Development of background-free tame fluorescent probes for intracellular live cell imaging

• Published in: Nature communications Vol. 7; no. 1; p. 11964
• Main Authors: Alamudi, Samira Husen, Satapathy, Rudrakanta, Kim, Jihyo, Su, Dongdong, Ren, Haiyan, Das, Rajkumar, Hu, Lingna, Alvarado-Martínez, Enrique, Lee, Jung Yeol, Hoppmann, Christian, Peña-Cabrera, Eduardo, Ha, Hyung-Ho, Park, Hee-Sung, Wang, Lei, Chang, Young-Tae
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 20.06.2016; Nature Publishing Group; Nature Portfolio
• Subjects: 13/109; 14/19; 14/34; 14/35; 14/63; 639/638/11/874; 639/638/403; 639/638/439/942; 639/638/92/630; 96/98; Animals; Automation; Azides - chemistry; Boron Compounds - chemistry; Cell Line, Tumor; Cell Nucleolus - metabolism; Cell Nucleolus - ultrastructure; CHO Cells; Cricetulus; Cyclooctanes - chemistry; Drug Design; Fluorescent Dyes - chemical synthesis; Fluorescent Dyes - metabolism; Gene Expression; Golgi Apparatus - metabolism; Golgi Apparatus - ultrastructure; High-Throughput Screening Assays; Humanities and Social Sciences; Humans; Labeling; Lysosomes - metabolism; Lysosomes - ultrastructure; Mitochondria - metabolism; Mitochondria - ultrastructure; Molecular Imaging - methods; multidisciplinary; Osteoblasts - metabolism; Osteoblasts - ultrastructure; Permeability; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Science; Science (multidisciplinary); Signal-To-Noise Ratio; Staining and Labeling - methods; South Korea; Singapore; California; United States > US
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms11964

Fluorescence labelling of an intracellular biomolecule in native living cells is a powerful strategy to achieve in-depth understanding of the biomolecule’s roles and functions. Besides being nontoxic and specific, desirable labelling probes should be highly cell permeable without nonspecific interactions with other cellular components to warrant high signal-to-noise ratio. While it is critical, rational design for such probes is tricky. Here we report the first predictive model for cell permeable background-free probe development through optimized lipophilicity, water solubility and charged van der Waals surface area. The model was developed by utilizing high-throughput screening in combination with cheminformatics. We demonstrate its reliability by developing CO-1 and AzG-1, a cyclooctyne- and azide-containing BODIPY probe, respectively, which specifically label intracellular target organelles and engineered proteins with minimum background. The results provide an efficient strategy for development of background-free probes, referred to as ‘tame’ probes, and novel tools for live cell intracellular imaging. The success of a fluorescent dye as a molecular probe to monitor the intracellular activity of biomolecules depends on its physicochemical characteristics. Here, the authors use a predictive model to identify key features that allow them to design cell permeable, background-free fluorescent probes.