C-13-NMR RELAXATION IN 3 DNA OLIGONUCLEOTIDE DUPLEXES - MODEL-FREE ANALYSIS OF INTERNAL AND OVERALL MOTION

Natural-abundance C-13-NMR spectra of [d(TCGCG)](2) (1), [d(CGCGCG)](2) (2), and [d(GGTATACC)](2) (3) were measured at 90.6 MHz to obtain C-13-H-1 NOEs and T-1 relaxation times; relaxation data were also measured at 125.7 MHz for 1 and 2 and at 62.9 MHz far 1. Analysis of the relaxation data was performed in the context of the ''model-free'' approach of Lipari and Szabo [Lipari, G., and Szabo, A, (1982) J. Am. Chem. Sec. 104, 4546-4559], leading to the following conclusions: (i) Optimized values for the overall correlation times of 0.9 ns for 1 and 1.4 ns for 2 are close to those predicted by light-scattering results on similar molecules [Eimer et al. (1990) Biochemistry 29, 799-811]. (ii) For the nonterminal residues, the ''order parameter'', S-2, is around 0.8 for the protonated base carbons and 0.6 for the sugar carbons, indicating less spatial restriction on the sugar carbons (in the model-free approach, the order parameter is 1 for a rigid body and 0 for a system with completely unrestricted internal motion). (iii) The order parameters for the terminal residues vary over a wide range with the smallest values around 0.2-0.3 for the HO-(13)C5' and the (13)C3'-OH; rational trends are seen in the variation of S-2 With chain position in the terminal residues. (iv) The analysis shows that the order parameters are accurate within 15%. (V) The ''effective internal correlation time'', tau is very short for the sugar carbons (30-300 ps) and less well-defined, but probably also short, for the bases. (vi) The analysis indicates that most of the relaxation in DNA is accounted for by S-2 and that tau(e), is so short that a good approximation to any relaxation property, P (e.g., T-1, T-2, C-13-H-1 NOE, H-1-H-1 cross-relaxation rate), is P = (SPrigid)-P-2, where P-rigid is the value for the property in a system without internal motion (the analysis assumes the same isotropic overall motion for both the rigid and flexible bodies).