title: Binding studies of a large antiviral polyamide to a natural HPV sequence.
abstract: PA1 is a large hairpin polyamide (dImPyPy-β-PyPyPy-γ-PyPy-β-PyPyPyPy-β-Ta; Py = pyrrole, Im = imidazole, β = beta alanine) that targets the sequence 5'-WWGWWWWWWW-3' (W = A or T) and is effective in eliminating HPV16 in cell culture (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res. 91 (2011) 177-186). Described here are its DNA binding properties toward a natural DNA, a 523 bp portion of HPV16 (2150-2672) containing three predicted perfect match sites. Strategies for obtaining binding data on large fragments using capillary electrophoresis are also described. Using an Fe EDTA conjugate of PA1, 19 affinity cleavage (AC) patterns were detected for this fragment. In many cases, there are multiple possible binding sequences (perfect, single and double mismatch sites) consistent with the AC data. Quantitative DNase I footprinting analysis indicates that perfect and most single mismatch sites bind PA1 with Kds between 0.7 and 4 nM, indicating excellent tolerance for the latter. Double mismatch sites exhibit Kds between 12 and 62 nM. A large fraction of the accessible sequence is susceptible to PA1 binding, much larger than predicted based on the literature of polyamide-DNA recognition rules.
authors.affiliation: Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States.
authors.forename: Gaofei
authors.initials: G
authors.lastname: He
authors.affiliation: Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States.
authors.forename: Elena
authors.initials: E
authors.lastname: Vasilieva
authors.affiliation: Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States.
authors.forename: George Davis
authors.initials: GD
authors.lastname: Harris
authors.affiliation: Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Koeller
authors.affiliation: Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States. Electronic address: bashkinj@umsl.edu.
authors.forename: James K
authors.initials: JK
authors.lastname: Bashkin
authors.affiliation: Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States. Electronic address: cdup@umsl.edu.
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Dupureur
mesh_terms: D000409:Alanine / Q000737:chemistry; D000998:Antiviral Agents / Q000737:chemistry / Q000494:pharmacology*; D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D052162:Human papillomavirus 16 / Q000737:chemistry* / Q000235:genetics; D007093:Imidazoles / Q000737:chemistry; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D009757:Nylons / Q000737:chemistry / Q000494:pharmacology*; D011758:Pyrroles / Q000737:chemistry
chemical_list: D000998:Antiviral Agents; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; C029899:imidazole; D004247:DNA; D000409:Alanine
keywords: Affinity cleavage; Binding constant; Footprinting; HPV; Polyamide