6I4N

Dodecamer DNA containing the synthetic base pair P-Z in complex with a pyrrole-imidazole polyamide


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 5000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with acceptable covalent geometry 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components.

Padroni, G.Withers, J.M.Taladriz-Sender, A.Reichenbach, L.F.Parkinson, J.A.Burley, G.A.

(2019) J Am Chem Soc 141: 9555-9563

  • DOI: 10.1021/jacs.8b12444
  • Primary Citation of Related Structures:  
    6I4N, 6I4O, 6RIO

  • PubMed Abstract: 
  • The structural basis of minor groove recognition of a DNA duplex containing synthetic genetic information by hairpin pyrrole-imidazole polyamides is described. Hairpin polyamides induce a higher melting stabilization of a DNA duplex containing the unnatural P·Z base-pair when an imidazole unit is aligned with a P nucleotide ...

    The structural basis of minor groove recognition of a DNA duplex containing synthetic genetic information by hairpin pyrrole-imidazole polyamides is described. Hairpin polyamides induce a higher melting stabilization of a DNA duplex containing the unnatural P·Z base-pair when an imidazole unit is aligned with a P nucleotide. An NMR structural study showed that the incorporation of two isolated P·Z pairs enlarges the minor groove and slightly narrows the major groove at the site of this synthetic genetic information, relative to a DNA duplex consisting entirely of Watson-Crick base-pairs. Pyrrole-imidazole polyamides bind to a P·Z-containing DNA duplex to form a stable complex, effectively mimicking a G·C pair. A structural hallmark of minor groove recognition of a P·Z pair by a polyamide is the reduced level of allosteric distortion induced by binding of a polyamide to a DNA duplex. Understanding the molecular determinants that influence minor groove recognition of DNA containing synthetic genetic components provides the basis to further develop unnatural base-pairs for synthetic biology applications.


    Organizational Affiliation

    Department of Pure and Applied Chemistry , University of Strathclyde , Thomas Graham Building, 295 Cathedral Street , Glasgow G1 1XL , United Kingdom.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3')A, B12synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    K4Z
    Query on K4Z

    Download Ideal Coordinates CCD File 
    C [auth B]3-[3-[[4-[[4-[[4-[[4-[[(2~{R})-2-azaniumyl-4-[[1-methyl-4-[[1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]butanoyl]amino]-1-methyl-imidazol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]propanoylamino]propyl-dimethyl-azanium
    C58 H74 N22 O10
    ZZDDBKPURCHKIT-LDLOPFEMSA-P
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 5000 
    • Conformers Submitted: 10 
    • Selection Criteria: structures with acceptable covalent geometry 
    • OLDERADO: 6I4N Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2019-06-12
      Type: Initial release
    • Version 1.1: 2019-07-10
      Changes: Data collection, Database references