1XCI

Mispair Aligned N3T-Butyl-N3T Interstrand Crosslink


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 15 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Intrastrand base-stacking buttresses widening of major groove in interstrand cross-linked B-DNA.

da Silva, M.W.Bierbryer, R.G.Wilds, C.J.Noronha, A.M.Colvin, O.M.Miller, P.S.Gamcsik, M.P.

(2005) Bioorg.Med.Chem. 13: 4580-4587

  • DOI: 10.1016/j.bmc.2005.03.032

  • PubMed Abstract: 
  • The introduction of a covalent interstrand cross-link induces changes in the intrinsic structure and deformability of the DNA helix that are recognized by elements of the DNA repair apparatus. In this context, the solution structure of the undecamer ...

    The introduction of a covalent interstrand cross-link induces changes in the intrinsic structure and deformability of the DNA helix that are recognized by elements of the DNA repair apparatus. In this context, the solution structure of the undecamer d(CGAAAT*TTTCG)2, where T* represents a N3T-butyl-N3T interstrand cross-link, was determined using molecular dynamics calculations restrained by NOE and dihedral angle data obtained from NMR spectroscopy. The structure of this cross-linked undecamer shows dramatic widening of the major groove of the B-DNA stem without disruption of Watson-Crick base pairing. This change in tertiary structure illustrates the cumulative effect of cooperativity in intrastrand base stacking of an A-tract of three adenines. Further, it is the direct result from the imposition of geometric angular constraints by the cross-link chain on an ApT* and T*pT steps in the segment AAAT*T. The widening of the major groove is due to the dominant contribution of base stacking to the stability of the ApT compared to the TpT step suggesting that the latter is more deformable within a DNA stem. Compared to earlier structures of ethyl cross-linked oligonucleotides, this unique perturbation induced by the butyl moiety offers a new probe for systematic studies of DNA repair mechanisms.


    Organizational Affiliation

    Department of Medicine, Duke University Medical Center, DUMC Box 2638, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3'A,B11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TTM
Query on TTM
A, B
DNA LINKINGC12 H19 N2 O8 PDT
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 15 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance