In organello footprinting analysis of rat mitochondrial DNA: protein interaction upstream of the Ori-L

Biochem Biophys Res Commun. 1997 Feb 24;231(3):856-60. doi: 10.1006/bbrc.1997.6203.


An in organello footprinting approach has been used to probe a protein-DNA interaction of a nuclear coded 25 kDa protein, previously isolated in our laboratory, that binds "in vitro" a region within the ND2 gene, located upstream of the Ori-L. Footprinting studies with the purine-modifying reagent dimethyl sulfate and the pirimidine-modifying reagent potassium permanganate were carried out in isolated mitochondria from rat liver. Dimethyl sulfate footprinting has allowed the detection of a protein-DNA interaction within the curved ND2 region with contact sites located in both the strands. Potassium permanganate footprinting allowed detection of an adjacent permanganate-reactive region. We hypothesize that the permanganate-reactive region is a single stranded DNA due to a profound helix distortion induced by a 25 kDa protein binding to the nearest region.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • DNA Footprinting*
  • DNA Replication
  • DNA, Mitochondrial / metabolism*
  • DNA, Mitochondrial / ultrastructure
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Deoxyribonucleoproteins / chemistry
  • Mitochondria, Liver / chemistry
  • Mitochondria, Liver / ultrastructure*
  • Molecular Weight
  • Nucleic Acid Conformation
  • Potassium Permanganate / chemistry
  • Protein Binding
  • Rats
  • Sulfuric Acid Esters / chemistry


  • DNA, Mitochondrial
  • DNA-Binding Proteins
  • Deoxyribonucleoproteins
  • Sulfuric Acid Esters
  • Potassium Permanganate
  • dimethyl sulfate

Grant support