Rolling hairpin replication

Rolling hairpin replication (RHR) is a unidirectional, strand displacement form of DNA replication used by parvoviruses, a group of viruses that constitute the family Parvoviridae. Parvoviruses have linear, single-stranded DNA (ssDNA) genomes in which the coding portion of the genome is flanked by telomeres at both ends that form hairpin loops. During RHR, these hairpins unfold and refold to change the direction of DNA replication to progress in a continuous manner back and forth across the genome. This creates a replicative form (RF) molecule that contains numerous copies of the genome. Progeny genomes are then excised from the RF molecule by excisions made by the viral replication initiator protein. RHR is similar to rolling circle replication and can be considered a variation of it used for linear ssDNA genomes.

Before RHR begins, a host cell DNA polymerase converts the genome to a duplex form in which the coding portion is double-stranded and connected to the terminal hairpins. Messenger RNA (mRNA) that encodes the viral initiator protein is then transcribed and translated to synthesize the protein. The initiator protein commences RHR by binding to and nicking the genome in a region at the base of the hairpin called the origin while establishing a replication fork. Nicking leads to the hairpin unfolding into a linear, extended form. The telomere is then replicated and both strands of the telomere refold back in on themselves to their original hairpin forms, which repositions the replication fork to switch templates to the other strand and move in the opposite direction to the other end of the RF molecule.

Parvoviruses vary in whether both hairpins are the same or different. Homotelomeric parvoviruses such as adeno-associated viruses (AAVs), i.e. those that have similar or identical telomeres, have both ends replicated by terminal resolution, the previously described process. Heterotelomeric parvoviruses such as minute virus of mice (MVM), i.e. those that have different telomeres, have one end replicated by terminal resolution and the other end by an asymmetric process called junction resolution. During asymmetric junction resolution, the duplex extended form of the telomere reorganizes into a cruciform-shaped junction, which enables the correct orientation of the telomere to be replicated off the lower arm of the cruciform. Because of their means of resolving termini, homotelomeric parvoviruses usually package an equal number of positive- and negative-sense strands into progeny capsids, while heterotelomeric parvoviruses typically package negative-sense strands.