IRDye® 800 phosphoramidite | CAS 211380-08-4

IRDye® 800 phosphoramidite is a near-infrared (NIR) fluorescent labeling building block supplied as a phosphoramidite, enabling efficient incorporation into oligonucleotides via standard solid-phase DNA/RNA synthesis workflows. Its NIR emission supports low-background fluorescence imaging and is frequently used to generate fluorescent oligo probes for molecular imaging, nucleic acid analysis, and fluorescence-based readouts where visible dyes may be less convenient.

1. Nucleic Acid Hybridization Probes

IRDye® 800 phosphoramidite is widely used to prepare fluorescent DNA and RNA hybridization probes for fluorescence detection of complementary sequences in research and assay development settings. Researchers incorporate the phosphoramidite into oligonucleotides to create labeled targets for microarray-style workflows, blotting formats, and solution-based hybridization assays, where NIR readout can reduce interference from autofluorescence. The resulting IRDye® 800-labeled probes are particularly useful when downstream instrumentation supports NIR channel detection for sensitive visualization and quantification of hybridization signals.

2. qPCR And Real-Time Amplification Assays

IRDye® 800 phosphoramidite is commonly employed to construct real-time PCR and nucleic-acid amplification assay reagents that require a fluorescent reporter compatible with NIR detection. By integrating the phosphoramidite into primers or probe oligonucleotides during synthesis, assay developers generate reporter-labeled constructs that can be paired with appropriate quenchers or assay chemistries to produce time-resolved fluorescence signals during amplification. This application is favored in laboratories that prefer NIR reporters for multiplexing compatibility and reduced background from biological samples.

3. Fluorescent Sequencing And Fragment Analysis

IRDye® 800 phosphoramidite supports fluorescent oligonucleotide labeling for nucleic acid fragment analysis workflows, including research-grade sequencing and size/identity verification assays. Incorporation into primers or internal oligo tags enables detection of extension products and labeled fragments using NIR-capable imaging or detection systems. In practice, teams use IRDye® 800-labeled oligos to streamline downstream readout when NIR channels are available, improving signal clarity in complex mixtures relative to purely visible fluorophores.

4. Molecular Imaging Of Oligonucleotide Targets

IRDye® 800 phosphoramidite is used to generate NIR fluorescent oligonucleotide imaging reagents for tracking labeled nucleic acids in molecular imaging experiments. Researchers synthesize IRDye® 800-bearing oligos to visualize uptake, localization, or binding to nucleic-acid-containing targets in model systems, leveraging NIR emission for improved contrast against background fluorescence. This approach is frequently adopted in fluorescence imaging studies where labeled oligonucleotides serve as molecular reporters and the experimental setup supports NIR detection.