The Jain Lab focuses on understanding how RNA structure, dynamics, and molecular recognition regulate biological function. We use solution-state NMR spectroscopy, RNA biochemistry, and complementary biophysical approaches to study structured RNAs, RNA-protein interactions, and RNA-ligand recognition.
Structural and dynamic characterization of functional RNA motifs, non-coding RNAs,and regulatory RNA elements, with a focus on how these RNAs recognize and interact with small-molecule ligands and proteins. The work combines structural, dynamic, and folding studies to understand RNA architecture and the principles governing RNA–small molecule and RNA–protein interactions.
Structure–function studies of long non-coding RNAs (lncRNAs) and their functional motifs, aimed at understanding how these transcripts adopt defined structural elements that underlie their biological roles. This work focuses on characterizing the discrete structured regions within lncRNAs and elucidating how these functional motifs mediate interactions with proteins and other RNA elements. By resolving the architecture of these motifs and the molecular basis of their recognition events, the research seeks to connect specific structural features to the regulatory functions that lncRNAs carry out within the cell.
Our lab investigates the thermodynamic and energetic principles governing CRISPR-Cas9 molecular recognition. Having mapped the thermodynamic landscape of guide RNA and target DNA binding, our ongoing work extends to the energetic determinants of expanded PAM recognition, connecting the energetics of RNA–DNA recognition to gene-editing precision, efficiency, and PAM flexibility.
Our work explores how chemical modifications, particularly N6-methyladenosine (m6A), the most prevalent internal modification in eukaryotic mRNA, influence RNA structure and function. We investigate how m6A reshapes local RNA conformation, base-pairing, and stability, and how these structural changes in turn modulate the recognition of RNA by reader proteins and other binding partners. By connecting the structural consequences of m6A to its effects on protein recognition, this research aims to clarify how a single modification can fine-tune RNA folding and the downstream regulatory events that depend on it.
Current projects explore RNA structural dynamics, RNA-protein recognition, non-coding RNA biology, RNA structural motifs in disease pathways, and environmental modulation of RNA structure and function.