 |
PDBsum entry 1ekd
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for g.U pairs: one hydrogen bond for each g.U pair in r(ggcgugcc)(2) and two for each g.U pair in r(gagugcuc)(2).
|
|
|
Authors
|
|
X.Chen,
J.A.Mcdowell,
R.Kierzek,
T.R.Krugh,
D.H.Turner.
|
|
|
Ref.
|
|
Biochemistry, 2000,
39,
8970-8982.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
G.U pairs occur frequently and have many important biological functions. The
stability of symmetric tandem G.U motifs depends both on the adjacent
Watson-Crick base pairs, e.g., 5'G > 5'C, and the sequence of the G.U pairs,
i.e., 5'-UG-3' > 5'-GU-3', where an underline represents a nucleotide in a
G.U pair [Wu, M., McDowell, J. A., and Turner, D. H. (1995) Biochemistry 34,
3204-3211]. In particular, at 37 degrees C, the motif 5'-CGUG-3' is less stable
by approximately 3 kcal/mol compared with other symmetric tandem G.U motifs with
G-C as adjacent pairs: 5'-GGUC-3', 5'-GUGC-3', and 5'-CUGG-3'. The solution
structures of r(GAGUGCUC)(2) and r(GGCGUGCC)(2) duplexes have been determined by
NMR and restrained simulated annealing. The global geometry of both duplexes is
close to A-form, with some distortions localized in the tandem G.U pair region.
The striking discovery is that in r(GGCGUGCC)(2) each G.U pair apparently has
only one hydrogen bond instead of the two expected for a canonical wobble pair.
In the one-hydrogen-bond model, the distance between GO6 and UH3 is too far to
form a hydrogen bond. In addition, the temperature dependence of the imino
proton resonances is also consistent with the different number of hydrogen bonds
in the G.U pair. To test the NMR models, U or G in various G.U pairs were
individually replaced by N3-methyluridine or isoguanosine, respectively, thus
eliminating the possibility of hydrogen bonding between GO6 and UH3. The results
of thermal melting studies on duplexes with these substitutions support the NMR
models.
|
|
|
|
|
|
|
|
Headers
|
|
|
|
|
|
