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.

No abstract

The opening of base pairs of double-stranded DNA is an important process, being a prerequisite for replication and transcription and possibly a factor in the recognition, flexibility and structure of DNA. The kinetics of base-pair opening have, however, been controversial. Base-pair opening can be studied by following the exchange of protons from imino groups with water, a process that seems only to occur from open base pairs. We have recently demonstrated catalysis by proton acceptors of imino proton exchange in nucleic acids. This has enabled us to determine the base-pair lifetimes, which are in the region of 10 ms at room temperature. In earlier reports it had been considered that proton exchange is limited by the rate of base-pair opening, which had led to estimates of base-pair lifetimes that were larger by one or two orders of magnitude. There are also important discrepancies between recent and early estimates of the base-pair dissociation constant. Earlier estimates of base-pair lifetimes correspond in fact to the time required for proton exchange in the absence of added catalyst (AAC exchange). This could be a distinct mode of base-pair opening with a very long open lifetime, different from the mode revealed by the effect of catalyst. The evidence reported here suggests on the contrary that there is only a single mode of here suggests on the contrary that there is only a single mode of base-pair opening and that proton exchange in the absence of added catalyst is in fact catalysed by a proton acceptor intrinsic to the nucleic acid, most probably the other base of the open pair.