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 

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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 Biol 6: 854-859

  • DOI: 10.1038/12313
  • Primary Citation of Related Structures:  
    1B4Y

  • 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 time how in an H-DNA isomer the purine strand extension interacts with the triplex loop ...

    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
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (H-Y5 TRIPLE HELIX)A30N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 12 
  • Selection Criteria: LOW ENERGIES 
  • OLDERADO: 1B4Y Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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