-COSY) experiments. The value of J3′-4′ has also been estimated from the magnitude of H-3′-H-4′ cross-peaks in DQF-COSY spectra and H-1′-H-4′ coherence transfer cross-peaks in two-dimensional homonuclear Hartman-Hahn spectroscopy (HOHAHA) spectra. The data were analysed, in terms of a dynamic equilibrium between North (C-3′-endo) and South (C-2′-endo) conformers, by using the graphical-analysis methods described by Rinkel & Altona [(1987) J. Biomol. Struct. Dyn. 4,621-649]. The data reveal that the sugars of the 2C-5G and 3A-4T base-pairs, which form the drug-intercalation site, have strikingly different properties. The deoxyribose rings of the 2C-5G base-pair are best described in terms of an equilibrium heavily weighted in favour of the C-2′-endo geometry (greater than 95% ‘S’), with a phase angle, P, lying in the range 170-175 degrees and amplitude of pucker between 35 and 40 degrees, as typically found for B-DNA. For the deoxyribose rings of the 3A-4T base-pair, however, the analysis shows that, for 3A, the C-2′-endo and C3′-endo conformers are equally populated, whereas a more limited data set for the 4T nucleotide restricts the equilibrium to within 65-75% C-2′-endo. The deoxyribose rings of the 1G-6C base-pair have populations of 70-80% C-2′-endo, typical of nucleotides at the ends of a duplex. Although drug-base-pair stacking interactions are an important determinant of the enhanced duplex stability of the complex [Searle, Hall, Denny, & Wakelin (1988) Biochemistry 27, 4340-4349], the current findings make it clear that the same interactions can be associated with considerable variations in the degree of local structural dynamics at the level of the sugar puckers.
Conformation and dynamics of the deoxyribose rings of a (nogalamycin)2–d (5′-GCATGC)2 complex studied in solution by 1H-n.m.r. spectroscopy
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M S Searle, L P Wakelin; Conformation and dynamics of the deoxyribose rings of a (nogalamycin)2–d (5′-GCATGC)2 complex studied in solution by 1H-n.m.r. spectroscopy. Biochem J 15 July 1990; 269 (2): 341–346. doi: https://doi.org/10.1042/bj2690341
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