Conformations of the alternating (C-T)n sequence under neutral and low pH

T. N. Jaishree, Andrew H.J. Wang

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


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-depedent confonnational 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.

Original languageEnglish
Pages (from-to)139-144
Number of pages6
JournalFEBS Letters
Issue number2
Publication statusPublished - Jan 10 1994
Externally publishedYes


  • Modified DNA base
  • Nuclear Overhauser effect
  • Unusual DNA conformation

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology


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