Abstract HIV-1 integrase (IN) is essential for viral replication and catalyzes integration of viral DNA into the host chromosome. A new class of allosteric IN inhibitors (ALLINIs) has recently been reported to be capable of inhibiting the enzyme function by promoting aberrant IN multimerization. Unexpectedly, in infected cells, these compounds potently impaired the late stage of HIV-1 replication by triggering significant viral core morphology defects. This phenotype suggested that in addition to its known catalytic function during the early steps of HIV-1 replication, IN also plays an important, non-catalytic role during the late steps of viral replication. Our preliminary studies reveal that IN tightly binds to select highly structured viral RNA elements both in vitro and in properly matured virions. In addition, we were able to observe that an ALLINI is capable of modulating this interaction in the virion. The following two aims will extend these preliminary observations. Aim 1 will map the viral RNA binding sites on IN and determine the functional significance of the identified interacting amino acids. Aim 2 will determine how ALLINIs affect IN interactions with viral RNA during virion morphogenesis. Taken together, we will use a combination of virology and biochemical approaches to allow us to examine the potential link between IN interactions with viral RNA genome and formation of properly matured virions. Structural details that will emerge from these studies will increase our understanding of how IN functions during the late stage of HIV-1 replication as well as elucidate the mode of action for the recently discovered ALLINIs.