PDBsum entry 103d

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PDB id:
Name: DNA
Title: The unusual structure of the human centromere (gga)2 motif: unpaired guanosine residues stacked between sheared g(dot) a pairs
Structure: DNA (5'-d( Gp Tp Gp Gp Ap Ap Tp Gp Gp Ap Ap C)- 3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized
NMR struc: 1 models
Authors: S.-H.Chou,L.Zhu,B.R.Reid
Key ref: S.H.Chou et al. (1994). The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs. J Mol Biol, 244, 259-268. PubMed id: 7966337
16-Dec-94     Release date:   31-Mar-95    


J Mol Biol 244:259-268 (1994)
PubMed id: 7966337  
The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs.
S.H.Chou, L.Zhu, B.R.Reid.
The centromere of human chromosomes contains multiple repeats of the DNA sequence d(TGGAA)n. This sequence has the interesting property of pairing with itself to form stable duplexes. We have determined the solution structure of the unusual DNA duplex 5'-TGGAATGGAA:TGGAATGGAA-3' at atomic resolution. The duplex contains unpaired staggered guanosine residues, which co-stack by intercalation between sheared G.A and A.G base-pairs to form an interesting new structural motif, the GA-bracketed G-stack. The TGGAA repeat unit contains six "steps", four of which are not Watson-Crick base-pairs.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20859962 D.A.Malyshev, D.A.Pfaff, S.I.Ippoliti, G.T.Hwang, T.J.Dwyer, and F.E.Romesberg (2010).
Solution structure, mechanism of replication, and optimization of an unnatural base pair.
  Chemistry, 16, 12650-12659.
PDB code: 2lho
19380271 M.Ting, R.Raich, and A.O.Hero Iii (2009).
Sparse image reconstruction for molecular imaging.
  IEEE Trans Image Process, 18, 1215-1227.  
18653524 C.Mura, and J.A.McCammon (2008).
Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation.
  Nucleic Acids Res, 36, 4941-4955.  
15324813 P.J.Paukstelis, J.Nowakowski, J.J.Birktoft, and N.C.Seeman (2004).
Crystal structure of a continuous three-dimensional DNA lattice.
  Chem Biol, 11, 1119-1126.
PDB code: 1p1y
12622812 C.H.Huang, C.Y.Chen, H.H.Tsai, C.Chen, Y.S.Lin, and C.W.Chen (2003).
Linear plasmid SLP2 of Streptomyces lividans is a composite replicon.
  Mol Microbiol, 47, 1563-1576.  
12736295 S.H.Chou, K.H.Chin, and A.H.Wang (2003).
Unusual DNA duplex and hairpin motifs.
  Nucleic Acids Res, 31, 2461-2474.  
12011426 S.H.Chou, K.H.Chin, and F.M.Chen (2002).
Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.
  Proc Natl Acad Sci U S A, 99, 6625-6630.
PDB code: 1l1v
10805729 A.Cortés, and F.Azorín (2000).
DDP1, a heterochromatin-associated multi-KH-domain protein of Drosophila melanogaster, interacts specifically with centromeric satellite DNA sequences.
  Mol Cell Biol, 20, 3860-3869.  
10393197 A.Cortés, D.Huertas, L.Fanti, S.Pimpinelli, F.X.Marsellach, B.Piña, and F.Azorín (1999).
DDP1, a single-stranded nucleic acid-binding protein of Drosophila, associates with pericentric heterochromatin and is functionally homologous to the yeast Scp160p, which is involved in the control of cell ploidy.
  EMBO J, 18, 3820-3833.  
10425682 A.Kettani, S.Bouaziz, E.Skripkin, A.Majumdar, W.Wang, R.A.Jones, and D.J.Patel (1999).
Interlocked mismatch-aligned arrowhead DNA motifs.
  Structure, 7, 803-815.
PDB code: 1b3p
9663678 C.H.Huang, Y.S.Lin, Y.L.Yang, S.W.Huang, and C.W.Chen (1998).
The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures.
  Mol Microbiol, 28, 905-916.  
9687367 W.Shepard, W.B.Cruse, R.Fourme, la Fortelle, and T.Prangé (1998).
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
  Structure, 6, 849-861.
PDB code: 376d
9057846 S.J.Berners-Price, A.Corazza, Z.Guo, K.J.Barnham, P.J.Sadler, Y.Ohyama, M.Leng, and D.Locker (1997).
Structural transitions of a GG-platinated DNA duplex induced by pH, temperature and box A of high-mobility-group protein 1.
  Eur J Biochem, 243, 782-791.  
8901550 L.Zhu, S.H.Chou, and B.R.Reid (1996).
A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins.
  Proc Natl Acad Sci U S A, 93, 12159-12164.
PDB code: 1xue
7583654 L.Zhu, S.H.Chou, J.Xu, and B.R.Reid (1995).
Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA.
  Nat Struct Biol, 2, 1012-1017.
PDB code: 1zhu
7583631 M.Kochoyan, and J.L.Leroy (1995).
Hydration and solution structure of nucleic acids.
  Curr Opin Struct Biol, 5, 329-333.  
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