13C-NMR relaxation in three DNA oligonucleotide duplexes: model-free analysis of internal and overall motion

Philip N. Borer

Research output: Contribution to journalArticle

85 Scopus citations

Abstract

Natural-abundance 13C-NMR spectra of [d(TCGCG)]2 (1), [d(CGCGCG)]2 (2), and [d(GGTATACC)]2 (3) were measured at 90.6 MHz to obtain 13C-1H NOEs and T, relaxation times; relaxation data were also measured at 125.7 MHz for 1 and 2 and at 62.9 MHz for 1. Analysis of the relaxation data was performed in the context of the "model-free" approach of Lipari and Szabo [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 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", S2, 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-13C5′ and the 13C3′-OH; rational trends are seen in the variation of S2 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", τe, 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 S2 and that τe is so short that a good approximation to any relaxation property, P (e.g., T1, T2, 13C-1H NOE, 1H-1H cross-relaxation rate), is P = S2Prigid, where Prigid 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).

Original languageEnglish (US)
Pages (from-to)2441-2450
Number of pages10
JournalBiochemistry
Volume33
Issue number9
StatePublished - 1994

ASJC Scopus subject areas

  • Biochemistry

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