Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication.

Mammalian mitochondrial DNAs contain a conserved origin of light-strand replication that supports accurate initiation of DNA synthesis in vitro. This provides an opportunity to examine the sequence requirements for initiation through in vitro analysis of a series of deleted and mutagenized DNA templates. These assays use enzymes isolated from human mitochondria and single-stranded DNA templates containing deletions or substitutions in the known origin region. The data indicate that accurate and efficient light-strand replication in vitro requires the previously identified stem-loop structure located within a tRNA cluster. In addition, the template sequence 3'-GGCCG-5', located immediately adjacent to the stem, is necessary for efficient replication. This sequence, the complement of which encodes the 3' end of tRNACys, may be the site of transition from RNA primer synthesis to DNA synthesis. Surprisingly, substitutions within a region located in the loop of this origin do not reduce levels of replication.