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 many chloroplasts and mitochondria have a single circular chromosome like bacteria instead of the linear chromosomes found in eukaryotes. However, it should be remembered that many cloroplastss and mitochondria have a linear chromosome, and D-loop replication is not important in these organelles.
In many organisms, one strand of DNA in the plastid comprises heavier nucleotides (relatively more purines: adenine and guanine). This strand is called the H (heavy) strand. The L (light) strand comprises 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.