Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite | CAS 289712-99-8

Name: Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite
Brand: BOC Sciences
Rating: 5 (1 reviews)

Catalog Number	A01-0019
Category	Fluorescent Proteins & Nucleotides
Molecular Formula	C79H89N6O17P
Molecular Weight	1425.57

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Product Introduction

Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite is a specialized nucleoside analog that incorporates a fluorescein moiety, known for its xanthene-based chromophore, into oligonucleotide synthesis. This compound features a 3'-CE phosphoramidite group, facilitating its integration into DNA or RNA strands during automated synthesis, thereby enabling the introduction of fluorescence for bioimaging and molecular tracking applications. Its structural design supports efficient energy transfer and fluorescence emission, making it suitable for use in fluorescence resonance energy transfer (FRET) studies and other fluorescence-based assays.

Chemical Information
Product Specification
Application

Chemical Information

Related CAS	1194507-30-6 (6-Fluorescein dT phosphoramidite)
Synonyms	Propanoic acid, 2,2-dimethyl-, 5-[[[6-[[3-[5-[5-O-[bis(4-methoxyphenyl)phenylmethyl]-3-O-[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]-2-deoxy-β-D-erythro-pentofuranosyl]-3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl]-1-oxo-2-propenyl]amino]hexyl]amino]carbonyl]-3-oxospiro[isobenzofuran-1(3H),9'-[9H]xanthene]-3',6'-diyl ester; Fluorescein-deoxy-pU Phosphoramidite; Fluorescein 5-methyl-2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite; 6-Fluorescein 5-methyl-2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite
Purity	≥95%
IUPAC Name	[5-[6-[3-[5-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyoxolan-2-yl]-2,4-dioxopyrimidin-1-yl]prop-2-enoylamino]hexylcarbamoyl]-6'-(2,2-dimethylpropanoyloxy)-3-oxospiro[2-benzofuran-1,9'-xanthene]-3'-yl] 2,2-dimethylpropanoate
SMILES	CC(C)N(C(C)C)P(OCCC#N)OC1CC(OC1COC(C2=CC=CC=C2)(C3=CC=C(C=C3)OC)C4=CC=C(C=C4)OC)C5=CN(C(=O)NC5=O)C=CC(=O)NCCCCCCNC(=O)C6=CC7=C(C=C6)C8(C9=C(C=C(C=C9)OC(=O)C(C)(C)C)OC1=C8C=CC(=C1)OC(=O)C(C)(C)C)OC7=O
InChI	InChI=1S/C79H89N6O17P/c1-49(2)85(50(3)4)103(96-42-20-38-80)102-67-46-64(99-68(67)48-95-78(52-21-16-15-17-22-52,53-24-28-55(93-11)29-25-53)54-26-30-56(94-12)31-27-54)60-47-84(75(92)83-71(60)88)41-37-69(86)81-39-18-13-14-19-40-82-70(87)51-23-34-61-59(43-51)72(89)101-79(61)62-35-32-57(97-73(90)76(5,6)7)44-65(62)100-66-45-58(33-36-63(66)79)98-74(91)77(8,9)10/h15-17,21-37,41,43-45,47,49-50,64,67-68H,13-14,18-20,39-40,42,46,48H2,1-12H3,(H,81,86)(H,82,87)(H,83,88,92)/t64-,67+,68-,103?/m1/s1
InChIKey	WHVKLEUMJJAXRZ-PCLSEREPSA-N
Appearance	Off-white powder

Product Specification

Storage

Store at 2-8 °C

Application

Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite is a fluorescein-modified nucleoside phosphoramidite designed for incorporation into oligonucleotides during solid-phase DNA/RNA synthesis. The fluorescein reporter enables fluorescence-based readouts in nucleic acid workflows, while the DMT-protected functionality and phosphoramidite format support standard automated synthesis and downstream conjugate handling. This reagent is commonly used when a site-specific fluorescein tag is required for probe construction, hybridization assays, or fluorescence imaging of nucleic acid structures.

1. Fluorescent Oligonucleotide Probes

Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite is used to generate fluorescent oligonucleotide probes where a defined fluorescein label is positioned within an RNA or DNA sequence context. Researchers incorporate this phosphoramidite into custom probes for hybridization-based detection formats, including strand-displacement and nucleic acid binding studies, where fluorescence readout is driven by probe presence and hybridization state. The nucleoside-based design supports site-specific labeling strategies that are valuable for comparing probe variants with the same sequence backbone but different label positions.

2. Molecular Beacons And Hybridization Assays

Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite is well suited for constructing fluorescence-reporting nucleic acid probes such as molecular beacons and other hybridization-responsive systems. By placing fluorescein into the beacon or probe strand during synthesis, users can monitor target-dependent changes in fluorescence during annealing and dissociation workflows. This approach is frequently adopted in assay development labs that need sequence-defined fluorescent reporters for real-time monitoring of nucleic acid interactions using plate readers or fluorescence-capable imaging instruments.

3. Fluorescence In Situ Hybridization Probes

Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite supports the preparation of fluorescent ISH probes for microscopy-based localization of nucleic acid targets in fixed sample workflows. Site-specific incorporation of fluorescein into the probe strand helps standardize labeling across probe batches, which is particularly useful when comparing spatial patterns across experimental conditions. Imaging teams commonly use fluorescein-labeled oligonucleotides to visualize target distribution in cell culture formats and tissue sections with fluorescence microscopy systems configured for fluorescein excitation and emission.

4. Nucleic Acid Tracing In Bioanalytical Workflows

Fluorescein 2'-deoxy-5'-O-DMT-pseudouridine 3'-CE phosphoramidite is also employed to build fluorescently tagged nucleic acid reagents for tracing and quantification in bioanalytical experiments. After incorporation into defined oligonucleotide constructs, fluorescein enables monitoring of labeled strands in electrophoretic or chromatography-adjacent workflows and supports downstream fluorescence readout for binding or processing studies. This reagent is a practical choice for teams that require a chemically defined, sequence-integrated fluorescein label rather than post-labeling dyes that can introduce heterogeneous substitution.