15N NMR of RNA Fragments Containing Specifically Labeled GU and GC Pairs

15N and 13C NMR have been used to study three specifically labeled RNA fragments that include two tandem GU wobble pairs of different thermal stability and a tetraloop GU pair. The data are also compared to earlier 15N NMR work on an isolated, intrahelical GU pair. The results provide qualitative information on the relative contributions by stacking and hydrogen bonding to chemical shift changes at specific sites in a variety of GU pairs. Chemical shifts for the unpaired guanine amino groups in the isolated and both tandem wobble pairs are all significantly upfield of corresponding paired GC aminos. The guanine amino of the tetraloop is further downfield, as expected for a base paired hydrogen bond donor. Thus, 15N NMR can be diagnostic for the presence of base−base pairing in RNA. Chemical shifts of the guanine N1 in all four GU pairs show significant shielding effects, particularly those of the more stable tandem GU pair. Similar shielding is also seen in the 13C data for the C2 atom of the GU wobble pairs. Our results demonstrate that these adjacent ring atoms (N1 and C2) are in the shielding regions of neighboring bases, and that specific labeling can provide information on base stacking. Thus, where global structure is known, specific labeling can be invaluable as a complement to probe local interactions. It is likely, however, that the most important use of specific labeling will be with complex systems in which global structural information is incomplete.