A tetrameric DNA structure with protonated cytosine.cytosine base pairs

Nature. 1993 Jun 10;363(6429):561-5. doi: 10.1038/363561a0.


Oligomers containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5'-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and constrained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs H1'-H1', H1'-H2" and H1'-H4'. These NOEs are probably diagnostic for such tetrameric structures.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Cytosine / chemistry*
  • DNA / chemistry*
  • Hydrogen-Ion Concentration
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Protons


  • Protons
  • Cytosine
  • DNA