1CYZ

NMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 11 
  • Conformers Submitted: 
  • Selection Criteria: REFINED AVERAGE STRUCTURE 

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This is version 1.2 of the entry. See complete history


Literature

Imidazole-imidazole pair as a minor groove recognition motif for T:G mismatched base pairs

Yang, X.-L.Hubbard IV, R.B.Lee, M.Tao, Z.-F.Sugiyama, H.Wang, A.H.-J.

(1999) Nucleic Acids Res 27: 4183-4190

  • DOI: 10.1093/nar/27.21.4183
  • Primary Citation of Related Structures:  
    1CYZ

  • PubMed Abstract: 
  • The T:G mismatched base pair is associated with many genetic mutations. Understanding its biological consequences may be aided by studying the structural perturbation of DNA caused by a T:G base pair and by specific probing of the mismatch using small molecular ligands ...

    The T:G mismatched base pair is associated with many genetic mutations. Understanding its biological consequences may be aided by studying the structural perturbation of DNA caused by a T:G base pair and by specific probing of the mismatch using small molecular ligands. We have shown previously that AR-1-144, a tri-imidazole (Im-Im-Im) minor groove binder, recognizes the sequence CCGG. NMR structural analysis of the symmetric 2:1 complex of AR-1-144 and GAACCGGTTC revealed that each AR-1-144 binds to four base pairs with the guanine N2 amino group forming a bifurcated hydrogen bond to a side-by-side Im/Im pair. We predicted that the free G-N2 amino group in a T:G wobble base pair can form two individual hydrogen bonds to a side-by-side Im/Im pair. Thus an Im/Im pair may be a good recognition motif for a T:G base pair in DNA. Cooperative and tight binding of an AR-1-144 homodimer to GAACTGGTTC permits a detailed structural analysis by 2D NOE NMR refinement and the refined structure confirms our prediction. Surprisingly, AR-1-144 does not bind to GAATCGGTTC. We further show that both the Im-Im-Im/Im-Py-Im heterodimer and the Im-Im-Im/Im-Im-Im homodimer bind strongly to the CACGGGTC + GACTCGTG duplex. These results together suggest that an Im/Im pair can specifically recognize a single T:G mismatch. Our results may be useful in future design of molecules (e.g. linked dimers) that can recognize a single T:G mismatch with specificity.


    Related Citations: 
    • Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy
      Yang, X.-L., Kaenzig, C., Lee, M., Wang, A.H.-J.
      (1999) Eur J Biochem 263: 646

    Organizational Affiliation

    Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*AP*AP*CP*TP*GP*GP*TP*TP*C)-3'A, B10N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    AR1 (Subject of Investigation/LOI)
    Query on AR1

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth B](2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM
    C20 H28 N11 O4
    PFRKDKQPQSBYQX-UHFFFAOYSA-O
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 11 
    • Conformers Submitted: 
    • Selection Criteria: REFINED AVERAGE STRUCTURE 
    • OLDERADO: 1CYZ Olderado

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1999-09-14
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance