title: Targeting the ICB2 site of the topoisomerase IIalpha promoter with a formamido-pyrrole-imidazole-pyrrole H-pin polyamide.
abstract: The synthesis, DNA binding characteristics and biological activity of an N-formamido pyrrole- and imidazole-containing H-pin polyamide (f-PIP H-pin, 2) designed to selectively target the ICB2 site on the topoIIalpha promoter, is reported herein. Thermal denaturation, circular dichroism, isothermal titration calorimetry, surface plasmon resonance and DNase I footprinting studies demonstrated that 2 maintained the selectivity of the unlinked parent monomer f-PIP (1) and with a slight enhancement in binding affinity (K(eq)=5 x 10(5)M(-1)) to the cognate site (5'-TACGAT-3'). H-pin 2 also exhibited comparable ability to inhibit NF-Y binding to 1, as demonstrated by gel shift studies. However, in stark contrast to monomer 1, the H-pin did not affect the up-regulation of topoisomerase IIalpha (topoIIalpha) in cells (Western blot), suggesting that the H-pin does not enter the nucleus. This study is the first to the authors' knowledge that reports such a markedly different cellular response between two compounds of almost identical binding characteristics.
authors.affiliation: Division of Natural and Applied Sciences, Department of Chemistry, Hope College, Holland, MI 49423, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Franks
authors.forename: Christopher
authors.initials: C
authors.lastname: Tronrud
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Kiakos
authors.forename: Jerome
authors.initials: J
authors.lastname: Kluza
authors.forename: Manoj
authors.initials: M
authors.lastname: Munde
authors.forename: Toni
authors.initials: T
authors.lastname: Brown
authors.forename: Hilary
authors.initials: H
authors.lastname: Mackay
authors.forename: W David
authors.initials: WD
authors.lastname: Wilson
authors.forename: Daniel
authors.initials: D
authors.lastname: Hochhauser
authors.forename: John A
authors.initials: JA
authors.lastname: Hartley
authors.forename: Moses
authors.initials: M
authors.lastname: Lee
mesh_terms: D000818:Animals; D000951:Antigens, Neoplasm / Q000235:genetics*; D001665:Binding Sites; D002151:Calorimetry; D002460:Cell Line; D002942:Circular Dichroism; D004250:DNA Topoisomerases, Type II / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D005559:Formamides / Q000737:chemistry*; D007093:Imidazoles / Q000737:chemistry*; D051379:Mice; D009757:Nylons / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D011401:Promoter Regions, Genetic; D011489:Protein Denaturation; D011758:Pyrroles / Q000737:chemistry*; D020349:Surface Plasmon Resonance; D044366:Transition Temperature
chemical_list: D000951:Antigens, Neoplasm; D004268:DNA-Binding Proteins; D005559:Formamides; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; C029899:imidazole; D004250:DNA Topoisomerases, Type II