An unusual DMA structure detected in a telomeric sequence under superhelical stress and at low pH

Abstract

TELOMERIC sequences of DNA, which are found at the ends of linear chromosomes, have been attracting attention as potential sites for the formation of unusual DNA structures. They consist of (G_nT_m) or (G_n AT_m) motifs (n ≥ m) and, in the single-stranded state, form hairpins stabilized by non-canonical G-G pairs¹. In the duplex state and under superhelical stress they exhibit hyper-sensitivity to SI nuclease² which by analogy with homopurine-homopyrimidine sequences^3–5 may reflect the formation of an unusual structure. To determine whether this is the case we have inserted into a plasmid the Tetmhymenatelomeric motif (G₄T₂)·(A₂C₄) and probed it by two-dimensional gel electrophoresis, chemical modification and oligonucleotide binding. Our data demonstrate that, under superhelical stress and at low pH, the insert does indeed adopt a novel DNA conformation. We have concluded that in this structure the C-rich strand forms a hairpin stabilized by non-Watson–Crick base pairs C·C⁺ and A·A⁺, whereas the G-rich strand remains unstructured. We term this new DNA structure the (C, A)-hairpin.