1B4Y

STRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF AN INTRAMOLECULAR DNA TRIPLE HELIX.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 12 
  • Selection Criteria: LOW ENERGIES 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix.

van Dongen, M.J.Doreleijers, J.F.van der Marel, G.A.van Boom, J.H.Hilbers, C.W.Wijmenga, S.S.

(1999) Nat.Struct.Mol.Biol. 6: 854-859

  • DOI: 10.1038/12313

  • PubMed Abstract: 
  • H-DNA, thought to play a regulatory role in transcription, exists in two isomeric forms, H-y3 and H-y5. We present the first solution structure of a DNA fragment representing the H-y5 fold. The structure shows the H-y5 triple helix, and for the first ...

    H-DNA, thought to play a regulatory role in transcription, exists in two isomeric forms, H-y3 and H-y5. We present the first solution structure of a DNA fragment representing the H-y5 fold. The structure shows the H-y5 triple helix, and for the first time how in an H-DNA isomer the purine strand extension interacts with the triplex loop. It gives direct insight into the mechanism of H-DNA formation, and explains a host of biochemical and biophysical data on the relative stability of the H-DNA isomers. In addition, the observed interaction of the purine strand extension and the triplex loop provides new clues to the design of clamp-type triple helix-forming oligonucleotides.


    Organizational Affiliation

    NSR Centre for Molecular Structure, Design, and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (H-Y5 TRIPLE HELIX)A30N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 12 
  • Selection Criteria: LOW ENERGIES 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance