Rolling circle replication

Rolling circle replication describes a process of nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids. It is also thought that some viruses may replicate their DNA via a rolling circle mechanism.

Circular DNA replication
Rolling circle DNA replication is initiated by an initiator protein encoded by the plasmid or bacteriophage DNA, which nicks one strand of the double-stranded, circular DNA molecule at a site called the double-strand origin, or DSO. The initiator protein remains bound to the 5' phosphate end of the nicked strand, and the free 3' hydroxyl end is released to serve as a primer for DNA synthesis by DNA polymerase III. Using the unnicked strand as a template, replication proceeds around the circular DNA molecule, displacing the nicked strand as single-stranded DNA. Displacement of the nicked strand is carried out by a host-encoded helicase called PcrA (the abbreviation standing for plasmid copy reduced) in the presence of the plasmid replication initiation protein.

Continued DNA synthesis can produce multiple single-stranded linear copies of the original DNA in a continuous head-to-tail series called a concatemer. These linear copies can be converted to double-stranded circular molecules through the following process:

First, the initiator protein makes another nick to terminate synthesis of the first (leading) strand. RNA polymerase and DNA polymerase III then replicate the single-stranded origin (SSO) DNA to make another double-stranded circle. DNA polymerase I removes the primer, replacing it with DNA, and DNA ligase joins the ends to make another molecule of double-stranded circular DNA.

A striking feature of rolling circle replication is the uncoupling of the replication of the two strands of the DNA molecule. In contrast to common modes of DNA replication where both the parental DNA strands are replicated simultaneously, in rolling circle replication one strand is replicated first (which protrudes after being displaced, giving the characteristic appearance) and the second strand is replicated after completion of the first one.

Rolling circle replication has found wide uses in academic research and biotechnology, and has been successfully used for amplification of DNA from very small amounts of starting material.

Circular RNA replication
Viroids are small, circular RNA molecules that act as plant pathogens. They replicate inside the host cell without a helper virus. Viroid RNA typically is folded into a double strand with some unpaired regions, being similar in size to a DNA doublestrand molecule. This enables DNA-dependent RNA polymerase II to recognize the viroid molecule as a template. The host enzyme essentially replicates the viroid by "transcribing" it in a rolling circle-type mechanism. The resulting RNA molecule is processed into mature viroid particles through the action of host RNases and ligases.