title: Footprinting and missing nucleoside analysis of transcription factor-DNA complexes.
abstract: In the following chapter we describe methods and protocols to analyze the interaction of proteins with DNA using footprinting and related techniques based on the modification of DNA with either hydroxyl radicals or methylating agents. Footprinting, based on the protection from chemical modification of DNA through the specific binding of a protein, gives information about the nucleotides that are in close contact with the protein upon binding. The derived missing nucleoside and interference techniques identify nucleotides that are energetically important for protein binding. These methods are highly valuable to study in detail the interaction of a transcription factor with nucleotides on both strands of its target DNA sequence.
authors: Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Universidad Nacional del Litoral, Santa Fe, Argentina. iviola@fbcb.unl.edu.ar
authors: Ivana L
authors: IL
authors: Viola
authors: Daniel H
authors: DH
authors: Gonzalez
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D018983:DNA Footprinting / Q000379:methods*; D018744:DNA, Plant / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D017665:Hydroxyl Radical; D008745:Methylation; D008958:Models, Molecular; D017422:Sequence Analysis, DNA / Q000379:methods; D013194:Staining and Labeling / Q000379:methods; D014157:Transcription Factors / Q000032:analysis* / Q000235:genetics / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D017665:Hydroxyl Radical