Repurposing genetically encoded fluorophore-binding RNA aptamers for high precision NanoMapping

• Applicant: Dr. Murat Sünbül
• Subject Area: Biological and Biomimetic Chemistry
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 503107812

Besides encoding proteins, RNAs play a myriad of key functions in cellular processes including catalysis, gene regulation and cellular signaling. These processes are flawlessly orchestrated by interactions with proteins and other RNA molecules. Any perturbation of this RNA interactome may lead to cellular malfunction and diseases. Therefore, it is of high importance to unravel the roles of RNAs and to discover new RNA interacting biomolecules. However, simple, versatile and low-cost methods enabling the comprehensive discovery of RNA-RNA and RNA-protein interactions in vivo with high precision are still needed. We envision that a methodology based on light-triggered proximity labeling by repurposed fluorescent light-up RNA aptamers (FLAPs) has the potential to decipher complex RNA networks. Typically, FLAPs bind fluorogenic dyes, resulting in fluorescence increase and are used for RNA imaging. In this proposal, we will design and synthesize new dyes for FLAPs, and use them as versatile tools to decipher RNA interactomes rather than as imaging tags. Harnessing synthetic chemistry, biophysics and molecular biology, we aim to develop a new technology (called “NanoMapping”) for tagging endogenous proteins and RNAs in the vicinity of a specific RNA and their subsequent genome-wide identification with high precision. Applying the NanoMapping technology to RNAs related to diseases such as Huntington, Fragile X syndrome and cancer will facilitate discovering novel RNA-RNA and RNA-protein interactions, unravelling fundamental molecular mechanisms of RNA diseases and developing new therapeutic approaches.

• DFG Programme: Research Grants