Analysis of intrasugar interproton NOESY cross-peaks as an aid to determine sugar geometries in DNA fragments.
A systematic analysis of the conformation of deoxyribofuranose rings in DNA fragments has been described using two-dimensional nuclear Overhauser effect spectroscopy (2D NOESY). The approach is based on the interpretation of the intrasugar proton-proton distances which can be estimated using a low-mixing-time pure-absorption mode w1-scaled NOESY spectrum. The experimental distances are compared with the theoretical values calculated as a function of pseudorotation phase angle (P) describing the sugar geometries. The approach can be used as a complementary aid to J couplings for establishing sugar conformations in individual nucleotide units of DNA fragments. Using this strategy on d-ACATCGATGT, we observed that individual nucleotides exhibit O4'-endo sugar pucker. The results rule out possibilities of the existence of a fast equilibrium (on the NMR time scale) between C2'-endo (or S-domain) and C3'-endo (or N-domain) sugar puckers.
Chary
K V
KV
Chemical Physics Group, Tata Institute of Fundamental Research, Bombay, India.
Modi
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D001483:Base Sequence; D004247:DNA; D003855:Deoxyribose; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides
D009838:Oligodeoxyribonucleotides; D003855:Deoxyribose; D004247:DNA