title: Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates.
abstract: BACKGROUND
  Pyrrole-imidazole polyamides are synthetic ligands that recognize predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA-binding proteins. As a result of their DNA-binding properties, polyamides could deliver reactive moieties for covalent reaction at specific DNA sequences and thereby inhibit DNA-protein interactions. Site-specific alkylation of DNA could be a useful tool for regulating gene expression. As a minimal first step, we set out to design and synthesize a class of hairpin polyamides equipped with DNA alkylating agents and characterize the specificity and yield of covalent modification.
  
  
  RESULTS
  Bis(dichloroethylamino)benzene derivatives of the well-characterized chlorambucil (CHL) were attached to the gamma turn of an eight-ring hairpin polyamide targeted to the HIV-1 promoter. We found that a hairpin polyamide-CHL conjugate binds and selectively alkylates predetermined sites in the HIV promoter at subnanomolar concentrations. Cleavage sites were determined on both strands of a restriction fragment containing the HIV-1 promoter, revealing good specificity and a high yield of alkylation.
  
  
  CONCLUSIONS
  The ability of polyamide-CHL conjugates to sequence specifically alkylate double-stranded DNA in high yield and at low concentrations sets the stage for testing their use as regulators of gene expression in cell culture and ultimately in complex organisms.
authors.affiliation: Arnold and Mabel Beckman Laboratories of Chemical Synthesis, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: N R
authors.initials: NR
authors.lastname: Wurtz
authors.forename: P B
authors.initials: PB
authors.lastname: Dervan
mesh_terms: D000478:Alkylation; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D019175:DNA Methylation; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016325:HIV Long Terminal Repeat; D006801:Humans; D007093:Imidazoles; D066298:In Vitro Techniques; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009757:Nylons; D011758:Pyrroles
chemical_list: D004279:DNA, Viral; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles