spacer
spacer

PDBsum entry 3ibk

Go to PDB code: 
dna_rna metals links
RNA PDB id
3ibk
Jmol
Contents
DNA/RNA
Metals
__K ×2
Waters ×45
PDB id:
3ibk
Name: RNA
Title: Crystal structure of a telomeric RNA quadruplex
Structure: RNA (5'-r( (5Bu)p Ap Gp Gp Gp Up Up Ap Gp Gp Gp U chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence occurs naturally in humans
Resolution:
2.20Å     R-factor:   0.216     R-free:   0.231
Authors: G.W.Collie,S.Neidle,G.N.Parkinson
Key ref: G.W.Collie et al. (2010). A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex. Nucleic Acids Res, 38, 5569-5580. PubMed id: 20413582
Date:
16-Jul-09     Release date:   12-May-10    
 Headers
 References

 

 
Nucleic Acids Res 38:5569-5580 (2010)
PubMed id: 20413582  
 
 
A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex.
G.W.Collie, S.M.Haider, S.Neidle, G.N.Parkinson.
 
  ABSTRACT  
 
DNA telomeric repeats in mammalian cells are transcribed to guanine-rich RNA sequences, which adopt parallel-stranded G-quadruplexes with a propeller-like fold. The successful crystallization and structure analysis of a bimolecular human telomeric RNA G-quadruplex, folded into the same crystalline environment as an equivalent DNA oligonucleotide sequence, is reported here. The structural basis of the increased stability of RNA telomeric quadruplexes over DNA ones and their preference for parallel topologies is described here. Our findings suggest that the 2'-OH hydroxyl groups in the RNA quadruplex play a significant role in redefining hydration structure in the grooves and the hydrogen bonding networks. The preference for specific nucleotides to populate the C3'-endo sugar pucker domain is accommodated by alterations in the phosphate backbone, which leads to greater stability through enhanced hydrogen bonding networks. Molecular dynamics simulations on the DNA and RNA quadruplexes are consistent with these findings. The computations, based on the native crystal structure, provide an explanation for RNA G-quadruplex ligand binding selectivity for a group of naphthalene diimide ligands as compared to the DNA G-quadruplex.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21416510 H.Bertrand, A.Granzhan, D.Monchaud, N.Saettel, R.Guillot, S.Clifford, A.Guédin, J.L.Mergny, and M.P.Teulade-Fichou (2011).
Recognition of G-quadruplex DNA by triangular star-shaped compounds: with or without side chains?
  Chemistry, 17, 4529-4539.  
21113023 I.Prislan, J.Lah, M.Milanic, and G.Vesnaver (2011).
Kinetically governed polymorphism of d(G₄T₄G₃) quadruplexes in K+ solutions.
  Nucleic Acids Res, 39, 1933-1942.  
21301727 Y.Xu (2011).
Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA.
  Chem Soc Rev, 40, 2719-2740.  
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.