Single-molecule RNA structural probing for the study of viral RNA genome structures
RNA folds into complex shapes, building the interface for interactions with proteins, RNA and other molecules. A prime example of this are the genome ends of RNA virus genomes, which have an essential function for the viral life cycle as promoters of viral RNA replication and transcription for the viral RNA polymerase. Recently, alternative viral RNA structures in the HIV genome have gained attention as important regulatory and functional domains.
However, current methods to study these structures largely generate consensus-level data that can produce information about alternative structures only at high sequencing depths and across short sequences, which makes the identification of alternative structures, if possible, experimentally expensive. We aim to develop a single‑molecule RNA probing method that solves this issue to enable the efficient identification of RNA structural ensembles. We will then apply this method to identify critical and variable RNA structure ensembles in viral genomes to deepen our understanding of the mechanisms of viral RNA replication and transcription, and to guide the design of inhibitory molecules.