Aminoallyl-UTP-Cy3 (ethyl)

Aminoallyl-UTP-Cy3 (ethyl) is a Cy3-based fluorescent nucleotide analog designed for post-incorporation fluorescent labeling of RNA by aminoallyl chemistry. After incorporation of the UTP analog into nucleic acids, the pendant aminoallyl handle enables covalent coupling to amine-reactive dyes and fluorescent labeling workflows, supporting visualization and tracking of RNA in molecular biology and nucleic acid analysis. Cy3 emission in the visible red range makes it compatible with standard fluorescence microscopy and many fluorescence detection platforms used for nucleic acid imaging and assay development.

1. RNA Fluorescent Labeling

Aminoallyl-UTP-Cy3 (ethyl) is used by molecular biology groups to generate Cy3-labeled RNA probes for hybridization-based experiments, RNA tracking studies, and fluorescence readouts in nucleic acid workflows. Researchers commonly incorporate the analog into RNA transcripts during in vitro synthesis, then use the Cy3 functionality to obtain a fluorescent RNA species for imaging, localization, and downstream fluorescence detection. This reagent is particularly valuable when a Cy3-tagged RNA probe is needed to monitor RNA abundance or distribution in experimental systems that rely on red-channel fluorescence.

2. Fluorescence In Situ Hybridization

Aminoallyl-UTP-Cy3 (ethyl) supports fluorescence in situ hybridization workflows where fluorescent RNA probes are required to visualize target RNA within fixed cells or tissue sections. Cell biology and pathology research laboratories use Cy3-labeled RNA to map expression patterns and compare relative localization across samples using fluorescence microscopy. The Cy3 labeling provides a robust red-emitting signal for imaging workflows that separate nucleic-acid fluorescence from other fluorophores in multicolor experiments, helping streamline probe-based microscopy studies.

3. Microarray and Hybridization Assays

Aminoallyl-UTP-Cy3 (ethyl) is applied in nucleic acid hybridization and array-based assay development where fluorescently labeled RNA or RNA-derived probes are used for detection. Molecular diagnostics research teams and genomics laboratories often use Cy3-labeled nucleic acid reagents to quantify hybridization signals and to compare binding patterns across experimental conditions. In these workflows, the fluorescent tag enables direct readout by fluorescence scanners and plate-based fluorescence systems, supporting assay development for RNA analysis and probe optimization.

4. RNA Tracking in Live-Cell Studies

Aminoallyl-UTP-Cy3 (ethyl) is used in RNA tracking experiments where fluorescent RNA is followed over time to study RNA localization dynamics and transport behaviors in cellular models. Chemical biology and cell imaging laboratories employ Cy3-labeled RNA to visualize where RNA accumulates and how it changes during experimental perturbations, using fluorescence microscopy readouts. The Cy3 fluorophore supports time-resolved imaging in setups designed for visible-channel fluorescence monitoring, enabling researchers to connect RNA distribution with experimental variables in mechanistic studies.