A new chemical approach for proximity labelling of chromatin-associated RNAs and proteins with visible light irradiation

Abstract

A new nucleus-localized singlet oxygen generator was designed and synthesized.

Chemical Tools for Endogenous Protein Labeling and Profiling

“…High spatiotemporal control of labeling can be achieved by the use of light and the small intracellular diffusion radius of singlet oxygen (10-20 nm) in cells (Moan and Berg, 1991;Tamura et al, 2020). In recent examples, Li et al (2019) and Tamura et al (2020) have developed nucleus-localized singlet oxygen generators to achieve the spatially restricted tagging of nuclear proteins in the presence of propargylamine or an o-phenylenediamine-based labeling reagent upon light irradiation. Very recently, Macmillan and colleagues have reported a novel concept, termed MicroMap (mMap), to map microenvironments with high precision by exploiting photocatalytic carbene generation to identify PPIs on the cell surface.…”

Organelle specific protein profiling with light mediated proximal labeling in living cells

“…LIMPLA2 is inspired by the method for RNA and protein labeling mediated by fluorophore eosin, 23-26 in which eosin is spatially confined in subcellular region via conjugation with halo tag protein or other subcellular targeting moiety, and then eosin will mediate PA for labeling proximal macromolecule upon illumination. However, eosin derivatives in this method are not commercially available and lengthy chemical synthesis work is unavoidable; eosin may be relatively toxic to cultured cell even under natural light compared with common dye as eosin is always used as a photosensitizer and has high singlet oxygen quantum yield, 27, 28 which also means eosin may have higher photo-labeling efficiency.…”

“…However, reactive molecules may react with highly abundant proteins while the molecules cross through the cytosol to mitochondria, which leads to artifacts and the MRMs labeling process requires starvation of serum for 6 h, which affects expression and phosphorylation of multiple proteins [16][17] . A fluorophore eosin mediated RNA and protein labeling method [18][19][20][21] is inspiring and powerful, in which eosin is spatially confined via conjugated with halo tag protein or other subcellular targeting moiety, and then eosin will activate PA for labeling proximal macromolecule catalyzed by visible light (LIMPLA2 is similar with this method). In this method, eosin derivatives are not commercial available which means much chemical synthesis work is indispensable; eosin may be relatively toxic to cultured cell even under natural light compared with common dye as eosin is always used as a photosensitizer which also means eosin may have higher photo-labeling efficiency.…”

Photocatalysis in Chemical Biology: Extending the Scope of Optochemical Control and Towards New Frontiers in Semisynthetic Bioconjugates and Biocatalysis

“…Local generation of singlet oxygen has also been used in proximity protein-labeling reactions with a ligand-photocatalyst conjugate (Figure 3,C). [27,28] Using a well-known DNA minor groove binder (Hoechst) conjugated to a fluorescein derivative, labeling of nearby RNA and proteins was achieved. Most recently, it was shown that singlet oxygen can react with histidine, converting the nucleophilic heterocycle into an electrophile that undergoes reaction with 1-methyl-4-aryl-urazole (MAUra, Figure 3,D).…”

“…Local generation of singlet oxygen has also been used in proximity protein‐labeling reactions with a ligand‐photocatalyst conjugate ( Figure 3 ,C ) [27,28] . Using a well‐known DNA minor groove binder ( Hoechst ) conjugated to a fluorescein derivative, labeling of nearby RNA and proteins was achieved.…”