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Acid-soluble proteins able to form DNA-protein complexes in the presence of physiological concentration of NaCl were isolated from rat liver mitochondria. Electrophoretic analysis of these proteins in 15% polyacrylamide gel showed that mitochondrial acid-soluble proteins include of approximately 20 polypeptides with molecular weight of 10–120 kDa. The fraction of acid-soluble proteins can be separated into basic and acidic proteins by chromatography on DEAE cellulose. Some of acidic proteins are tightly bound to the basic proteins and can be separated from them in the presence of 5 mM dithiothreitol. It is discovered that the fraction of acidic proteins contains proteases (including DNA-activated ones), which cleave different polypeptides of the basic proteins with different efficiency. Possibly, mitochondrial DNA-binding proteins and DNA-activated proteases are involved in the regulation of structural organization and functional activity of mitochondrial DNA.