Sequence and structure in double-stranded ribonucleic acid: (A-G-C-U)2 and (A-C-G-U)2

Abstract

Comparative studies of the thermally induced helix-coil transition in ribosyl (A-G-C-U)2 and (A-C-G-U)2 are described. Ordered structures form at low temperatures where the ribofuranose rings adopt the 3''-endo conformation and both oligomer helices have base-paired stacking arrangements qualitatively similar to the A-RNA family configuration. Especially for (A-C-G-U)2, there is a lack of quantitative agreement between the A-family base overlap and the 1H NMR data; ring-current and atomic diamagnetic anisotropies using A-form structures fail to predict 5 of the 7 aromatic C-H resonances within 0.2 ppm. The NMR results are in better agreement with the A form for (A-G-C-U)2. For both oligomers, the changes in chemical shift for the anomeric (H1'') resonances indicate substantial (.gtoreq. 20.degree.) changes in the average glycosidic torsion angle upon base pairing and stacking for the adenosine and cytidine residues; this angle in uridine and guanosine residues must change only slightly.