1C11

INTERCALATED D(TCCCGTTTCCA) DIMER, NMR, 7 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: STRUCTURE CONVERGENCE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Centromeric pyrimidine strands fold into an intercalated motif by forming a double hairpin with a novel T:G:G:T tetrad: solution structure of the d(TCCCGTTTCCA) dimer.

Gallego, J.Chou, S.H.Reid, B.R.

(1997) J.Mol.Biol. 273: 840-856

  • DOI: 10.1006/jmbi.1997.1361

  • PubMed Abstract: 
  • The solution structures of the oligodeoxynucleotides d(CCCGTTTCC) and d(TCCCGTTTCCA) have been determined by two-dimensional NMR spectroscopy. These oligomers are part of a DNA box in human centromeric alpha satellite targeted by the centromere prote ...

    The solution structures of the oligodeoxynucleotides d(CCCGTTTCC) and d(TCCCGTTTCCA) have been determined by two-dimensional NMR spectroscopy. These oligomers are part of a DNA box in human centromeric alpha satellite targeted by the centromere protein B (CENP-B). Both CENP-B and its recognition box in alphoid DNA are conserved in mammals, suggesting an important biological role. At acidic pH, d(CCCGTTTCC), d(TCCCGTTTCCA) and the full d(TCCCGTTTCCAACGAAG) CENP-B box strand all fold and dimerize in solution forming a stable bimolecular structure containing two GTTT hairpin loops that interact through a novel T : G : G : T tetrad. The stem region of the dimer is a four-stranded intercalated motif in which the hairpin monomers are parallel and held together by C : C+ hydrogen-bonding and intercalation. The loops are at the same end of the dimer and lie across the narrow grooves of the tetraplex. They are remarkably structured and stabilized by base-base cross-stacking, sugar-base stacking, and parallel G:G and antiparallel G:T pairing. In the d(TCCCGTTTCCA)2 structure, the intercalated motif is continued at the other end of the dimer with unpaired but stacked adenine and thymine bases. The possible biological implications of these structures are discussed.


    Organizational Affiliation

    Chemistry Department, University of Washington Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*CP*CP*GP*TP*TP*TP*CP*CP*A)-3')A,B11N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: STRUCTURE CONVERGENCE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance