A tetrameric DNA structure with protonated cytosine.cytosine base pairs

Overview of Gehring K. et al.

AuthorsGehring K., Leroy J.L., Guéron M.
AffiliationGroupe de Biophysique de l'Ecole Polytechnique et de l'URA D1254 du CNRS, 91128 Palaiseau, France  
JournalNature
Year 1993

Abstract


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.