PDBsum entry 2rmq

Go to PDB code: 
ligands links
PDB id:
Name: DNA
Title: Solution structure of fully modified 4'-thiodna with the sequence of d(cgcgaattcgcg)
Structure: DNA (5'-d( (C4s)p (S4g)p (C4s)p (S4g)p (S4a) p (S4a)p (T49)p (T49)p (C4s)p (S4g)p (C4s)p (S4g))-3'). Chain: a, b. Engineered: yes. Other_details: 4'-thio-DNA
Source: Synthetic: yes. Other_details: chemically synthesized
NMR struc: 1 models
Authors: A.Matsugami,T.Ohyama,M.Inada,M.Katahira
Key ref: A.Matsugami et al. (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. PubMed id: 18252770
12-Nov-07     Release date:   15-Apr-08    


Nucleic Acids Res 36:1805-1812 (2008)
PubMed id: 18252770  
Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.
A.Matsugami, T.Ohyama, M.Inada, N.Inoue, N.Minakawa, A.Matsuda, M.Katahira.
Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an RNA molecule, but no details of its structure beyond the results of circular dichroism analysis are available. Here, we have determined the structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG) by NMR. Most sugars take on the C3'-endo conformation. The major groove is narrow and deep, while the minor groove is wide and shallow. Thus, fully modified 4'-thioDNA takes on the A-form characteristic of RNA, both locally and globally. The only structure reported for 4'-thioDNA showed that partially modified 4'-thioDNA that contained some 2'-deoxy-4'-thionucleosides took on the B-form in the crystalline form. We have determined the structure of 4'-thioDNA in solution for the first time, and demonstrated unexpected differences between the two structures. The origin of the formation of the A-form is discussed. The remarkable biochemical properties reported for fully modified 4'-thioDNA, including nuclease-resistance, are rationalized in the light of the elucidated structure.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21297374 A.Matsuda (2011).
[Development of highly nuclease-resistant chemically-modified oligonucleotides].
  Yakugaku Zasshi, 131, 285-298.  
19151085 M.Takahashi, N.Minakawa, and A.Matsuda (2009).
Synthesis and characterization of 2'-modified-4'-thioRNA: a comprehensive comparison of nuclease stability.
  Nucleic Acids Res, 37, 1353-1362.  
19666719 T.Mashima, A.Matsugami, F.Nishikawa, S.Nishikawa, and M.Katahira (2009).
Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein.
  Nucleic Acids Res, 37, 6249-6258.
PDB code: 2rqj
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.