Solution conformation and dynamics of the octadeoxy-nucleotide d(CACTAGTG)2: a multinuclear n.m.r. relaxation study

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The conformation and internal dynamics of the octadeoxynucleotide d(CACTAGTG)2 have been examined by 1H- and 13C-n.m.r. relaxation. All the non-exchangeable protons, the seven phosphate resonances, and most of the 13C resonances of the proton-bearing carbons have been assigned by conventional two-dimensional n.m.r. methods. The average conformations of each nucleotide have been determined using time-dependent one-dimensional n.O.e.'s and 3JHH values derived from both NOESY and 2-quantum-filtered COSY experiments. All glycosidic torsion angles are anti, and in the range -95 to 125°, in which the pyrimidines have a significantly larger angle than the purines. All sugars were found mainly (> 80%) in the conformation range C-2′ endo to C-3′exo. The DNA fragment is within the B-family of conformations. The cytosine H-6-H-5 vectors move with an apparent correlation time of 3 ns at 25°. Cross-relaxation rate constants for the H-1′-H-2b vectors and some H-2a-H-2b and H-2a-H-3′ vectors were measured, from which order parameters were determined. The order parameters are all in the range 0.7-0.9, which is consistent with only moderate internal mobility on the sub-ns time scale. The {1H}-13C n.O.e. and the spin-lattice relaxation rate constant show that the terminal residues are relatively more mobile than the internal residues, and that the C-2′-H and C-3′%z.sbnd;-H vectors move with order parameters of 0.6-0.75.

Original languageEnglish
Pages (from-to)123-144
Number of pages22
JournalCarbohydrate Research
Issue number1
StatePublished - Dec 16 1991

Bibliographical note

Funding Information:
This work was supported by the Medical Research Council. for the purification of the oligonucleotide, and Dr. J. Feeney for

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Organic Chemistry


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