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15N NMR of RNA Fragments Containing Specifically Labeled GU and GC Pairs
journal contribution
posted on 1998-01-16, 00:00 authored by Xiaohu Zhang, Barbara L. Gaffney, Roger A. Jones15N 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.