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PDBsum entry 230d

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DNA PDB id
230d
Jmol
Contents
DNA/RNA
PDB id:
230d
Name: DNA
Title: Solution structures of unimolecular quadruplexes formed by oligonucleotides containing oxytricha telomere repeats
Structure: Quadruplexes DNA. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized
NMR struc: 7 models
Authors: F.W.Smith,P.Schultze,J.Feigon
Key ref:
F.W.Smith et al. (1995). Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats. Structure, 3, 997. PubMed id: 8590010 DOI: 10.1016/S0969-2126(01)00236-2
Date:
24-Aug-95     Release date:   15-Oct-95    
 Headers
 References

 

 
DOI no: 10.1016/S0969-2126(01)00236-2 Structure 3:997 (1995)
PubMed id: 8590010  
 
 
Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats.
F.W.Smith, P.Schultze, J.Feigon.
 
  ABSTRACT  
 
BACKGROUND: Oligonucleotides containing the guanine-rich telomeric sequence of Oxytricha chromosomes (dT4G4) have previously been shown to form DNA quadruplexes comprising guanine quartets stabilized by cations. Two different structures have been reported for both d(G4T4G4) (Oxy1.5) and d(G4T4G4T4G4T4G4) (Oxy3.5). RESULTS: Here we present the solution structure of a uracil- and inosine-containing derivative of Oxy3.5, d(G4TUTUG4T4G4UUTTG3I) (Oxy3.5-U4128), determined using two-dimensional 1H and 31P NMR techniques. This oligonucleotide forms a unimolecular quadruplex that is very similar to the dimeric Oxy1.5 solution structure, in that it contains a loop spanning the diagonal of an end quartet. The groove widths, strand polarities, and positions of the syn bases along the G4 tracts and within the quartets are all as reported for Oxy1.5. The first and third pyrimidine tracts form parallel loops spanning a wide groove and a narrow groove respectively. CONCLUSIONS: Both Oxy3.5 and Oxy3.5-U(4)128 form unimolecular quadruplexes in solution with a diagonal central T4 loop. These results conflict with those reported for d(G4TUTUG4TTUUG4UUTTG4) in solution, in which the central loop spans a wide groove.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic model structures of (a) Oxy1.5 solution NMR structure [33], (b) Oxy1.5 crystal structure [28], (c) Oxy3.5 [31] and Oxy3.5-U[4]128 NMR structure (this work) and (d) Oxy3.5-U6 NMR model reported by Wang et al. [30]. Shading indicates syn residues. Figure 1. Schematic model structures of (a) Oxy1.5 solution NMR structure [[3]33], (b) Oxy1.5 crystal structure [[4]28], (c) Oxy3.5 [[5]31] and Oxy3.5-U[4]128 NMR structure (this work) and (d) Oxy3.5-U6 NMR model reported by Wang et al. [[6]30]. Shading indicates syn residues.
Figure 6.
Figure 6. Structural features of Oxy3.5-U[4]I28 and Oxy1.5. (a) Stereoview looking into one of the medium-width grooves of the seven Oxy3.5-U[4]I28 structures with the lowest total energies out of a set of 80 calculations. The color scheme is as follows: the first and last G tracts are green; the second and third G tracts are red; the central thymine loop is orange, and the first and third thymine loops are yellow. (b) Stereoview of the eight Oxy1.5 structures with the lowest total energies out of a set of 20 calculations (from [33]). The color scheme is as follows: the two different strands have green guanines and yellow thymines and red guanines and orange thymines, respectively. The view is the same as in (a). (c) Stereoview of the seven lowest-energy structures of Oxy3.5-U[4]I28 showing the interactions of T7 and T23 (blue) in the two edge loops. The narrow groove is towards the left and the medium groove is towards the right side of the view shown. The color scheme is the same as in (a). The white ribbons trace the fold of the backbone. (d) Stereoview of the lowest-energy structure of Oxy3.5-U[4]I28, showing the stacking of T7 and T23 (blue). The color scheme is the same as in (a). Figure 6. Structural features of Oxy3.5-U[4]I28 and Oxy1.5. (a) Stereoview looking into one of the medium-width grooves of the seven Oxy3.5-U[4]I28 structures with the lowest total energies out of a set of 80 calculations. The color scheme is as follows: the first and last G tracts are green; the second and third G tracts are red; the central thymine loop is orange, and the first and third thymine loops are yellow. (b) Stereoview of the eight Oxy1.5 structures with the lowest total energies out of a set of 20 calculations (from [[6]33]). The color scheme is as follows: the two different strands have green guanines and yellow thymines and red guanines and orange thymines, respectively. The view is the same as in (a). (c) Stereoview of the seven lowest-energy structures of Oxy3.5-U[4]I28 showing the interactions of T7 and T23 (blue) in the two edge loops. The narrow groove is towards the left and the medium groove is towards the right side of the view shown. The color scheme is the same as in (a). The white ribbons trace the fold of the backbone. (d) Stereoview of the lowest-energy structure of Oxy3.5-U[4]I28, showing the stacking of T7 and T23 (blue). The color scheme is the same as in (a).
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 997-0) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18274682 J.Talib, C.Green, K.J.Davis, T.Urathamakul, J.L.Beck, J.R.Aldrich-Wright, and S.F.Ralph (2008).
A comparison of the binding of metal complexes to duplex and quadruplex DNA.
  Dalton Trans, (), 1018-1026.  
18663013 N.Borovok, N.Iram, D.Zikich, J.Ghabboun, G.I.Livshits, D.Porath, and A.B.Kotlyar (2008).
Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition.
  Nucleic Acids Res, 36, 5050-5060.  
17486674 K.C.Gornall, S.Samosorn, J.Talib, J.B.Bremner, and J.L.Beck (2007).
Selectivity of an indolyl berberine derivative for tetrameric G-quadruplex DNA.
  Rapid Commun Mass Spectrom, 21, 1759-1766.  
17972263 M.Webba da Silva (2007).
Geometric formalism for DNA quadruplex folding.
  Chemistry, 13, 9738-9745.  
16511573 L.Oganesian, I.K.Moon, T.M.Bryan, and M.B.Jarstfer (2006).
Extension of G-quadruplex DNA by ciliate telomerase.
  EMBO J, 25, 1148-1159.  
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.  
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.  
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.  
12087187 J.Chen, L.R.Zhang, J.M.Min, and L.H.Zhang (2002).
Studies on the synthesis of a G-rich octaoligoisonucleotide (isoT)2(isoG)4(isoT)2 by the phosphotriester approach and its formation of G-quartet structure.
  Nucleic Acids Res, 30, 3005-3014.  
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.  
10740289 H.Han, and L.H.Hurley (2000).
G-quadruplex DNA: a potential target for anti-cancer drug design.
  Trends Pharmacol Sci, 21, 136-142.  
11745109 M.A.Keniry (2000).
Quadruplex structures in nucleic acids.
  Biopolymers, 56, 123-146.  
9145109 A.Kettani, S.Bouaziz, W.Wang, R.A.Jones, and D.J.Patel (1997).
Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads.
  Nat Struct Biol, 4, 382-389.
PDB code: 1aff
9331414 S.Nonin, A.T.Phan, and J.L.Leroy (1997).
Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.
  Structure, 5, 1231-1246.
PDB code: 1bae
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.