PDBsum entry 1fqp

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PDB id:
Name: DNA
Title: Intramolecular quadruplex DNA with three gggg repeats, nmr, ph 6.7, 0.1 m na+ and 4 mm (strand concentration), 5 structures
Structure: DNA (5'-d(gp Gp Gp Tp Tp Tp Tp Gp Gp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
NMR struc: 5 models
Authors: M.A.Keniry,G.D.Strahan,E.A.Owen,R.H.Shafer
Key ref: M.A.Keniry et al. (1995). Solution structure of the Na+ form of the dimeric guanine quadruplex [d(G3T4G3)]2. Eur J Biochem, 233, 631-643. PubMed id: 7588810
01-Aug-96     Release date:   12-Feb-97    


Eur J Biochem 233:631-643 (1995)
PubMed id: 7588810  
Solution structure of the Na+ form of the dimeric guanine quadruplex [d(G3T4G3)]2.
M.A.Keniry, G.D.Strahan, E.A.Owen, R.H.Shafer.
The solution structure of the DNA quadruplex formed by the association of two strands of the DNA oligonucleotide, d(G3T4G3), in NaCl solution has been determined by 1H two-dimensional NMR techniques, full relaxation matrix calculations and restrained molecular dynamics. The refined structure incorporates the sequences 5'-G1sG2AG3AT4AT5AT6AT7AG8sG9AG10A-3' and 5'-G11sG12AG13AT14AT15AT16AT17AG18sG19sG20A-3' (where S and A denote syn and anti, respectively) in a three-quartet, diagonal-looped structure that we [Strahan, G. D., Shafer, R. H. & Keniry, M. A. (1994) Nucleic Acids Res. 22, 5447-5455] and others [Smith, F. W., Lau, F. W. & Feigon, J. (1994) Proc. Natl. Acad. Sci. USA 91, 10546-10550] have described. The loop structure is compact and incorporates many of the features found in duplex hairpin loops including base stacking, intraloop hydrogen bonding and extensive van der Waals' interactions. The first and third loop thymines stack over the outermost G-quartet and are also associated by hydrogen bonding. The second and the fourth loop thymines fold inwards in order to enhance van der Waals' interactions. The unexpected sequential syn-syn deoxyguanosines in the quadruplex stem appear to be a direct consequence of the way DNA oligonucleotides fold and the subsequent search for the most stable loop structure. The implications of loop sequence and length on the structure of quadruplexes are discussed.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20440429 S.Masiero, R.Trotta, S.Pieraccini, S.De Tito, R.Perone, A.Randazzo, and G.P.Spada (2010).
A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures.
  Org Biomol Chem, 8, 2683-2692.  
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.  
17013819 I.V.Smirnov, and R.H.Shafer (2007).
Electrostatics dominate quadruplex stability.
  Biopolymers, 85, 91.  
17576685 P.A.Rachwal, I.S.Findlow, J.M.Werner, T.Brown, and K.R.Fox (2007).
Intramolecular DNA quadruplexes with different arrangements of short and long loops.
  Nucleic Acids Res, 35, 4214-4222.  
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.  
15849241 E.E.Merkina, and K.R.Fox (2005).
Kinetic stability of intermolecular DNA quadruplexes.
  Biophys J, 89, 365-373.  
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.  
15141030 A.Risitano, and K.R.Fox (2004).
Influence of loop size on the stability of intramolecular DNA quadruplexes.
  Nucleic Acids Res, 32, 2598-2606.  
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.  
11861867 J.Suzuki, N.Miyano-Kurosaki, T.Kuwasaki, H.Takeuchi, G.Kawai, and H.Takaku (2002).
Inhibition of human immunodeficiency virus type 1 activity in vitro by a new self-stabilized oligonucleotide with guanosine-thymidine quadruplex motifs.
  J Virol, 76, 3015-3022.  
11891627 J.Sühnel (2001).
Beyond nucleic acid base pairs: from triads to heptads.
  Biopolymers, 61, 32-51.  
11405224 T.Simonsson (2001).
G-quadruplex DNA structures--variations on a theme.
  Biol Chem, 382, 621-628.  
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.  
10454595 P.Schultze, N.V.Hud, F.W.Smith, and J.Feigon (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.
PDB code: 1k4x
10358100 T.Simonsson, and R.Sjöback (1999).
DNA tetraplex formation studied with fluorescence resonance energy transfer.
  J Biol Chem, 274, 17379-17383.  
9675197 G.D.Strahan, M.A.Keniry, and R.H.Shafer (1998).
NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald molecular dynamics simulations.
  Biophys J, 75, 968-981.  
9336473 M.A.Keniry, E.A.Owen, and R.H.Shafer (1997).
The contribution of thymine-thymine interactions to the stability of folded dimeric quadruplexes.
  Nucleic Acids Res, 25, 4389-4392.  
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