Distinctive features of the self-association of deoxyhexanucleotide 5'-D(GpCpApTpGpC) in aqueous solution: 1H NMR analysis

The self-association of self-complementary deoxyhexanucleotide d(GCATGC) was investigated in aqueous salt solution. Homonuclear 1H NMR correlation spectroscopy (2D-TOCSY and 2D-NOESY) was used for complete assignments of nonexchangeable protons of the hexamer. The equilibrium reaction constants and...

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Bibliographic Details
Published inBiofizika Vol. 49; no. 5; p. 781
Main Authors Veselkov, A N, Pakhomov, V I, Rogova, O V, Volynkina, V S, Dymant, L N, Eaton, R J, Davies, D B
Format Journal Article
LanguageRussian
Published Russia (Federation) 01.09.2004
Subjects
Base Sequence
DNA - chemistry
Models, Molecular
Nuclear Magnetic Resonance, Biomolecular
Nucleic Acid Conformation
Oligodeoxyribonucleotides - chemistry
Solutions - chemistry
Thermodynamics
Water - chemistry
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Summary:The self-association of self-complementary deoxyhexanucleotide d(GCATGC) was investigated in aqueous salt solution. Homonuclear 1H NMR correlation spectroscopy (2D-TOCSY and 2D-NOESY) was used for complete assignments of nonexchangeable protons of the hexamer. The equilibrium reaction constants and thermodynamical parameters of duplex d(GCATGC)2 formation were determined from experimental concentration and temperature dependences of proton chemical shifts of the deoxyhexanucleotide. Distinctive features of the concentration dependences in the range of small concentrations at relatively low temperatures of solution enable one to assume that one single-stranded hexamer sequence forms a compact structure (similar to a hairpin) in aqueous solution. A possible spatial hairpin structure of the hexamer was proposed. Comparative analysis of the experimental and theoretical (using the "nearest neighbor" model) thermodynamical parameters of duplex formation was made.
ISSN:0006-3029