Human cytomegalovirus (HCMV) lytic DNA replication is initiated at the complex cis-acting oriLyt region, which spans nearly 3 kb. DNA synthesis requires six core proteins together with UL84 and IE2. Previously, two essential regions were identified within oriLyt. Essential region I (nucleotides [nt] 92209 to 92573) can be replaced with the constitutively active simian virus 40 promoter, which in turn eliminates the requirement for IE2 in the origin-dependent transient-replication assay. Essential region II (nt 92979 to 93513) contains two elements of interest: an RNA/DNA hybrid domain and an inverted repeat sequence capable of forming a stem-loop structure. Our studies now reveal for the first time that UL84 interacts with a stem-loop RNA oligonucleotide in vitro, and although UL84 interacted with other nucleic acid substrates, a specific interaction occurred only with the RNA stem-loop. Increasing concentrations of purified UL84 produced a remarkable downward-staircase pattern, which is not due to a nuclease activity but is dependent upon the presence of secondary structures, suggesting that UL84 modifies the conformation of the RNA substrate. Cross-linking experiments show that UL84 possibly changes the conformation of the RNA substrate. The addition of purified IE2 to the in vitro binding reaction did not affect binding to the stem-loop structure. Chromatin immunoprecipitation assays performed using infected cells and purified virus show that UL84 is bound to oriLyt in a region adjacent to the RNA/DNA hybrid and the stem-loop structure. These results solidify UL84 as the potential initiator of HCMV DNA replication through a unique interaction with a conserved RNA stem-loop structure within oriLyt.The mechanism of initiation of human cytomegalovirus (HCMV) lytic DNA replication is largely undefined. The process of HCMV lytic DNA replication requires six core replication proteins: UL54 (polymerase), UL44 (polymerase accessory protein), UL57 (single-stranded DNA binding protein), UL70 (primase), UL102 (primase-associated factor), and UL105 (helicase) (13, 30). These six core proteins make up the generic replication machinery responsible for lytic DNA replication of the HCMV genome (27). Although the proposed activities of these components are postulated through homology to other herpesvirus systems, the exact mechanism of their assembly at the site of the origin is unknown. Our laboratory seeks to understand the early events in HCMV origin-dependent DNA replication that lead to the assembly and function of the HCMV DNA replication machinery.Most herpesviruses, as well as many other DNA viruses, encode an initiation factor, or origin binding protein (OBP), responsible for recognizing the lytic origin and creating a local environment where DNA is separated and the replication machinery can assemble. Many initiation proteins such as those for simian virus 40 (SV40) T antigen, papillomavirus E1, and herpes simplex virus type 1 (HSV-1) UL9 have enzymatic activities such as DNA-dependent nucleoside triphosphatase acti...