Conformations of the alternating (C-T)n sequence under neutral and low pH.
The structures of the (C-T)n sequence at two different pHs have been analyzed by 500 MHz 2D-NMR using a modified DNA decamer d(CT[m5C]TCU[m5C]UCT) as a model system. The chemical modifications serve to perturb the monotonous C-T repeat, and consequently to yield a better chemical shift dispersion. The results reinforce our earlier suggestion that there are three major pH-dependent conformational species: two antiparallel-stranded (APS) duplexes at pH 7 and pH 3, and a different structure near pH 5. Structural refinement of the decamer duplexes at pH = 7.5 and pH = 2.9 using 2D-NOE data suggests that the C:T or C+:T base pairs are continuously stacked. Exchangeable proton NMR spectra at pH 7.5 and pH 2.9 are consistent with C:T or C+:T base pairing schemes in which a water molecule bridges the two bases.
Jaishree
T N
TN
Biophysics Division, University of Illinois at Urbana-Champaign 61801.
Wang
A H
AH
D044503:5-Methylcytosine; D001482:Base Composition; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives; D004247:DNA / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D009843:Oligoribonucleotides / Q000737:chemistry; D011089:Polydeoxyribonucleotides / Q000737:chemistry; D013941:Thymine
D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D011089:Polydeoxyribonucleotides; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA; D013941:Thymine