Dye Phosphoramidites

Dye Phosphoramidites

CAS: 204697-37-0 Molecular Formula: C46H58N3O10P Molecular Weight: 843.94
CAS: 147566-42-5 Molecular Formula: C45H56N3O10P Molecular Weight: 829.91
Molecular Formula: C58H64Cl2N3O10P Molecular Weight: 1065
Molecular Formula: C58H64Cl2N3O10P Molecular Weight: 1065
Molecular Formula: C66ClH75N4O4P Molecular Weight: 1054.75
Molecular Formula: C68H77IN4O4P Molecular Weight: 1172.24
Molecular Formula: C52H62Cl2N3O12P Molecular Weight: 1021.34
Molecular Formula: C73H83N6O13P Molecular Weight: 870.85
Molecular Formula: C66H77N6O10P Molecular Weight: 1145.3
CAS: 288631-58-3 Molecular Formula: C30H45N6O3P Molecular Weight: 568.69
CAS: 351186-76-0 Molecular Formula: C60H72N4O4P Molecular Weight: 944.21
CAS: 718594-66-2 Molecular Formula: C58H70N4O4P Molecular Weight: 918.17
CAS: 1360547-55-2 Molecular Formula: C46H52N3O10Cl6P Molecular Weight: 1050.61
CAS: 877049-90-6 Molecular Formula: C46H54N3O10Cl4P Molecular Weight: 981.72

Dye phosphoramidites are used by introducing a variety of dye molecules, which in turn exert their effects with various characteristics. We offer products such as fluorescein phosphoramidites, cyanine phosphoramidites, TAMRA phosphoramidites, JOE phosphoramidites, etc. These molecules are used in genome research, molecular diagnostics, and other fields.

Molecular structures of the cyanine dye phosphoramidites.Fig 1. Molecular structures of the cyanine dye phosphoramidites. (Kretschy et al., 2014)

What are Dye Phosphoramidite?

Dye phosphoramidite is a modified nucleotide monomer for DNA synthesis and sequencing, designed for the detection and analysis of DNA sequences. Dye phosphoramidite is a chemical reagent that functions by introducing a fluorescent dye during the synthesis of DNA strands. Dye phosphoramidites are usually used in conjunction with standard nucleotide phosphoramidites to introduce fluorescent dyes at specific locations on the DNA strand. These dyes emit fluorescence at specific wavelengths so that DNA sequences can be detected and analyzed using the appropriate fluorescence detection systems.

Types of Dye Phosphoramidites

  • Fluorescein Phosphoramidites

Fluorescein is one of the common fluorescent dyes. It reacts with strong bases to form fluorescein salts, which are easily soluble in water and have strong green fluorescence, and can make many organisms fluorescent substances. The fluorescein phosphoramidite products we offer are made from 6-carboxyfluorescein derivatives.

  • SIMA Phosphoramidite

SIMA (dichlorodiphenylfluorescein) is an xanthene dye with spectral properties similar to HEX but with higher quantum yield. SIMA phosphoramidites are used in oligonucleotide synthesis to produce fluorescently labeled primers and hybridization probes for quantitative PCR.

  • Cyanine Phosphoramidites

Cy (Cyanine) series fluorescent dyes are a class of synthetic fluorescent dyes characterized by the chemical structure of polymeric hypromellitic bridges. The hypromellitic bridges of Cy dyes are often connected to two nitrogen atoms at the ends of the bridges, and one of the nitrogen atoms is charged positively, so that the Cy dyes form mesoionic compounds with an out-of-region positive charge effect. The introduction of anthocyanins into phosphoramidites enables fluorescent labeling and detection of oligonucleotides.

  • JOE phosphoramidite

The fluorescent dye JOE is a fluorescein derivative containing two chlorine atoms and two methoxy groups. Based on its spectral properties, JOE is intermediate between FAM and lTAMRA/ROX, and this fluorescent quantification is commonly used for multiplexed assays, including detection during DNA sequencing.

  • TAMRA Phosphoramidite

TAMRA is the most commonly used rhodamine dye for oligonucleotide applications. TAMRA phosphoramidite phosphoramidites are used to synthesize oligonucleotides of TAMRA, which in turn are used in genome research, molecular diagnostics and molecular biology.

Quality Control

From material procurement to final quality control and product release is monitored for batch-to-batch reproducibility. The purity of each phosphoramidite batch can be assessed by HPLC, NMR and Karl Fischer determination of moisture. Our tightly controlled manufacturing process helps minimize the level of reactive impurities that can be incorporated into oligonucleotides during synthesis and lead to the accumulation of by-products.

Advantages of BOC Sciences' Dye Phosphoramidites

  • Long-term Availability - Long-term supply to manufacturers and research organizations in a variety of industries to support emerging diagnostic assays.
  • Superior Service - Short response time to orders and customized product offerings.
  • High-quality Products - All products undergo stringent quality control and are guaranteed to be consistent with high purity and efficiency.
  • Flexible Product Solutions - The dyes in dye phosphoramidite can be matched to different fluorescent dyes and the products can be customized according to customer needs (position of dye introduction or density of introduction), this flexibility of dye combination facilitates diversity analysis and multi-pathway detection.


  1. Kretschy N, Somoza M M. Comparison of the sequence-dependent fluorescence of the cyanine dyes Cy3, Cy5, DyLight DY547 and DyLight DY647 on single-stranded DNA[J]. PloS one, 2014, 9(1): e85605.
* Only for research. Not suitable for any diagnostic or therapeutic use.
Inquiry Basket