title: A recommended workflow for DNase I footprinting using a capillary electrophoresis genetic analyzer.
abstract: Fragment analysis was developed to determine the sizes of DNA fragments relative to size standards of known lengths using a capillary electrophoresis genetic analyzer. This approach has since been adapted for use in DNA footprinting. However, DNA footprinting requires accurate determination of both fragment length and intensity, imposing specific demands on the experimental design. Here we delineate essential considerations involved in optimizing the fragment analysis workflow for use in DNase I footprinting to ensure that changes in DNase I cleavage patterns may be reliably identified.
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Smitha
authors.initials: S
authors.lastname: Sivapragasam
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Anuja
authors.initials: A
authors.lastname: Pande
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. Electronic address: agrove@lsu.edu.
authors.forename: Anne
authors.initials: A
authors.lastname: Grove
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D018983:DNA Footprinting / Q000379:methods*; D003850:Deoxyribonuclease I / Q000378:metabolism*; D019075:Electrophoresis, Capillary / Q000379:methods*; D011401:Promoter Regions, Genetic; D048372:Streptomyces coelicolor / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D057188:Workflow
chemical_list: D014157:Transcription Factors; D004247:DNA; D003850:Deoxyribonuclease I
keywords: Capillary electrophoresis; DNase I footprinting; Fragment analysis; Single hit