Book of Abstracts: Albany 2003
June 17-21 2003
Sheared Ganti·Csyn Base Pair: A Unique d(GXC) Loop Closure Motif
Stable DNA loop structures closed by a G·C base pair have been determined for the single-residue d(GXC) loops (X = A, T, G, C) in low salt solution by high resolution nuclear magnetic resonance (NMR) techniques. The closing G·C base pair in these loops is not of the canonical Watson-Crick type, but adopts instead a unique sheared mode as those of the mismatched sheared G·A or A·C base pair to draw near the two opposite strands. The cytidine residue in the closing base pair is transformed into the rare syn conformation to form two H-bonds with the guanine base and to prevent the possible steric clash between the G2NH2 and the CH5 protons. Besides, the sugar pucker of the syn cytidine retains in the regular C2?-endo domain, unlike the C3?-endo domain adopted in the pyrimidines of the out-of-alternation left-handed Z-DNA structure. The facile formation of compact d(GXC) loops closed by a unique sheared Ganti·Csyn base pair demonstrates the great potential of the single-stranded d(GXC) triplet repeats to fold into stable hairpins.
1Institute of Biochemistry