201D

SOLUTION STRUCTURE OF THE OXYTRICHA TELOMERIC REPEAT D[G4(T4G4)3] G-TETRAPLEX

  • Classification: DNA

  • Deposited: 1995-03-16 Released: 1995-07-31 
  • Deposition Author(s): Wang, Y., Patel, D.J.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the Oxytricha telomeric repeat d[G4(T4G4)3] G-tetraplex.

Wang, Y.Patel, D.J.

(1995) J.Mol.Biol. 251: 76-94

  • DOI: 10.1006/jmbi.1995.0417

  • PubMed Abstract: 
  • The solution structure of Oxytricha telomere sequence d[G4(T4G4)3] in 0.1 M Na+ containing solution has been determined using a combined NMR-molecular dynamics approach including relaxation matrix refinement. This four G4 repeat sequence folds intram ...

    The solution structure of Oxytricha telomere sequence d[G4(T4G4)3] in 0.1 M Na+ containing solution has been determined using a combined NMR-molecular dynamics approach including relaxation matrix refinement. This four G4 repeat sequence folds intramolecularly into a right-handed G-tetraplex containing four stacked G-tetrads which are connected by two lateral T4 loops and a central diagonal T4 loop. The guanine glycosidic bonds adopt a syn-anti alternation along the full length of the d[G4(T4G4)3] sequence while the orientation around adjacent G-tetrads switches between syn.syn.anti.anti and anti.anti.syn.syn alignments. Four distinct grooves are formed by the parallel (two of medium width) and anti-parallel (one wide and one narrow width) alignment of adjacent G-G-G-G segments in the G-tetraplex. The T4 residues in the diagonal loop are well-defined while the T4 residues in both lateral loops are under-defined and sample multiple conformations. The solution structure of the Na(+)-stabilized Oxytricha d[G4(T4G4)3] G-tetraplex and an earlier solution structure reported from our laboratory on the Na(+)-stabilized human d[AG3(T2AG3)3] G-tetraplex exhibit a common folding topology defined by the same syn/anti distribution of guanine residues along individual strands and around individual G-tetrads, as well as a common central diagonal loop which defines the strand directionalities. The well-resolved proton NMR spectra associated with the d[G4(T4G4)3] G-tetraplex opens the opportunity for studies ranging from cation-dependent characterization of G-tetraplex conformation and hydration to ligand and protein recognition of the distinct grooves associated with this folding topology.


    Organizational Affiliation

    Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
INTRAMOLECULAR G-TETRAPLEX DNAA28N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-03-16 
  • Released Date: 1995-07-31 
  • Deposition Author(s): Wang, Y., Patel, D.J.

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance