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PDBsum entry 376d
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dna_rna ligands links
DNA PDB id
376d

 

 

 

 

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Contents
DNA/RNA
Ligands
NCO
Waters ×18
PDB id:
376d
Name: DNA
Title: A zipper-like DNA duplex d(gcgaaagct)
Structure: DNA (5'-d( Gp (Cbr)p Gp Ap Ap Ap Gp Cp T)-3'). Chain: a. Engineered: yes
Source: not given
Biol. unit: Dimer (from PDB file)
Resolution:
2.10Å     R-factor:   0.189     R-free:   0.241
Authors: W.B.T.Cruse,W.Shepard,T.Prange,E.Delalfortelle,R.Fourme
Key ref:
W.Shepard et al. (1998). A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution. Structure, 6, 849-861. PubMed id: 9687367 DOI: 10.1016/S0969-2126(98)00087-2
Date:
22-Jan-98     Release date:   26-Oct-99    
 Headers
 References

DNA/RNA chain
  G-CBR-G-A-A-A-G-C-T 9 bases

 

 
DOI no: 10.1016/S0969-2126(98)00087-2 Structure 6:849-861 (1998)
PubMed id: 9687367  
 
 
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
W.Shepard, W.B.Cruse, R.Fourme, E.de la Fortelle, T.Prangé.
 
  ABSTRACT  
 
BACKGROUND: The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these sequences often show exceptional stability which is associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. Nuclear magnetic resonance (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like repeats dimerise into unusual duplexes. The factors stabilising these unusual secondary structure elements in ssDNA, however, are poorly understood. RESULTS: The nonamer d(GCGAAAGCT) was crystallised as a bromocytosine derivative in the presence of cobalt hexammine. The crystal structure, solved by the multiple wavelength anomalous dispersion (MAD) method at the bromine K-edge, reveals an unexpected zipper-like motif in the middle of a standard B-DNA duplex. Four central adenines, flanked by two sheared G.A mismatches, are intercalated and stacked on top of each other without any interstrand Watson-Crick base pairing. The cobalt hexammine cation appears to participate only in crystal cohesion. CONCLUSIONS: The GAAA consensus sequence can dimerise into a stable zipper-like duplex as well as forming a hairpin loop. The arrangement closes the minor groove and exposes the intercalated, unpaired, adenines to the solvent and DNA-binding proteins. Such a motif, which can transform into a hairpin, should be considered as a structural option in modelling DNA and as a potential binding site, where it could have a role in DNA replication, nuclease resistance, ssDNA genome packaging and centromere function.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo view of the zipper-like motif. A closeup view of the central adenine tract cut out from the duplex. The figure illustrates the substantial buckling of the sheared G·A mismatch located at the bottom of the figure. Atoms are shown in standard colours.
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 849-861) copyright 1998.  
  Figure was selected by an automated process.  

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
12770867 K.Réblová, N.Spacková, R.Stefl, K.Csaszar, J.Koca, N.B.Leontis, and J.Sponer (2003).
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.
  Biophys J, 84, 3564-3582.  
12777806 P.Retailleau, and T.Prangé (2003).
Phasing power at the K absorption edge of organic arsenic.
  Acta Crystallogr D Biol Crystallogr, 59, 887-896.
PDB code: 1n4f
12736295 S.H.Chou, K.H.Chin, and A.H.Wang (2003).
Unusual DNA duplex and hairpin motifs.
  Nucleic Acids Res, 31, 2461-2474.  
12012446 J.Kypr, and M.Vorlícková (2002).
Circular dichroism spectroscopy reveals invariant conformation of guanine runs in DNA.
  Biopolymers, 67, 275-277.  
12466550 T.Sunami, J.Kondo, T.Kobuna, I.Hirao, K.Watanabe, K.Miura, and A.Takénaka (2002).
Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs.
  Nucleic Acids Res, 30, 5253-5260.
PDB code: 1ixj
11526315 M.L.Coté, and M.M.Georgiadis (2001).
Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase.
  Acta Crystallogr D Biol Crystallogr, 57, 1238-1250.
PDB code: 1i6j
10957631 M.L.Coté, S.J.Yohannan, and M.M.Georgiadis (2000).
Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs.
  Acta Crystallogr D Biol Crystallogr, 56, 1120-1131.
PDB code: 1d1u
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
10600106 Y.G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, and A.H.Wang (1999).
Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.
  Biochemistry, 38, 16452-16460.
PDB codes: 1d8x 1d9r 1dcr
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.

 

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