PDBsum entry 1k4x

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PDB id:
Name: DNA
Title: Potassium form of oxy-1.5 quadruplex DNA
Structure: DNA (5'-d( Gp Gp Gp Gp Tp Tp Tp Tp Gp Gp Gp G)- 3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: sequence from oxytricha nova
NMR struc: 8 models
Authors: P.Schultze,N.V.Hud,F.W.Smith,J.Feigon
Key ref: P.Schultze et al. (1999). The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G(4)T(4)G(4)). Nucleic Acids Res, 27, 3018-3028. PubMed id: 10454595
08-Jun-99     Release date:   23-Jun-99    


Nucleic Acids Res 27:3018-3028 (1999)
PubMed id: 10454595  
The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G(4)T(4)G(4)).
P.Schultze, N.V.Hud, F.W.Smith, J.Feigon.
The DNA sequence d(G(4)T(4)G(4)) [Oxy-1.5] consists of 1.5 units of the repeat in telomeres of Oxytricha nova and has been shown by NMR and X-ray crystallographic analysis to form a dimeric quadruplex structure with four guanine-quartets. However, the structure reported in the X-ray study has a fundamentally different conformation and folding topology compared to the solution structure. In order to elucidate the possible role of different counterions in this discrepancy and to investigate the conformational effects and dynamics of ion binding to G-quadruplex DNA, we compare results from further experiments using a variety of counterions, namely K(+), Na(+)and NH(4)(+). A detailed structure determination of Oxy-1.5 in solution in the presence of K(+)shows the same folding topology as previously reported with the same molecule in the presence of Na(+). Both conformations are symmetric dimeric quadruplexes with T(4)loops which span the diagonal of the end quartets. The stack of quartets shows only small differences in the presence of K(+)versus Na(+)counterions, but the T(4)loops adopt notably distinguishable conformations. Dynamic NMR analysis of the spectra of Oxy-1.5 in mixed Na(+)/K(+)solution reveals that there are at least three K(+)binding sites. Additional experiments in the presence of NH(4)(+)reveal the same topology and loop conformation as in the K(+)form and allow the direct localization of three central ions in the stack of quartets and further show that there are no specific NH(4)(+)binding sites in the T(4)loop. The location of bound NH(4)(+)with respect to the expected coordination sites for Na(+)binding provides a rationale for the difference observed for the structure of the T(4)loop in the Na(+)form, with respect to that observed for the K(+)and NH(4)(+)forms.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20700418 F.Rosu, V.Gabelica, N.Smargiasso, G.Mazzucchelli, K.Shin-Ya, and E.De Pauw (2010).
Cation involvement in telomestatin binding to g-quadruplex DNA.
  J Nucleic Acids, 2010, 0.  
20820501 K.Dutta, T.Fujimoto, M.Inoue, D.Miyoshi, and N.Sugimoto (2010).
Development of new functional nanostructures consisting of both DNA duplex and quadruplex.
  Chem Commun (Camb), 46, 7772-7774.  
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.  
19234874 F.Wei, and C.M.Ho (2009).
Aptamer-based electrochemical biosensor for Botulinum neurotoxin.
  Anal Bioanal Chem, 393, 1943-1948.  
19490102 P.Barros, F.Boán, M.G.Blanco, and J.Gómez-Márquez (2009).
Effect of monovalent cations and G-quadruplex structures on the outcome of intramolecular homologous recombination.
  FEBS J, 276, 2983-2993.  
18718931 A.N.Lane, J.B.Chaires, R.D.Gray, and J.O.Trent (2008).
Stability and kinetics of G-quadruplex structures.
  Nucleic Acids Res, 36, 5482-5515.  
18663011 S.Paramasivan, and P.H.Bolton (2008).
Mix and measure fluorescence screening for selective quadruplex binders.
  Nucleic Acids Res, 36, e106.  
18399214 X.Liu, X.Li, T.Zhou, Y.Wang, M.T.Ng, W.Xu, and T.Li (2008).
Site specific self-cleavage of certain assemblies of G-quadruplex.
  Chem Commun (Camb), (), 380-382.  
17430965 C.C.Chang, C.W.Chien, Y.H.Lin, C.C.Kang, and T.C.Chang (2007).
Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule.
  Nucleic Acids Res, 35, 2846-2860.  
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
17636049 C.G.Peng, and M.J.Damha (2007).
G-quadruplex induced stabilization by 2'-deoxy-2'-fluoro-D-arabinonucleic acids (2'F-ANA).
  Nucleic Acids Res, 35, 4977-4988.  
17136788 D.M.Tagore, K.I.Sprinz, S.Fletcher, J.Jayawickramarajah, and A.D.Hamilton (2007).
Protein recognition and denaturation by self-assembling fragments on a DNA quadruplex scaffold.
  Angew Chem Int Ed Engl, 46, 223-225.  
17972263 M.Webba da Silva (2007).
Geometric formalism for DNA quadruplex folding.
  Chemistry, 13, 9738-9745.  
17412708 P.Podbevsek, N.V.Hud, and J.Plavec (2007).
NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution.
  Nucleic Acids Res, 35, 2554-2563.  
17572101 X.Guo, S.Liu, and Z.Yu (2007).
Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS.
  J Am Soc Mass Spectrom, 18, 1467-1476.  
16902582 J.O.Bustamante (2006).
Current concepts in nuclear pore electrophysiology.
  Can J Physiol Pharmacol, 84, 347-365.  
16614450 J.T.Nielsen, K.Arar, and M.Petersen (2006).
NMR solution structures of LNA (locked nucleic acid) modified quadruplexes.
  Nucleic Acids Res, 34, 2006-2014.
PDB codes: 2chj 2chk
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
16678852 P.Buczek, and M.P.Horvath (2006).
Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain.
  J Mol Biol, 359, 1217-1234.  
16641317 P.Hazel, G.N.Parkinson, and S.Neidle (2006).
Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.
  Nucleic Acids Res, 34, 2117-2127.  
17012276 S.Burge, G.N.Parkinson, P.Hazel, A.K.Todd, and S.Neidle (2006).
Quadruplex DNA: sequence, topology and structure.
  Nucleic Acids Res, 34, 5402-5415.  
15731338 B.Saccà, L.Lacroix, and J.L.Mergny (2005).
The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides.
  Nucleic Acids Res, 33, 1182-1192.  
15817566 I.N.Rujan, J.C.Meleney, and P.H.Bolton (2005).
Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium.
  Nucleic Acids Res, 33, 2022-2031.  
16267597 N.M.Brown, P.A.Rachwal, T.Brown, and K.R.Fox (2005).
Exceptionally slow kinetics of the intramolecular quadruplex formed by the Oxytricha telomeric repeat.
  Org Biomol Chem, 3, 4153-4157.  
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.  
16045346 S.Rankin, A.P.Reszka, J.Huppert, M.Zloh, G.N.Parkinson, A.K.Todd, S.Ladame, S.Balasubramanian, and S.Neidle (2005).
Putative DNA quadruplex formation within the human c-kit oncogene.
  J Am Chem Soc, 127, 10584-10589.  
16052652 T.van Mourik, and A.J.Dingley (2005).
Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters.
  Chemistry, 11, 6064-6079.  
15240460 E.Fadrná, N.Spacková, R.Stefl, J.Koca, T.E.Cheatham, and J.Sponer (2004).
Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.
  Biophys J, 87, 227-242.  
12831878 S.Neidle, and G.N.Parkinson (2003).
The structure of telomeric DNA.
  Curr Opin Struct Biol, 13, 275-283.  
12682360 V.Dapić, V.Abdomerović, R.Marrington, J.Peberdy, A.Rodger, J.O.Trent, and P.J.Bates (2003).
Biophysical and biological properties of quadruplex oligodeoxyribonucleotides.
  Nucleic Acids Res, 31, 2097-2107.  
12235382 C.Krafft, J.M.Benevides, and G.J.Thomas (2002).
Secondary structure polymorphism in Oxytricha nova telomeric DNA.
  Nucleic Acids Res, 30, 3981-3991.  
12207360 F.Rosu, V.Gabelica, C.Houssier, P.Colson, and E.D.Pauw (2002).
Triplex and quadruplex DNA structures studied by electrospray mass spectrometry.
  Rapid Commun Mass Spectrom, 16, 1729-1736.  
11842096 J.L.Mergny, J.F.Riou, P.Mailliet, M.P.Teulade-Fichou, and E.Gilson (2002).
Natural and pharmacological regulation of telomerase.
  Nucleic Acids Res, 30, 839-865.  
11306347 H.Arthanari, and P.H.Bolton (2001).
Functional and dysfunctional roles of quadruplex DNA in cells.
  Chem Biol, 8, 221-230.  
11891627 J.Sühnel (2001).
Beyond nucleic acid base pairs: from triads to heptads.
  Biopolymers, 61, 32-51.  
11159416 R.Stefl, N.Spacková, I.Berger, J.Koca, and J.Sponer (2001).
Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.
  Biophys J, 80, 455-468.  
11745109 M.A.Keniry (2000).
Quadruplex structures in nucleic acids.
  Biopolymers, 56, 123-146.  
11745111 S.Neidle, and M.A.Read (2000).
G-quadruplexes as therapeutic targets.
  Biopolymers, 56, 195-208.  
10756199 V.M.Marathias, and P.H.Bolton (2000).
Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA.
  Nucleic Acids Res, 28, 1969-1977.
PDB codes: 1c32 1c34 1c35 1c38
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 code is shown on the right.