Synthesis and proton-NMR studies of oligonucleotides containing an apurinic (AP) site
- Gorlaeus Laboratories State Univ., Leiden (Netherland)
In order to elucidate the conformational properties of base-deleted oligodeoxyribonucleotides, the molecules d-CpS(pCpG)n (n = 1,2; S = sugar) were synthesized by the phosphotriester method and characterized by 1H-NMR spectroscopy. Complete assignment of all non-exchangeable proton resonances of both compounds was obtained by 1D- and 2D-NMR techniques. In combination with computer simulation, these spectra yielded proton-proton and proton-phosphorus coupling constants of high accuracy. These data provide valuable information about the sugar and the backbone conformation. It appears that d-Cp1Sp2Cp3G4 does not form a duplex under any of the conditions studied. On the contrary, the base-deleted hexamer d-Cp1Sp2Cp3Gp4Cp5G6 occurs as a right-handed' staggered' DNA duplex at 280 K: the core of this duplex is formed by the residues C(3)-G(6); two 'dangling' residues C(1) and S(2) are located at the two 5'-ends of the duplex. The assignment of the corresponding imino proton resonances for (d-CpS(pCpG)2)2 was based on their thermal behavior: the line broadening of these resonances was studied as a function of temperature. The chemical shift and the number of imino proton resonances accord well with the number and type of Watson-Crick base pairs which can be formed in the staggered duplex described above. Thermodynamic parameters of duplex formation were obtained from an analysis of the chemical shift versus temperature profiles of aromatic base and H-1' protons. It is suggested that the cytosine ring of C(1) stacks, at least part of the time, with the guanine ring on the nucleotide residue, G(6), situated in the complementary strand. The binding of Lys-Trp-Lys to (d-CpS(pCpG)2)2 as well as to (d-CpGpCpG)1 was investigated.
- OSTI ID:
- 6945661
- Journal Information:
- Journal of Biomolecular Structure and Dynamics; (USA), Vol. 5:2; ISSN 0739-1102
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
OLIGONUCLEOTIDES
MOLECULAR STRUCTURE
COMPUTERIZED SIMULATION
DEUTERIUM
NUCLEAR MAGNETIC RESONANCE
PROTONS
THERMODYNAMICS
TRACER TECHNIQUES
BARYONS
ELEMENTARY PARTICLES
FERMIONS
HADRONS
HYDROGEN ISOTOPES
ISOTOPE APPLICATIONS
ISOTOPES
LIGHT NUCLEI
MAGNETIC RESONANCE
NUCLEI
NUCLEIC ACIDS
NUCLEONS
ODD-ODD NUCLEI
ORGANIC COMPOUNDS
RESONANCE
SIMULATION
STABLE ISOTOPES
550201* - Biochemistry- Tracer Techniques