iEDDA-assisted Proximity Labeling for Dynamic Analysis near Nuclear Lamina

RNAs are dynamic biomolecules essential for cellular survival and development, with RNA localization being a pivotal aspect of RNA biology. However, current methods for studying RNA localization are limited, typically focusing on RNAs at a single location or time point. This limitation stems from the absence of chemical tools that can effectively differentiate RNAs across various locations or time intervals. Despite the availability of various chemical mechanisms for RNA proximity labeling in live cells, the prevalent use of terminal alkyne or direct conjugation of biotin moiety leads to limited diversity in RNA modification. In this study, we introduced inverse electron- demand Diels-Alder (iEDDA) into RNA proximity labeling, which serves as an orthogonal approach that matches the efficiency of copper-catalysed azide–alkyne cycloaddition (CuAAC). These two biotinylation methods can be integrated, enabling the monitoring of biomolecular dynamics across two different locations and two time points. We employ this new system to evaluate the biological impact of the proximity labeling step itself, resolving longstanding challenges associated with singlet oxygen-mediated proximity labeling. This foundational study not only addressed current limitations in RNA localization studies but also paves new pathways for exploring the complex roles of RNA in cellular functioning and development.