1N96

DIMERIC SOLUTION STRUCTURE OF THE CYCLIC OCTAMER CD(CGCTCATT)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.

Escaja, N.Gelpi, J.L.Orozco, M.Rico, M.Pedroso, E.Gonzalez, C.

(2003) J.Am.Chem.Soc. 125: 5654-5662

  • DOI: 10.1021/ja0344157

  • PubMed Abstract: 
  • The solution structure of a cyclic oligonucleotide d<pCGCTCATT> has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. Under the appropriate experimental conditions, this molecule self-associates, forming a symmetr ...

    The solution structure of a cyclic oligonucleotide d has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. Under the appropriate experimental conditions, this molecule self-associates, forming a symmetric dimer stabilized by four intermolecular Watson-Crick base pairs. The resulting four-stranded structure consists of two G:C:A:T tetrads, formed by facing the minor groove side of the Watson-Crick base-pairs. Most probably, the association of the base-pairs is stabilized by coordinating a Na(+) cation. This is the first time that this novel G:C:A:T tetrad has been found in an oligonucleotide structure. This observation increases considerably the number of sequences that may adopt a four-stranded architecture. Overall, the three-dimensional structure is similar to those observed previously in other quadruplexes formed by minor groove alignment of Watson-Crick base pairs. This resemblance strongly suggests that we may be observing a general motif for DNA-DNA recognition.


    Related Citations: 
    • NMR STRUCTURE OF TWO CYCLIC OLIGONUCLEOTIDES. A MONOMER DIMER EQUILIBRIUM BETWEEN DUMBELLL AND QUADRUPLEX STRUCTURES
      Gonzalez, C.,Escaja, N.,Rico, M.,Pedroso, E.
      (1998) J.Am.Chem.Soc. 120: 2176
    • Dimeric solution structure of two cyclic octamers: Four stranded DNA structures stabilized by A:T:A:T and C:G:C:G tetrads
      Escaja, N.,Pedroso, E.,Rico, M.,Gonzalez, C.
      (2000) J.Am.Chem.Soc. 122: 12732


    Organizational Affiliation

    Departament de Química Orgànica, Universitat de Barcelona, C/, Martí i Franquès 1-11, 08028 Barcelona, Spain.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
CYCLIC OLIGONUCLEOTIDE D(CGCTCATT)A,B8N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance