Stable sheared A.C pair in DNA hairpins.

Single-residue d(Pu1NPu2) (Pu1.Pu2=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(GTACANCGTAC) oligomers. Numerous idiosyncratic nuclear Overhauser enhancements, especially those across the A.C base-pair between C4NH2left and right arrow AH1', C4NH2left and right arrow AH2, and CH5left and right arrow 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.