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PDBsum entry 1f5h
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dna_rna links
RNA PDB id
1f5h

 

 

 

 

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Contents
DNA/RNA
PDB id:
1f5h
Name: RNA
Title: The g7(syn)-g4(anti) structure of r(gcaggcgugc)2
Structure: 5'-r( Gp Cp Ap Gp Gp Cp Gp Up Gp C)-3'. Chain: a, b. Engineered: yes
Source: Synthetic: yes
NMR struc: 26 models
Authors: M.E.Burkard,D.H.Turner
Key ref:
M.E.Burkard and D.H.Turner (2000). NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs. Biochemistry, 39, 11748-11762. PubMed id: 10995243 DOI: 10.1021/bi000720i
Date:
14-Jun-00     Release date:   26-Jun-00    
 Headers
 References

DNA/RNA chains
  G-C-A-G-G-C-G-U-G-C 10 bases
  G-C-A-G-G-C-G-U-G-C 10 bases

 

 
DOI no: 10.1021/bi000720i Biochemistry 39:11748-11762 (2000)
PubMed id: 10995243  
 
 
NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs.
M.E.Burkard, D.H.Turner.
 
  ABSTRACT  
 
Nucleotides in RNA that are not Watson-Crick-paired form unique structures for recognition or catalysis, but determinants of these structures and their stabilities are poorly understood. A single noncanonical pair of two guanosines (G) is more stable than other noncanonical pairs and can potentially form pairing structures with two hydrogen bonds in four different ways. Here, the energetics and structure of single GG pairs are investigated in several sequence contexts by optical melting and NMR. The data for r(5'GCAGGCGUGC3')(2), in which G4 and G7 are paired, are consistent with a model in which G4 and G7 alternate syn glycosidic conformations in a two-hydrogen-bond pair. The two distinct structures are derived from nuclear Overhauser effect spectroscopic distance restraints coupled with simulated annealing using the AMBER 95 force field. In each structure, the imino and amino protons of the anti G are hydrogen bonded to the O6 and N7 acceptors of the syn G, respectively. An additional hydrogen-bond connects the syn G amino group to the 5' nonbridging pro-R(p) phosphate oxygen. The GG pair fits well into a Watson-Crick helix. In r(5'GCAGGCGUGC3')(2), the G4(anti), G7(syn) structure is preferred over G4(syn), G7(anti). For single GG pairs in other contexts, exchange processes make interpretation of spectra more difficult but the pairs are also G(syn), G(anti). Thermodynamic data for a variety of duplexes containing pairs of G, inosine, and 7-deazaguanosine flanked by GC pairs are consistent with the structural and energetic interpretations for r(5'GCAGGCGUGC3')(2), suggesting similar GG conformations.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20123727 K.Onizuka, Y.Taniguchi, and S.Sasaki (2010).
A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA.
  Nucleic Acids Res, 38, 1760-1766.  
19178151 J.H.Chen, B.Gong, P.C.Bevilacqua, P.R.Carey, and B.L.Golden (2009).
A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme.
  Biochemistry, 48, 1498-1507.  
19591840 V.Venditti, L.Clos, N.Niccolai, and S.E.Butcher (2009).
Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.
  J Mol Biol, 391, 894-905.
PDB codes: 2kez 2kf0
18658118 W.Rypniewski, D.A.Adamiak, J.Milecki, and R.W.Adamiak (2008).
Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.
  RNA, 14, 1845-1851.
PDB codes: 3czw 3d0m
16710302 S.Chowdhury, C.Maris, F.H.Allain, and F.Narberhaus (2006).
Molecular basis for temperature sensing by an RNA thermometer.
  EMBO J, 25, 2487-2497.
PDB codes: 2gio 2gip
16982646 Z.J.Lu, D.H.Turner, and D.H.Mathews (2006).
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.
  Nucleic Acids Res, 34, 4912-4924.  
11327869 M.E.Burkard, T.Xia, and D.H.Turner (2001).
Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair.
  Biochemistry, 40, 2478-2483.  
11295748 S.J.Schroeder, M.E.Burkard, and D.H.Turner (1999).
The energetics of small internal loops in RNA.
  Biopolymers, 52, 157-167.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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