PDBsum entry 1c34

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PDB id:
Name: DNA
Title: Solution structure of a quadruplex forming DNA and its intermidiate
Structure: DNA (5'- d( Gp Gp Tp Tp Gp Gp Tp Gp Tp Gp Gp Tp Tp Gp G)-3'). Chain: a. Engineered: yes. Other_details: thrombin binding aptamer intermidiate
Source: Synthetic: yes
NMR struc: 11 models
Authors: P.H.Bolton,V.M.Marathias,K.Wang
Key ref: 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. PubMed id: 10756199 DOI: 10.1093/nar/28.9.1969
24-Jul-99     Release date:   18-Aug-99    


DOI no: 10.1093/nar/28.9.1969 Nucleic Acids Res 28:1969-1977 (2000)
PubMed id: 10756199  
Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA.
V.M.Marathias, P.H.Bolton.
Potassium can stabilize the formation of chair- or edge-type quadruplex DNA structures and appears to be the only naturally occurring cation that can do so. As quadruplex DNAs may be important in the structure of telomere, centromere, triplet repeat and other DNAs, information about the details of the potassium-quadruplex DNA interactions are of interest. The structures of the 1:1 and the fully saturated, 2:1, potassium-DNA complexes of d(GGTTGGTGTGGTTGG) have been determined using the combination of experimental NMR results and restrained molecular dynamics simulations. The refined structures have been used to model the interactions at the potassium binding sites. Comparison of the 1:1 and 2:1 potassium:DNA structures indicates how potassium binding can determine the folding pattern of the DNA. In each binding site potassium interacts with the carbonyl oxygens of both the loop thymine residues and the guanine residues of the adjacent quartet.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20434362 E.S.Hong, H.J.Yoon, B.Kim, Y.H.Yim, H.Y.So, and S.K.Shin (2010).
Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA.
  J Am Soc Mass Spectrom, 21, 1245-1255.  
20174694 L.Q.Gu, and J.W.Shim (2010).
Single molecule sensing by nanopores and nanopore devices.
  Analyst, 135, 441-451.  
19961180 R.D.Gray, L.Petraccone, J.O.Trent, and J.B.Chaires (2010).
Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence.
  Biochemistry, 49, 179-194.  
19957315 Y.Hong, H.Xiong, J.W.Lam, M.Häussler, J.Liu, Y.Yu, Y.Zhong, H.H.Sung, I.D.Williams, K.S.Wong, and B.Z.Tang (2010).
Fluorescent bioprobes: structural matching in the docking processes of aggregation-induced emission fluorogens on DNA surfaces.
  Chemistry, 16, 1232-1245.  
19112078 J.W.Shim, Q.Tan, and L.Q.Gu (2009).
Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity.
  Nucleic Acids Res, 37, 972-982.  
19865704 M.Trajkovski, P.Sket, and J.Plavec (2009).
Cation localization and movement within DNA thrombin binding aptamer in solution.
  Org Biomol Chem, 7, 4677-4684.  
17853398 D.M.Gray, J.D.Wen, C.W.Gray, R.Repges, C.Repges, G.Raabe, and J.Fleischhauer (2008).
Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities.
  Chirality, 20, 431-440.  
18563930 J.W.Shim, and L.Q.Gu (2008).
Encapsulating a single G-quadruplex aptamer in a protein nanocavity.
  J Phys Chem B, 112, 8354-8360.  
18663011 S.Paramasivan, and P.H.Bolton (2008).
Mix and measure fluorescence screening for selective quadruplex binders.
  Nucleic Acids Res, 36, e106.  
16896485 A.E.Radi, and C.K.O'Sullivan (2006).
Aptamer conformational switch as sensitive electrochemical biosensor for potassium ion recognition.
  Chem Commun (Camb), (), 3432-3434.  
16433524 J.Dai, T.S.Dexheimer, D.Chen, M.Carver, A.Ambrus, R.A.Jones, and D.Yang (2006).
An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution.
  J Am Chem Soc, 128, 1096-1098.  
16077025 B.I.Kankia, G.Barany, and K.Musier-Forsyth (2005).
Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein.
  Nucleic Acids Res, 33, 4395-4403.  
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.  
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.  
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.  
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.  
11772310 P.J.Perry, J.R.Arnold, and T.C.Jenkins (2001).
Telomerase inhibitors for the treatment of cancer: the current perspective.
  Expert Opin Investig Drugs, 10, 2141-2156.  
11739403 R.Strick, P.L.Strissel, K.Gavrilov, and R.Levi-Setti (2001).
Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes.
  J Cell Biol, 155, 899-910.  
11745109 M.A.Keniry (2000).
Quadruplex structures in nucleic acids.
  Biopolymers, 56, 123-146.  
11745112 R.H.Shafer, and I.Smirnov (2000).
Biological aspects of DNA/RNA quadruplexes.
  Biopolymers, 56, 209-227.  
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.