Description

2-[5-[1,3-Dihydro-1-[3-(4-methoxytriphenylmethoxy)propyl]-3,3-dimethyl-2H-indol-2-ylidene]-1,3-pentadien-1-yl]-1-[3-[N,N-diisopropylamino(2-cyanoethoxy)phosphinoxy]propyl]-3,3-dimethyl-3H-indolium is a specialized cyanine dye derivative, a key intermediate in the synthesis of oligonucleotide labeling reagents. Its primary value lies in its role as a phosphoramidite monomer for the automated solid-phase synthesis of fluorescently tagged DNA and RNA probes. This high-purity compound is essential for researchers and manufacturers in the molecular diagnostics, genomics, and biotechnology sectors who require reliable, high-performance reagents for sensitive detection applications.

Application

• Fluorescent Probe Synthesis: As a critical phosphoramidite building block for the automated synthesis of oligonucleotides labeled with cyanine dyes.
• Molecular Diagnostics: Manufacture of probes for fluorescence in situ hybridization (FISH), real-time PCR (qPCR), and microarray technologies.
• Genomic Research: Production of labeled nucleotides and primers for next-generation sequencing (NGS), SNP detection, and gene expression analysis.
• Bioconjugation: Intermediate for creating dye-labeled antibodies, peptides, or other biomolecules for imaging and detection.
• Pharmaceutical R&D: Development of diagnostic kits and therapeutic oligonucleotides requiring precise fluorescent tagging.

Basic Information

Product Name	2-[5-[1,3-Dihydro-1-[3-(4-methoxytriphenylmethoxy)propyl]-3,3-dimethyl-2H-indol-2-ylidene]-1,3-pentadien-1-yl]-1-[3-[N,N-diisopropylamino(2-cyanoethoxy)phosphinoxy]propyl]-3,3-dimethyl-3H-indolium
CAS No.	351186-76-0
Molecular Formula	C61H75N4O5P
Molecular Weight	975.24 g/mol
Synonyms	Cy5 Phosphoramidite; Cyanine 5 Phosphoramidite; 5-[1,3-Dihydro-3,3-dimethyl-1-(3-{[4-methoxytriphenylmethyl]oxy}propyl)-2H-indol-2-ylidene]-1,3-pentadien-1-yl]-3-[3-({[2-cyanoethoxy)(diisopropylamino)phosphino]oxy}propyl)-3,3-dimethyl-3H-indolium; Cy5-dye phosphoramidite; Cy5 CPG precursor; Fluorescent dye phosphoramidite monomer; Cy5-oligonucleotide synthesis reagent
EINECS	Contact for details

Quality Control

This high-value biochemical intermediate is manufactured under strict quality control protocols to ensure batch-to-batch consistency and optimal performance in oligonucleotide synthesis. Our rigorous testing includes HPLC for purity, NMR for structural confirmation, and moisture analysis. A comprehensive Certificate of Analysis (COA) detailing identity, purity (typically >95%), and impurity profile is provided with each shipment to support your quality assurance and regulatory documentation.

Storage

Preserve in a tightly closed container, protected from light. Store desiccated at -20°C or below under an inert atmosphere (argon or nitrogen) to maximize stability and shelf life. Allow the sealed vial to equilibrate to room temperature before opening to prevent moisture condensation.

Specification

Item	Specification
Appearance	Blue to dark blue solid or film
Identification (HPLC)	Conforms to reference standard
Identification (NMR)	Conforms to structure
Purity (HPLC)	≥ 95.0%
Water Content (KF)	≤ 1.0%
Solubility	Soluble in anhydrous acetonitrile, DCM

Note: Specifications can be tailored. Please contact us for the detailed technical data sheet of a specific grade.