1TNE

NMR STUDY OF Z-DNA AT PHYSIOLOGICAL SALT CONDITIONS, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

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This is version 1.4 of the entry. See complete history


Literature

Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions.

Sugiyama, H.Kawai, K.Matsunaga, A.Fujimoto, K.Saito, I.Robinson, H.Wang, A.H.

(1996) Nucleic Acids Res 24: 1272-1278

  • DOI: https://doi.org/10.1093/nar/24.7.1272
  • Primary Citation of Related Structures:  
    1TNE

  • PubMed Abstract: 

    Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction Of M8G into DNA sequences markedly stabilizes the Z conformation under low salt conditions. The hexamer d(CGC[M8G]CG)2 exhibits a CD spectrum characteristic of the Z conformation under physiological salt conditions. The NOE-restrained refinement unequivocally demonstrated that d(CGC[m8G]CG)2 adopts a Z structure with all guanines in the syn conformation. The refined NMR structure is very similar to the Z form crystal structure of d(CGCGCG)2, with a root mean square deviation of 0.6 between the two structures. The contribution of m8G to the stabilization of Z-DNA has been estimated from the mid-point NaCl concentrations for the B-Z transition of various m8G-containing oligomers. The presence of m8G in d(CGC[m8G]CG)2 stabilizes the Z conformation by at least deltaG = -0.8 kcal/mol relative to the unmodified hexamer. The Z conformation was further stabilized by increasing the number of m8Gs incorporated and destabilized by incorporating syn-A or syn-T, found respectively in the (A,T)-containing alternating and non-alternating pyrimidine-purine sequences. The results suggest that the chemically less reactive m8G base is a useful agent for studying molecular interactions of Z-DNA or other DNA structures that incorporate syn-G conformation.


  • Organizational Affiliation

    Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Japan.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*(8MG)P*CP*G)-3')
A, B
6N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-05-22
    Changes: Data collection