2MH6

Solution structure of DNA duplex containing N3T-ethylene-N1I interstrand cross-link


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 25 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the least restraint violations and the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

NMR Structure of an Ethylene Interstrand Cross-Linked DNA which Mimics the Lesion Formed by 1,3-Bis(2-chloroethyl)-1-nitrosourea.

O'Flaherty, D.K.Denisov, A.Y.Noronha, A.M.Wilds, C.J.

(2014) Chemmedchem 9: 2099-2103

  • DOI: 10.1002/cmdc.201402121

  • PubMed Abstract: 
  • The bisalkylating agent 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU), used in cancer chemotherapy to hinder cellular proliferation, forms lethal interstrand cross-links (ICLs) in DNA. BCNU generates an ethylene linkage connecting the two DNA strands a ...

    The bisalkylating agent 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU), used in cancer chemotherapy to hinder cellular proliferation, forms lethal interstrand cross-links (ICLs) in DNA. BCNU generates an ethylene linkage connecting the two DNA strands at the N1 atom of 2'-deoxyguanosine and N3 atom of 2'-deoxycytidine, which is a synthetically challenging probe to prepare. To this end, an ICL duplex linking the N1 atom of 2'-deoxyinosine to the N3 atom of thymidine via an ethylene linker was devised as a mimic. We have solved the structure of this ICL duplex by a combination of molecular dynamics and high-field NMR experiments. The ethylene linker is well-accommodated in the duplex with minimal global and local perturbations relative to the unmodified duplex. These results may account for the substantial stabilization of the ICL duplex observed by UV thermal denaturation experiments and provides structural insights of a probe that may be useful for DNA repair studies.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, Concordia University, Montréal, QC H4B 1R6 (Canada).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3'A8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3'B8N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
EDI
Query on EDI
B
DNA LINKINGC12 H16 I N4 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 25 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the least restraint violations and the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references