Sequence and Structure in Double-Stranded Ribonucleic Acid: (A-G-C-U)2 and (A-C-G-U)2

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 five of the seven aromatic C-H resonances within 0.2 ppm. The NMR results are in better agreement with the A form for (A-G-CU) 2. For both oligomers, the changes in chemical shift for the anomeric (HU) resonances indicate substantial (≥20°) 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.