Solution Structure of a DNA Double Helix Incorporating
Four Consecutive Non-Canonical Base Pairs

Ko-Hsin Chin & Shan-Ho Chou*

Institute of Biochemistry

National Chung-Hsing University, Taichung, 40227, Taiwan


A series of DNA 21-mers containing a variety of the 4 x 4 internal loop sequence 5’-CAAG-3’/3’-ACGT-5’ were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG) /molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the well characterization of a DNA hairpin incorporating a track of four different non-canonical base pairs in the stem, which include a wobble C·A base pair, a sheared A·C base pair, a sheared A·G base pair, and a wobble G·T base pair. Excellent intra-strand and inter-strand base stacking is observed within the four consecutive mismatches and the surrounding canonical base pairs, which explain why it exhibits a decent UV-melting temperature of 52 °C even five out of ten base pairs in the stem adopt non-canonical H-bonding. The 4 x 4 internal loop fits into a B-DNA double helix very well with no significant change in the backbone torsion angles; only z torsion angles between the tandem sheared base pairs are changed from the gauche- domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The four consecutive non-canonical base pairs observed in this manuscript greatly increase the limited repertoire of irregular DNA folds known to date.