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PDBsum entry 1s47

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dna_rna metals links
DNA PDB id
1s47
Jmol
Contents
DNA/RNA
Metals
_NA ×7
_TL ×6
Waters ×86
PDB id:
1s47
Name: DNA
Title: Crystal structure analysis of the DNA quadruplex d(tggggt)s2
Structure: 5'-d( Tp Gp Gp Gp Gp T)-3'. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence occurs naturally in tetrahymena.
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.224     R-free:   0.311
Authors: C.Caceres,G.Wright,C.Gouyette,G.Parkinson,J.A.Subirana
Key ref: C.Cáceres et al. (2004). A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions. Nucleic Acids Res, 32, 1097-1102. PubMed id: 14960719 DOI: 10.1093/nar/gkh269
Date:
15-Jan-04     Release date:   24-Feb-04    
 Headers
 References

 

 
DOI no: 10.1093/nar/gkh269 Nucleic Acids Res 32:1097-1102 (2004)
PubMed id: 14960719  
 
 
A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions.
C.Cáceres, G.Wright, C.Gouyette, G.Parkinson, J.A.Subirana.
 
  ABSTRACT  
 
We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG1-3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3'ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na+ or Tl+ ions. We show that by using MAD methods, Tl+ can be unambiguously located and distinguished from Na+. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19757406 F.Cesare Marincola, A.Virno, A.Randazzo, F.Mocci, G.Saba, and A.Lai (2009).
Competitive binding exchange between alkali metal ions (K(+), Rb(+), and Cs(+)) and Na(+) ions bound to the dimeric quadruplex [d(G(4)T(4)G(4))](2): a (23)Na and (1)H NMR study.
  Magn Reson Chem, 47, 1036-1042.  
19321501 J.Viladoms, N.Escaja, M.Frieden, I.Gómez-Pinto, E.Pedroso, and C.González (2009).
Self-association of short DNA loops through minor groove C:G:G:C tetrads.
  Nucleic Acids Res, 37, 3264-3275.
PDB codes: 2k8z 2k90 2k97
17505106 C.Creze, B.Rinaldi, R.Haser, P.Bouvet, and P.Gouet (2007).
Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions.
  Acta Crystallogr D Biol Crystallogr, 63, 682-688.
PDB code: 2o4f
17719795 C.L.Mazzitelli, J.Wang, S.I.Smith, and J.S.Brodbelt (2007).
Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulations.
  J Am Soc Mass Spectrom, 18, 1760-1773.  
17308634 R.Ida, I.C.Kwan, and G.Wu (2007).
Direct 23Na NMR observation of mixed cations residing inside a G-quadruplex channel.
  Chem Commun (Camb), (), 795-797.  
16235233 G.Oliviero, J.Amato, N.Borbone, A.Galeone, M.Varra, G.Piccialli, and L.Mayol (2006).
Synthesis and characterization of DNA quadruplexes containing T-tetrads formed by bunch-oligonucleotides.
  Biopolymers, 81, 194-201.  
16945956 M.L.Gill, S.A.Strobel, and J.P.Loria (2006).
Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex.
  Nucleic Acids Res, 34, 4506-4514.
PDB code: 2hbn
16607659 N.Escaja, I.Gómez-Pinto, J.Viladoms, M.Rico, E.Pedroso, and C.González (2006).
Induced-fit recognition of DNA by small circular oligonucleotides.
  Chemistry, 12, 4035-4042.  
15914667 J.L.Huppert, and S.Balasubramanian (2005).
Prevalence of quadruplexes in the human genome.
  Nucleic Acids Res, 33, 2908-2916.  
15642696 J.L.Mergny, A.De Cian, A.Ghelab, B.Saccà, and L.Lacroix (2005).
Kinetics of tetramolecular quadruplexes.
  Nucleic Acids Res, 33, 81-94.  
16282586 J.Zhou, S.Krueger, and S.K.Gregurick (2005).
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution.
  Nucleic Acids Res, 33, 6361-6371.  
16299826 M.Roitzsch, and B.Lippert (2005).
Inverting the charges of natural nucleobase quartets: a planar platinum-purine quartet with pronounced sulfate affinity.
  Angew Chem Int Ed Engl, 45, 147-150.  
16221978 M.Vorlícková, J.Chládková, I.Kejnovská, M.Fialová, and J.Kypr (2005).
Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats.
  Nucleic Acids Res, 33, 5851-5860.  
15985684 P.Sket, M.Crnugelj, and J.Plavec (2005).
Identification of mixed di-cation forms of G-quadruplex in solution.
  Nucleic Acids Res, 33, 3691-3697.  
15556400 M.Egli (2004).
Nucleic acid crystallography: current progress.
  Curr Opin Chem Biol, 8, 580-591.  
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.