13C-NMR of Ribosyl ApApA, ApApG and ApUpG

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Abstract
The chemical shifts as well as the 13C-31P coupling constants of the carbon-13 nuclei in single-stranded ApApA, ApApG, and ApUpG are sensitive to sequence and temperature. ApApA and ApApG have similar properties with large shielding (up to 1.7 ppm) of many of the base carbons upon decreasing the temperature from 70°C to 11°C; the base carbons have smaller shielding changes in ApUpG. Large shielding and deshielding effects are observed for the 1′, 3′, 4′ and 5′-carbons over this temperature range. Analysis of the 13C-31P couplings measured at the 4′ ribose carbons show that the population of the anti rotamer about 05′-C5′ varies from 98 to 75%, and is higher in ApApA and ApApG than in ApUpG. The CCOP coupling data at 2′ and 4′ is consistent with a blend of the -antiperiplanar/-synclinal nonclassical rotamers about the C3′-03′ bond, varying from 89/11% in ApApG to 55/45% in ApUpG. The coupling and chemical shift data support the thesis that ApUpG is stacked much less than the other two molecules. The stacked forms of all three trinucleotides is most easily interpreted by a standard A-RNA model. It is not necessary to invoke the “bulged base” hypothesis [Lee, C.-H. and Tinoco, Jr., I. (1981) Biophysical Chemistry 1, 283-294; Lankhorst, P.P., Wille, G., van Boom., J.H., Altona, C., and Haasnoot, C.A.G. (1983) Nucleic Acids Research 11, 2839-2856] to explain the contrast in 13C spectroscopic properties of ApUpG in comparison to ApApG and ApApA.

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