1FV7

A TWO B-Z JUNCTION CONTAINING DNA RESOLVES INTO AN ALL RIGHT HANDED DOUBLE HELIX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 11 
  • Selection Criteria: lower energy structures, restraints violations, and the average structure 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A two B-Z junction containing DNA resolves into an all right-handed double-helix.

Mauffret, O.El Amri, C.Santamaria, F.Tevanian, G.Rayner, B.Fermandjian, S.

(2000) Nucleic Acids Res. 28: 4403-4409


  • PubMed Abstract: 
  • Natural and artificial oligonucleotides are capable of assuming many different conformations and functions. Here we present results of an NMR restrained molecular modelling study on the conformational preferences of the modified decanucleotide d((m)C ...

    Natural and artificial oligonucleotides are capable of assuming many different conformations and functions. Here we present results of an NMR restrained molecular modelling study on the conformational preferences of the modified decanucleotide d((m)C1G2(m)C3G4C5(L)G6(L)(m)C7G8(m)C9G10) .d((m)C11G12(m)C13G14C15(L)G (L)16(m)C17-G18(m)C19G20 ) which contains L deoxynucleotides in its centre. This chimeric DNA was expected to form a right-left-right-handed B-type double-helix (BB*B) at low salt concentration. Actually, it matured into a fully right-handed double helix with its central C(L)pG(L) core forming a right-handed Z-DNA helix embedded in a B-DNA matrix (BZ*B). The interplay between base-base and base-sugar stackings within the core and its immediately adjacent residues was found to be critical in ensuring the stabilisation of the right-handed helix. The structure could serve as a model for the design of antisense oligonucleotides resistant to nucleases and capable of hybridising to natural DNAs and RNAs.


    Organizational Affiliation

    D├ępartement de Biologie et Pharmacologie Structurales, UMR 8532 CNRS, PR2, Institut Gustave-Roussy, 39 rue Camille-Desmoulins, 94805 Villejuif Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*(5CM)P*GP*(5CM)P*GP*(0DC)P*(0DG)P*(5CM)P*GP*(5CM)P*G)-3'A,B10N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
A, B
DNA LINKINGC10 H16 N3 O7 PDC
0DG
Query on 0DG
A, B
L-DNA LINKINGC10 H14 N5 O7 P

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0DC
Query on 0DC
A, B
L-DNA LINKINGC9 H14 N3 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 11 
  • Selection Criteria: lower energy structures, restraints violations, and the average structure 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-11
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-01
    Type: Structure summary