1,3,5,7-Tetramethyl-8-pentafluorophenyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene | CAS 1299467-50-7

1,3,5,7-Tetramethyl-8-pentafluorophenyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene is a boron-dipyrromethene (BODIPY)-based fluorescent dye that is widely used as a bright, photostable fluorophore scaffold for fluorescence labeling and imaging reagent development. Its aryl substitution pattern and BODIPY core support strong fluorescence for microscopy and plate-based readouts, while the pentafluorophenyl motif provides a convenient handle for downstream conjugation strategies in chemical biology workflows.

1. Fluorescent Labeling Conjugates

1,3,5,7-Tetramethyl-8-pentafluorophenyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene is commonly incorporated into fluorescent labeling conjugates for tracking biomolecules in research settings, including protein and peptide labeling used in binding studies, purification monitoring, and reagent characterization. Researchers frequently use this dye as a fluorophore component in conjugation pipelines to generate fluorescent standards and labeled affinity reagents that can be read on common fluorescence imaging and detection platforms.

2. Fluorescence Microscopy Tracing

1,3,5,7-Tetramethyl-8-pentafluorophenyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene supports cellular and materials microscopy workflows where a robust visible-range fluorophore is required for localization and co-localization experiments. Chemical biology groups use BODIPY-based labeling reagents derived from this dye to visualize labeled targets in fixed samples and to build multi-color imaging panels with spectrally compatible fluorophores, leveraging the dye's characteristic brightness for clear signal in microscopy.

3. Flow Cytometry Fluorescent Tags

1,3,5,7-Tetramethyl-8-pentafluorophenyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene is used as a fluorophore building block for preparing fluorescent tags that can be analyzed by flow cytometry in labeling and sorting assay development. In typical workflows, researchers generate dye-conjugated biomolecule reagents to quantify binding to cell-associated targets and to support fluorescence-based phenotyping experiments where consistent emission and stable dye performance are important for reproducible cytometry readouts.

4. Fluorescence Bioassay Reagents

1,3,5,7-Tetramethyl-8-pentafluorophenyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene is frequently selected for constructing fluorescence-based bioassay reagents and screening tools that rely on straightforward fluorescence readout. Assay developers incorporate this BODIPY dye into labeled components used in binding assays, reagent qualification, and fluorescence monitoring in microplate formats, where the dye's strong signal output helps support practical assay workflows for research and industrial R&D.