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PDBsum entry 1aff

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dna_rna links
DNA PDB id
1aff
Jmol
Contents
DNA/RNA
PDB id:
1aff
Name: DNA
Title: DNA quadruplex containing gggg tetrads and (t.A).A triads, nmr, 8 structures
Structure: Quadruplex DNA (5'-d(tp Ap Gp G)-3'). Chain: a, b, c, d. Engineered: yes
Source: Synthetic: yes. Other_details: truncated biological sequence
NMR struc: 8 models
Authors: A.Kettani,S.Bouaziz,W.Wang,R.A.Jones,D.J.Patel
Key ref: A.Kettani et al. (1997). Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads. Nat Struct Biol, 4, 382-389. PubMed id: 9145109
Date:
06-Mar-97     Release date:   20-Aug-97    
 Headers
 References

 

 
Nat Struct Biol 4:382-389 (1997)
PubMed id: 9145109  
 
 
Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads.
A.Kettani, S.Bouaziz, W.Wang, R.A.Jones, D.J.Patel.
 
  ABSTRACT  
 
A combined NMR-molecular dynamics approach has been applied to determine the solution structure of a truncated analogue of the Bombyx mori telomeric d(TTAGG) single repeat sequence in Na+ cation-containing aqueous solution. The two-fold symmetric four-stranded d(TAGG) quadruplex contains two adjacent G(syn).G(syn).G(anti).G(anti) G-tetrads sandwiched between novel (T.A).A triads with individual strands having both a parallel and antiparallel neighbour around the quadruplex. The (T.A).A triad represents the first experimental verification of a base triad alignment which constitutes a key postulate in the recently proposed model of triad-DNA. Further, the (T.A).A triad is generated by positioning an A residue through hydrogen bonding in the minor groove of a Watson-Crick T.A base pair and includes a T-A platform related to an A-A platform recently observed in the structure of the P4-P6 domain of the Tetrahymena self splicing group I ribozyme. The novel architecture of the truncated Bombyx mori quadruplex structure sets the stage for the design and potential identification of additional base tetrads and triads that could participate in pairing alignments of multi-stranded DNA structures during chromosome association and genetic recombination.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20849417 R.Basundra, A.Kumar, S.Amrane, A.Verma, A.T.Phan, and S.Chowdhury (2010).
A novel G-quadruplex motif modulates promoter activity of human thymidine kinase 1.
  FEBS J, 277, 4254-4264.  
19103662 S.Amrane, R.W.Ang, Z.M.Tan, C.Li, J.K.Lim, J.M.Lim, K.W.Lim, and A.T.Phan (2009).
A novel chair-type G-quadruplex formed by a Bombyx mori telomeric sequence.
  Nucleic Acids Res, 37, 931-938.  
17913750 D.J.Patel, A.T.Phan, and V.Kuryavyi (2007).
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
  Nucleic Acids Res, 35, 7429-7455.  
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
16408022 A.T.Phan, V.Kuryavyi, H.Y.Gaw, and D.J.Patel (2005).
Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.
  Nat Chem Biol, 1, 167-173.
PDB codes: 2a5p 2a5r
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.  
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.  
10358100 T.Simonsson, and R.Sjöback (1999).
DNA tetraplex formation studied with fluorescence resonance energy transfer.
  J Biol Chem, 274, 17379-17383.  
9469822 T.Simonsson, P.Pecinka, and M.Kubista (1998).
DNA tetraplex formation in the control region of c-myc.
  Nucleic Acids Res, 26, 1167-1172.  
9204276 A.Lebrun, and R.Lavery (1997).
Unusual DNA conformations.
  Curr Opin Struct Biol, 7, 348-354.  
9384529 C.H.Lin, and D.J.Patel (1997).
Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.
  Chem Biol, 4, 817-832.
PDB code: 1aw4
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.