The binding of polyribonucleotides to the complementary strands of mitochondrial DNA

Abstract

We have purified the complementary strands (H and L) of rat mtDNA by equilibrium centrifugation in alkaline CsCl and studied their interaction with polyribonucleotides in neutral CsCl. H, the strand with the higher density in alkaline CsCl, was shifted to a higher density by poly(C) (20 mg/cm 3), slightly shifted by alkali-degraded poly(U) (7 mg/cm 3) and not shifted by poly(I,G) or poly(I); L was displaced by 37 mg/cm 3 alkali-degraded poly(U), by alkali-degraded poly(I,G) > 50 mg/cm 3), by poly(I) (22 mg/cm 3) but not by poly(C). Poly(A) did not interact with either strand, even at 4°. These results suggest that H contains dG- and dT-rich clusters, and L dA- and dC-rich clusters and that these clusters bind the complementary ribopolymers by standard Watson-Crick base-pairing. To explain the lack of poly(A) binding we postulate that the dT-rich clusters contain enough dC residues to prevent formation of the complex of H and poly(A), whereas the dG residues in the dA-rich clusters on the other strand do not interfere with poly(U) binding.