Project Summary
HIV remains a significant problem worldwide. The CA protein of HIV is involved in several critical replication
events, including Gag oligomerization and viral assembly, maturation, reverse transcription (RT), trafficking to
the nucleus via interaction with host factors, nuclear import, integration, and evasion of host immune
responses. Despite significant advances in our understanding of the role of CA in replication, there are many
unresolved questions regarding CA structural dynamics during viral assembly and post-entry replication steps,
CA-host factor interactions, and the impact of these interactions on virus biology. The genetic fragility of CA and
difficulty of examining CA-host interactions in cells represent significant barriers to the resolution of these
questions. To address these challenges and knowledge gaps, we are working to identify and develop novel tools
capable of discriminating among different CA assembly forms. To date, we have identified RNA aptamers that
bind specifically to the CA lattice, but not other assembly forms, and those that bind both the CA lattice and CA
hexamer assembly forms. Aptamers represent unique tools particularly well-suited to the study of CA assembly
forms and interaction sites, as they bind targets with high specificity, discriminate among different conformations
of the same protein, can be expressed in or delivered to cells, can be used to outcompete other interacting
partners, and are amenable to a variety of different modifications. Interestingly, our aptamers identified to date
display different biological phenotypes, suggesting that they may target unique sites on CA or influence CA
function in distinct ways. Here, we propose two aims in support of our goal to develop aptamers as useful tools
for the field. The focus of Aim 1 is to identify new aptamers that target additional CA assembly forms, building
upon our prior work supporting feasibility of our approach. Our ultimate goal is to develop a panel of aptamers
with specificities to all relevant CA assembly states. The focus of Aim 2 is to develop an aptamer-mediated, CA
assembly state-specific affinity purification method paired with crosslinking mass spectrometry to identify novel
CA assembly state-associated host factors. Collectively, these tools will tremendously benefit the field, as there
are currently no tools available for the differentiation of CA assembly states. Importantly, aptamers are amenable
to a variety of modifications that will facilitate applications including affinity purification, microscopy-based
tracking of CA during replication, expression in cells for evaluation of replication effects and mechanistic studies,
and delivery to cells to compete for binding to specific CA sites. Furthermore, future determination of sites of
aptamer-CA interaction will help identify novel accessible sites on CA for potential therapeutic targeting.