Cy3.5 phosphoramidite

Cy3.5 phosphoramidite is a cyanine dye phosphoramidite designed for direct incorporation into oligonucleotides during solid-phase nucleic acid synthesis. Researchers use this reagent to generate Cy3.5-labeled DNA or RNA probes for fluorescence-based detection workflows where a red-shifted cyanine emission is advantageous for multiplexing and background management. Because the dye is introduced as part of the oligonucleotide backbone build, the resulting conjugates are routinely used in nucleic acid hybridization assays, fluorescence imaging of labeled strands, and quantitative fluorescence readouts.

1. Oligonucleotide Hybridization Probes

Cy3.5 phosphoramidite is used to construct fluorescent DNA or RNA hybridization probes for monitoring nucleic acid binding events by fluorescence microscopy, plate-based fluorescence, or capillary-style optical readouts. In these workflows, Cy3.5 labeling provides a bright, spectrally distinct signal for tracking target-dependent hybridization of complementary sequences, including probe/target formats used in research genotyping and sequence verification experiments.

2. Fluorescent FISH Labeling

Cy3.5 phosphoramidite supports the preparation of labeled probes for fluorescence in situ hybridization (FISH) and related spatial nucleic acid mapping studies. Lab teams incorporate Cy3.5 into oligonucleotide probes to visualize the presence and distribution of specific nucleic acid sequences within fixed samples, enabling researchers to correlate labeled targets with cellular or tissue context using standard fluorescence microscopy filter sets appropriate for Cy3.5 emission.

3. qPCR and Nucleic Acid Assay Development

Cy3.5 phosphoramidite is commonly used in assay development to generate fluorescently labeled oligonucleotide components for nucleic acid amplification and real-time fluorescence monitoring formats. Molecular biology groups incorporate Cy3.5 into primers or probe strands to produce fluorescence reagents for method optimization, assay chemistry screening, and platform transfer to instruments that support Cy3.5-compatible excitation/emission detection.

4. Sequencing And Fragment Tracing

Cy3.5 phosphoramidite is applied to produce labeled oligonucleotides for fluorescence-based nucleic acid analysis and fragment tracing experiments. Researchers use Cy3.5-labeled strands as fluorescent tags to follow strand identity, hybridization behavior, or separation outcomes in analytical workflows where a cyanine dye label provides strong optical contrast for downstream imaging or fluorescence measurement.