IRDye® 700 phosphoramidite | CAS 648882-22-8

IRDye® 700 phosphoramidite is a near-infrared (NIR) fluorescent labeling building block designed for incorporation into oligonucleotides during solid-phase nucleic acid synthesis. As a phosphoramidite, it provides a convenient way to generate site-specific NIR dye-DNA conjugates that are widely used for fluorescence-based nucleic acid analysis, imaging, and quantitative assays where low autofluorescence and deep tissue penetration are advantageous. Researchers leverage the IRDye 700 labeling format to produce sequence-defined probes and standards for fluorescence readouts on common NIR imaging and detection platforms.

1. Oligonucleotide Probe Labeling

IRDye® 700 phosphoramidite is used to prepare fluorescent DNA or RNA probes for hybridization-based workflows, including probe design for nucleic acid detection assays and sequence-specific binding studies. By installing the dye directly into the oligonucleotide backbone via solid-phase synthesis, users obtain defined dye-to-oligonucleotide stoichiometry that supports reproducible fluorescence signals in microarray formats, blotting workflows, and hybridization assays. This labeling approach is frequently selected when NIR emission is preferred to reduce background from biological matrices and to enable sensitive visualization with NIR-capable imaging systems.

2. qPCR And Amplification Assay Reagents

IRDye® 700 phosphoramidite is commonly incorporated into oligonucleotide components used in fluorescence amplification and real-time monitoring assay development, including probe-based formats where NIR fluorescence readout is desired. In these workflows, the dye-labeled oligonucleotide serves as a reporter for fluorescence measurements during thermal cycling, enabling quantitative monitoring of nucleic acid amplification products with instrumentation that supports the dye's NIR detection window. Molecular biology and assay development teams use this reagent to build sequence-defined reporter probes and to evaluate assay performance in multiplex-friendly NIR detection schemes.

3. Nucleic Acid Imaging Standards

IRDye® 700 phosphoramidite is applied to generate fluorescent nucleic acid standards and labeled reference materials for calibration, method development, and imaging-based analysis. Laboratories use IRDye 700-labeled oligonucleotides to validate imaging workflows, compare labeling batches, and establish consistent reference signals for gel imaging, capillary electrophoresis readouts, and NIR fluorescence documentation. Because the dye is introduced as a defined phosphoramidite building block, users can produce standardized conjugates that improve comparability across experiments and instruments.

4. Fluorescent Molecular Tracing Oligos

IRDye® 700 phosphoramidite is also used to create NIR fluorescent oligonucleotide tracers for molecular tracing experiments in chemical biology and biomolecular interaction studies. Researchers label oligos to follow binding, localization, and transport behaviors in experimental systems where NIR detection helps minimize interference from scattering and autofluorescence. This reagent is particularly useful when sequence-defined probes are needed for controlled labeling, enabling researchers to correlate fluorescence readouts with specific nucleic acid sequences in imaging and analytical studies.