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.
Fig 1. Molecular structures of the cyanine dye phosphoramidites. (Kretschy et al., 2014)
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.
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 (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.
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.
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 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.
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.
Dye phosphoramidites are used to introduce fluorescent dyes into DNA or RNA during oligonucleotide synthesis, enabling detection, sequence analysis, and multiplexed assays in genome research and molecular diagnostics.
Common types include fluorescein, SIMA, cyanine (Cy) dyes, JOE, and TAMRA phosphoramidites, each offering unique spectral properties suitable for different fluorescent labeling applications.
By customizing the dye type, position, or density of labeling, multiple targets can be simultaneously detected with distinct fluorescent signals, improving throughput and data diversity in quantitative assays.
Yes, dye phosphoramidites are typically incorporated alongside standard nucleotides during synthesis to label specific positions on oligonucleotides without affecting sequence integrity.
Each batch undergoes rigorous quality control, including HPLC, NMR, and moisture analysis, ensuring high purity, reproducibility, and minimal reactive impurities that could interfere with oligonucleotide synthesis.
BOC RNA offers flexible solutions to introduce dyes at desired positions or densities, allowing researchers to tailor oligonucleotide labeling for specialized detection strategies or complex assay designs.
Reference
| Catalog | CAS Number | Product Name | Molecular Formula | Molecular Weight | Price |
| BRP-02227 | 147566-42-5 | 5'-(5-Fluorescein) phosphoramidite | C46H58N3O10P | 843.94 | Inquiry |
| BRP-02228 | 1360547-55-2 | 6-Hexachloro-Fluorescein Phosphoramidite | C46H52N3O10Cl6P | 1050.61 | Inquiry |
| BRP-02229 | 288631-58-3 | 5'-Dabcyl Phosphoramidite | C30H45N6O3P | 568.69 | Inquiry |
| BRP-02230 | 1411797-05-1 | 6-SIMA phosphoramidite | C58H64Cl2N3O10P | 1065.02 | Inquiry |
| BRP-02231 | 289712-99-8 | Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite | C79H89N6O17P | 1425.57 | Inquiry |
| BRP-02232 | 5-SIMA phosphoramidite | C58H64Cl2N3O10P | 1065.02 | Inquiry | |
| BRP-02233 | 877049-90-6 | 6-Tetrachloro-Fluorescein Phosphoramidite | C46H54N3O10Cl4P | 981.72 | Inquiry |
| BRP-02234 | 718594-66-2 | Cyanine 3 Phosphoramidite | C58H70N4O4P | 918.17 | Inquiry |
| BRP-02235 | 351186-76-0 | Cyanine 5 Phosphoramidite | C60H72N4O4P | 944.21 | Inquiry |
| BRP-02236 | 916753-58-7 | Cyanine 5.5 Phosphoramidite | C68H76IN4O4P | 1171.24 | Inquiry |
| BRP-02237 | 6-JOE phosphoramidite | C48H60Cl2N3O12P | 972.88 | Inquiry | |
| BRP-02238 | 1266091-48-8 | TAMRA-dT phosphoramidite | C73H83N8O13P | 1311.48 | Inquiry |
| BRP-02239 | 6-TAMRA phosphoramidite | C66H77N6O10P | 1145.35 | Inquiry | |
| BRP-02240 | 204697-37-0 | 6-Fluorescein phosphoramidite | C46H58N3O10P | 843.94 | Inquiry |
