Stable sheared A•C pair in DNA hairpins

Single-residue d(Pu1NPu2) (Pu-1 . Pu-2 = G . A, G . G or A . A) hairpin loops can be stably closed by sheared purine purine pairs. These special motifs have been found in several important biological systems. We now extend these loop-closing base-pairs to a sheared purine pyrimidine (A . C) pair at a neutral pH condition. High-resolution NMR spectroscopy, distance geometry, and molecular dynamics methods were used to study d(GTA-CANCGTAC) oligomers. Numerous idiosyncratic nuclear Overhauser enhancements, especially those across the A C base-pair between (CNH2)-N-4 <-> AH1', (CNH2)-N-4 <-> AH2, and CH5 <->AH2 proton pairs, clearly define the novel sheared nature of the closing A . C base-pair. This novel base-pair is possibly present in several biological systems and in two single-stranded DNA aptamers selected from oligonucleotide libraries. (C) 1999 Academic Press.