Footprinting and Missing Nucleoside Analysis of Transcription Factor-DNA Complexes

VIOLA, IVANA L.; GONZALEZ, DANIEL H.

Plant Transcription Factors: Methods and Protocols

Springer Science+Business Media

Año: 2011; p. 259 - 275

In the folowing 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 of chemical modification of DNA by 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 each nucleotide of both strands of its target DNA sequence.