Aminoallyl-UTP-PEG5-AF594

Aminoallyl-UTP-PEG5-AF594 is an aminoallyl-modified uridine triphosphate analog bearing a PEG5 spacer and an AF594 fluorophore, designed for post-incorporation fluorescent labeling of nucleic acids. In typical workflows, the aminoallyl handle enables efficient coupling to amine-reactive chemistry after UTP analog incorporation, providing stable fluorescent tagging for microscopy and nucleic acid analysis. The AF594 dye supports fluorescence detection in standard visible-channel imaging and fluorescence-based readouts used in molecular biology and chemical biology research.

1. Fluorescent RNA Labeling

Aminoallyl-UTP-PEG5-AF594 is used to generate fluorescently labeled RNA for fluorescence imaging and downstream binding or hybridization experiments. Researchers incorporate the uridine analog during in vitro transcription to introduce the aminoallyl functionality at defined positions, then couple the AF594-containing labeling chemistry to obtain an RNA probe with a PEG5 spacer that helps reduce steric constraints during hybridization. This approach is commonly used in studies that track RNA localization, RNA-protein interactions, or RNA uptake in controlled experimental systems where fluorescence readout is required.

2. Fluorescent In Situ Hybridization

Aminoallyl-UTP-PEG5-AF594 supports fluorescence-based nucleic acid staining workflows where labeled RNA probes are hybridized to complementary targets in fixed samples. Chemical biology and cell biology laboratories use AF594-labeled RNA to visualize hybridization patterns with fluorescence microscopy, leveraging the dye's compatibility with common filter sets for visible-channel detection. The PEG5 spacer and nucleic acid-compatible design help maintain probe accessibility, which is particularly useful when probes need to hybridize efficiently while preserving fluorescence signal for imaging and quantitative analysis.

3. Flow Cytometry Nucleic Acid Probes

Aminoallyl-UTP-PEG5-AF594 is applied in fluorescence workflows that require nucleic acid labeling compatible with flow cytometry instrumentation. Labeled RNA or RNA-derived probes are used to report on nucleic acid hybridization events in suspension formats, enabling population-level quantification of probe binding. Researchers often choose AF594-labeled nucleic acid reagents when they need a robust fluorescent tag for multiplexing strategies that rely on distinct excitation/emission channels and consistent signal across many thousands of cells or particles.

4. Fluorescent Hybridization Assays

Aminoallyl-UTP-PEG5-AF594 is frequently incorporated into labeled nucleic acid probe preparations for fluorescence-based hybridization assays. Molecular imaging and diagnostic reagent development groups use AF594-tagged RNA probes to monitor target binding in plate-based or cuvette-based formats, including experiments designed to compare hybridization conditions, kinetics, or probe design variables. The aminoallyl/PEG5 architecture supports construction of fluorescent probes that remain functional for binding readouts while providing a stable fluorescence signal for quantitative fluorescence measurements.