Inducible tag-free degradation of endogenous proteins with AlissAID and development of a photoactivable inducer.

Protein analysis strategies involving targeted protein degradation are powerful approaches to determine gene functions. Auxin-inducible degron (AID) is among the most widely used methods for target protein knockdown. This system enables the rapid depletion of AID-tagged target proteins in an auxin-dependent manner. Various improved AID methods have been developed to date; however, the requirement to tag the target proteins remains a common challenge. Here, we demonstrated the efficiency of an affinity linker-based super-sensitive AID system for the conditional knockdown of target proteins in cultured animal cells and mouse embryos. This system combines the improved AID method with a small protein binder, enabling the control of green fluorescent protein and mCherry fusion proteins. Additionally, this system can be used to degrade tag-free targets, such as Ras proteins. We also developed caged 5-adamantyl-indole-3-acetic acid that precisely controlled targeted protein degradation under light irradiation. This advanced technique aids in the degradation of endogenous proteins of interest and can be used to develop new technologies for localized protein degradation.