Zipper-like Watson-Crick base-pairs

Abstract

A series of DNA heptadecamers containing the DNA analogues of RNA E-like 5′-d(GXA)/(AYG)-5′ motifs (X/Y is complementary T/A, A/T, C/G, or G/C pair) were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers reveal excellent resolution in NMR spectra and exhibit many unusual nuclear Overhauser effects (NOEs) that allow for good characterization of an unusual zipper-like conformation with zipper-like Watson-Crick base-pairs; the potential canonical X · Y H-bonding is not present, and the central X/Y pairs are transformed instead into inter-strand stacks that are bracketed by sheared G · A base-pairs. Such phenomenal structural change is brought about mainly through two backbone torsional angle adjustments, i.e. δ from C2′-endo to C3′-endo for the sugar puckers of unpaired residues and γ from gauche+ to trans for the following 3′-adenosine residues. Such motifs are analogous to the previously studied (GGA)2 motif presumably present in the human centromeric (TGGAA)n tandem repeat sequence. The novel zipper-like motifs are only 4–7 deg. C less stable than the (GGA)2 motif, suggesting that inter-strand base stacking plays an important role in stabilizing unusual nucleic acid structures. The discovery that canonical Watson-Crick G · C or A · T hydrogen-bonded pairs can be transformed into stacking pairs greatly increases the repertoire for unusual nucleic acid structural motifs.