title: Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis.
abstract: The mapping of DNA footprints and affinity cleavage sites for small DNA ligands is affected by the choice of sequencing chemistry and end label, and the potential for indexing errors can be significant when mapping small ligand-DNA interactions. Described here is a mechanism for avoiding such errors based on a summary of standard labeling, cleavage, and indexing chemistries and a comparison among them for analysis of these interactions by capillary electrophoresis. The length dependence of the difference between Sanger and Maxam-Gilbert indexing is examined for a number of duplexes of mixed sequence.
authors.affiliation: Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri-St. Louis, St. Louis, MO 63121, USA.
authors.forename: Gaofei
authors.initials: G
authors.lastname: He
authors.forename: Elena
authors.initials: E
authors.lastname: Vasilieva
authors.forename: James K
authors.initials: JK
authors.lastname: Bashkin
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Dupureur
mesh_terms: D002846:Chromatography, Affinity / Q000379:methods*; D018983:DNA Footprinting / Q000379:methods*; D019075:Electrophoresis, Capillary / Q000379:methods*; D006878:Hydroxides; D008024:Ligands
chemical_list: D006878:Hydroxides; D008024:Ligands; C031356:hydroxide ion
keywords: Capillary electrophoresis; DNA; Footprinting; Ligand–DNA interactions; Sequencing