HSV-1 origin binding protein UL9 forms intermolecular DNA tethers and intramolecular DNA loops

Herpesviruses are ubiquitous human pathogens, causing mild to severe symptoms ranging from cold sores to nasopharyngeal carcinoma. Even though replication of the dsDNA genome has been studied for decades, we still lack a complete molecular understanding of its mechanism. It has been previously proposed, but never shown directly, that the HSV-1 origin-binding protein UL9 interacts with two closely spaced sites within the oriS origin sequence, thereby mediating origin looping, which in turn facilitates replication initiation. Here, we use an array of single-molecule approaches to test this long-standing hypothesis directly. Surprisingly, the data show that UL9 does not efficiently loop oriS. However, we demonstrate that UL9 can form large DNA loops at non-origin sequences very efficiently, as well as tether two oriS DNA molecules intermolecularly. Contrary to the origin-bending hypothesis, our findings indicate that UL9 does not primarily loop oriS DNA but rather may play an alternative role in replication initiation, such as tethering two separate molecules to facilitate recombination.