D-loop replication

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D-loop replication is a process by which chloroplasts and mitochondria replicate their genetic material. An important component of understanding D-loop replication is that chloroplasts and mitochondria have a single circular chromosome like bacteria instead of the linear chromosomes found in eukaryotes.

In many organisms, one strand of DNA in the plastid is comprised of heavier nucleotides (relatively more purines: adenine and guanine). This strand is called the H (heavy) strand. The L (light) strand is comprised of lighter nucleotides (pyrimidines: thymine and cytosine). Replication begins with replication of the heavy strand starting at the D-loop (also known as the control region). An origin of replication opens, and the heavy strand is replicated in one direction. After heavy strand replication has continued for some time, a new light strand is also synthesized, through the opening of another origin of replication. When diagramed, the resulting structure looks like the letter D.

The D-loop region is important for phylogeographic studies. Because the region does not code for any genes, it is free to vary with only a few selective limitations on size and heavy/light strand factors. The mutation rate is among the fastest of anywhere in either the nuclear or mitochondrial genomes in animals. Mutations in the D-loop can effectively track recent and rapid evolutionary changes such as within species and among very closely related species.