PDBsum entry 233d

Go to PDB code: 
dna_rna links
Waters ×67
PDB id:
Name: DNA
Title: The crystal structure analysis of d(cgcgaasscgcg)2: a synthetic DNA dodecamer duplex containing four 4'-thio-2'- deoxythymidine nucleotides
Structure: DNA (5'-d( Cp Gp Cp Gp Ap Ap )-D( (T49)p (T49) p )-D( Cp Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
2.40Å     R-factor:   0.201    
Authors: T.J.Boggon,E.L.Hancox,K.E.Mcauley-Hecht,B.A.Connolly, W.N.Hunter,T.Brown,R.T.Walker,G.A.Leonard
Key ref: T.J.Boggon et al. (1996). The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides. Nucleic Acids Res, 24, 951-961. PubMed id: 8600465
16-Oct-95     Release date:   21-Jun-96    


Nucleic Acids Res 24:951-961 (1996)
PubMed id: 8600465  
The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides.
T.J.Boggon, E.L.Hancox, K.E.McAuley-Hecht, B.A.Connolly, W.N.Hunter, T.Brown, R.T.Walker, G.A.Leonard.
The crystal structure refinement of the synthetic dodecamer d(CGCGAASSCGCG), where S = 4'-thio-2'-deoxythymidine, has converged at R=0.201 for 2605 reflections with F > 2sigma(F) in the resolution range 8.0-2.4 A for a model consisting of the dodecamer duplex and 66 water molecules. A comparison of its structure with that of the native dodecamer d(CGCGAATTCGCG) has revealed that the major differences between the two structures is a change in the conformation of the sugar-phosphate backbone in the regions at and adjacent to the positions of the modified nucleosides. Examination of the fine structural parameters for each of the structures reveals that the thiosugars adopt a C3'-exo conformation in d(CGCGAASSCGCG), rather than the approximate C1'-exo conformation found for the analogous sugars in the structure of d(CGCGAATTCGCG). The observed differences in structure between the two duplexes may help to explain the enhanced resistance to nuclease digestion of synthetic oligonucleotides containing 4'-thio-2'-deoxynucleotides.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20087997 M.Egli, and P.S.Pallan (2010).
Crystallographic studies of chemically modified nucleic acids: a backward glance.
  Chem Biodivers, 7, 60-89.  
18252770 A.Matsugami, T.Ohyama, M.Inada, N.Inoue, N.Minakawa, A.Matsuda, and M.Katahira (2008).
Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.
  Nucleic Acids Res, 36, 1805-1812.
PDB code: 2rmq
18160414 K.Robeyns, P.Herdewijn, and L.Van Meervelt (2008).
Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG).
  Nucleic Acids Res, 36, 1407-1414.
PDB code: 2p8d
16855286 N.Inoue, N.Minakawa, and A.Matsuda (2006).
Synthesis and properties of 4'-ThioDNA: unexpected RNA-like behavior of 4'-ThioDNA.
  Nucleic Acids Res, 34, 3476-3483.  
15592840 F.Richardson, C.Black, K.Richardson, A.Franks, E.Wells, S.Karimi, G.Sennello, K.Hart, D.Meyer, D.Emerson, E.Brown, J.LeRay, C.Nilsson, B.Tomkinson, and R.Bendele (2005).
Incorporation of OSI-7836 into DNA of Calu-6 and H460 xenograft tumors.
  Cancer Chemother Pharmacol, 55, 213-221.  
16027443 P.Haeberli, I.Berger, P.S.Pallan, and M.Egli (2005).
Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine.
  Nucleic Acids Res, 33, 3965-3975.
PDB code: 2a0p
9204276 A.Lebrun, and R.Lavery (1997).
Unusual DNA conformations.
  Curr Opin Struct Biol, 7, 348-354.  
9097732 H.M.Berman (1997).
Crystal studies of B-DNA: the answers and the questions.
  Biopolymers, 44, 23-44.  
9354758 R.S.Lloyd, and X.Cheng (1997).
Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
  Biopolymers, 44, 139-151.  
9207024 S.Kumar, J.R.Horton, G.D.Jones, R.T.Walker, R.J.Roberts, and X.Cheng (1997).
DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
  Nucleic Acids Res, 25, 2773-2783.
PDB code: 6mht
8932360 G.D.Jones, E.A.Lesnik, S.R.Owens, L.M.Risen, and R.T.Walker (1996).
Investigation of some properties of oligodeoxynucleotides containing 4'-thio-2'-deoxynucleotides: duplex hybridization and nuclease sensitivity.
  Nucleic Acids Res, 24, 4117-4122.  
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.