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(Received for publication, March 27, 1995; and in revised form, August 14, 1995)
Footprinting studies with the purine-modifying reagent dimethyl
sulfate and with the single-stranded DNA probing reagent potassium
permanganate were carried out in isolated mitochondria from rat liver.
Dimethyl sulfate footprinting allowed the detection of protein-DNA
interactions within the rat analogues of the human binding sites for
the transcription termination factor mTERF and for the transcription
activating factor mtTFA. Although mTERF contacts were localized only at
the boundary between the 16S rRNA/tRNA genes, multiple mtTFA contacts were detected. Contact sites were
located in the light and the heavy strand promoters and, in agreement
with in vitro footprinting data on human mitochondria, between
the conserved sequence blocks (CSB) 1 and 2 and inside CSB-1. Potassium
permanganate footprinting allowed detection of a 25-base pair region
entirely contained in CSB-1 in which both strands were
permanganate-reactive. No permanganate reactivity was associated with
the other regions of the D-loop, including CSB-2 and -3, and with the
mTERF contact site. We hypothesize that the single-stranded DNA at
CSB-1 may be due to a profound helix distortion induced by mtTFA
binding or be associated with a RNA polymerase pause site. In any case
the location in CSB-1 of the 3` end of the most abundant replication
primer and of the 5` end of the prominent D-loop DNA suggests
that protein-induced DNA conformational changes play an important role
in directing the transition from transcription to replication in
mammalian mitochondria.
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