Using FLIM-FRET for Characterizing Spatial Interactions in the Spindle

Practical guide to fluorescence lifetime imaging microscopy

Fluorescence lifetime imaging microscopy (FLIM) has emerged as a powerful modality that offers sensitivity to molecular environments, fluorophore concentration independence, local environment sensing, characterization of molecular binding events with multiplexing capabilities, and monitoring metabolism. Recently, we adapted FLIM for quantitatively sensing RNAs in live cells, establishing the Riboglow-FLIM platform. More broadly, FLIM has the potential to complement and advance traditional intensity-based microscopy platforms. Here, we provide a practical guide to make use of FLIM for diverse fluorescence sensors. We discuss FLIM basics, the experimental setup, data-fitting principles, and real-world case studies of well-understood fluorescent proteins to demonstrate the applicability of these workflows. This perspective provides a basic "best practices" guide for designing and executing FLIM experiments, with the goal of introducing researchers to concepts that will help empower them to utilize this emerging technology.

FLIM-FRET Protein-Protein Interaction Assay

Fluorescence lifetime imaging performed under FRET conditions between two interacting molecules is a sensitive and robust way to quantify intermolecular interactions in cells. The fluorescence lifetime, an inherent property of the fluorophore, remains unaffected by factors such as concentration, laser intensity, and other photophysical artifacts. In the context of FLIM-FRET, the focus lies on measuring the fluorescence lifetime of the donor molecule, which diminishes upon interaction with a neighboring acceptor molecule. In this study, we present a step-by-step experimental protocol for applying FLIM-FRET to investigate protein-protein interactions involving various RAS isoforms and RAS effectors at the live cell's plasma membrane. By utilizing the FRET pair comprising enhanced green fluorescent protein (eGFP) and fluorescent mCherry, we demonstrate that the proximity and possible nanoclustering of eGFP-tagged KRAS4b G12D and mCherry-tagged KRAS4b WT led to a reduction in the donor eGFP's fluorescence lifetime. The donor lifetime of eGFP-tagged KRAS decreases even further when treated with a dimer-inducing small molecule, or in the presence of RAF proteins, suggesting a greater FRET efficiency, and thus less distance, between donor and acceptor.