METHODS
Footprinting reactions:
  • DNase I footprinting

  • genomic in situ DNAse I footprinting

  • competitive DNAse I footprint

  • methidiumpropyl-EDTA.Fe(II)

  • methidiumpropyl-EDTA.Fe(II) in nuclei

  • DNase II

  • hydroxyl radicals

  • photofootprinting in vivo

  • copper/phenanthroline footprinting

  • copper/phenanthroline footprinting in situ

  • neocarzinostatin footprinting

  • micrococcal nuclease

  • micrococcal nuclease in situ

  • nuclease P1 footprinting

  • in vivo DMS footprinting

    • Exonuclease digests:
  • exonuclease III

  • genomic / in vivo exonuclease III digest

  • competition exonuclease III digest

  • lambda exonuclease

  • T7 gene exonuclease

    • Gel retardation:
  • direct gel shift

  • supershift (antibody binding)

  • gel shift competition

    • DNA modification reactions:
  • methylation protection

  • in vivo / genomic methylation protection

  • methylation interference

  • Dam methylation

  • ethylation protection

  • ethylation interference

  • DEPC interference

  • KMnO4 modification

  • genomic demethylation

  • uracil interference

  • depurination interference

  • missing base interference

  • carboxymethylation interference

  • carboxyethylation interference

  • depyrimidination interference

  • cytosine and adenine interference

  • primer extension footprint

  • avidin-biotin complex DNA binding assay

  • Southwestern blotting / filter binding

  • nitrocellulose filter binding

  • southwestern blotting

    • UV:
  • UV-crosslinking

  • genomic UV-photofootprint

  • UV/primer extension

  • immunoprecipitation

  • affinity chromatography

  • crystallization

  • electron microscopy

  • chromatin immunoprecipitation procedure

  • yeast one hybrid system

    • Functional analysis