Genetically Encoded Near-Infrared Photocatalysis for Proximity Labeling of Subcellular Proteome

The spatial organization of proteins in eukaryotic cells plays essential roles in cellular functions. Genetically encoded proximity labeling methods offer spatially resolved and proteome-wide mapping of protein localization, yet existing techniques are limited to blue light activation, which has limited tissue penetration and causes a high cellular background. Here, we report the development of a near-infrared photocatalytic proximity labeling method, FLAPP, based on the engineered fluorogen-activating protein dL5**. Upon binding to the fluorogenic iodinated malachite green, the complex can efficiently absorb near-IR light to produce singlet oxygen that reacts in situ with nearby histidine residues. Unlike most existing near-infrared light-activated proximity labeling techniques that rely on antibody-dependent membrane targeting, FLAPP is a genetically encoded near-infrared light-activated proximity labeling technology. We demonstrate the high spatial specificity (96%) of FLAPP in the mitochondria and nucleus. FLAPP enables the deep tissue penetration of protein labeling, underscoring its potential for live animal applications.