Eclipse^® Quencher Phosphoramidite | CAS 916753-64-5

Name: Eclipse® Quencher Phosphoramidite
Brand: BOC Sciences
Rating: 5 (1 reviews)

Catalog Number	A20-0034
Category	Other Quencher
Molecular Formula	C52H61CIN7O8P
Molecular Weight	978.51

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Product Introduction

Eclipse® Quencher Phosphoramidite is a paramount constituent employed in the fabrication of oligonucleotides, emerges as a pivotal ensemble. Its functions lie in its ability to dampen the fluorescence signal within nucleotide probes, consequently facilitating meticulous identification of distinctive DNA or RNA sequences. It substantiates its worth by contributing to the proficiency of diagnostic assays and molecular biology research, consequently augmenting the detection and scrutiny of assorted maladies and genetic irregularities.

Chemical Information
Product Specification
Application

Chemical Information

Synonyms	EclipseQ Phosphoramidite; Eclipse Quencher Phosphoramidite; 4-N-methyl-N-(4'-nitro-2'-chloroazobenzen-4-yl)-aminobutanamido-1-(2-O-dimethoxytrityloxymethyl)-pyrrolidin-4-yl-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramdite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, (3R,5S)-5-[[bis(4-methoxyphenyl)phenylmethoxy]methyl]-1-[4-[[4-[2-(2-chloro-4-nitrophenyl)diazenyl]phenyl]methylamino]-1-oxobutyl]-3-pyrrolidinyl 2-cyanoethyl ester, rel-; rel-(3R,5S)-5-[[Bis(4-methoxyphenyl)phenylmethoxy]methyl]-1-[4-[[4-[2-(2-chloro-4-nitrophenyl)diazenyl]phenyl]methylamino]-1-oxobutyl]-3-pyrrolidinyl 2-cyanoethyl N,N-bis(1-methylethyl)phosphoramidite; 5'-Eclipse Amidite
IUPAC Name	rel-(3R,5S)-5-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-1-(4-((4-((2-chloro-4-nitrophenyl)diazenyl)phenyl)(methyl)amino)butanoyl)pyrrolidin-3-yl (2-cyanoethyl) diisopropylphosphoramidite
SMILES	N#CCCOP(OC1CN(C(=O)CCCN(C2=CC=C(N=NC3=CC=C(C=C3Cl)N(=O)=O)C=C2)C)C(COC(C=4C=CC=CC4)(C5=CC=C(OC)C=C5)C6=CC=C(OC)C=C6)C1)N(C(C)C)C(C)C
InChI	InChI=1/C52H61ClN7O8P/c1-37(2)59(38(3)4)69(67-32-12-30-54)68-48-33-45(36-66-52(39-13-9-8-10-14-39,40-16-25-46(64-6)26-17-40)41-18-27-47(65-7)28-19-41)58(35-48)51(61)15-11-31-57(5)43-22-20-42(21-23-43)55-56-50-29-24-44(60(62)63)34-49(50)53/h8-10,13-14,16-29,34,37-38,45,48H,11-12,15,31-33,35-36H2,1-7H3/t45-,48+,69?/s2
InChIKey	CXNVOZCFZYENEQ-SOWLJRCBNA-N
Appearance	Black solid
Boiling Point	962.2±65.0 °C (Predicted)

Product Specification

Storage

Store at -20°C

Application

Eclipse® Quencher Phosphoramidite is a quencher phosphoramidite designed for incorporation into oligonucleotides during solid-phase synthesis. As a fluorescence signal-suppression component, it is used to minimize background from fluorophores in proximity-based nucleic acid formats and distance-dependent fluorescence control systems. Its phosphoramidite functionality enables straightforward placement at defined positions within DNA or RNA probes, molecular beacons, and related hybridization or amplification constructs.

1. Molecular Beacon Signal Control

Eclipse® Quencher Phosphoramidite is frequently used by nucleic acid assay developers to build molecular beacons where fluorescence is suppressed in the unhybridized state and recovered upon target binding. Researchers place the quencher at a defined location relative to the beacon fluorophore to support distance-dependent quenching behavior, enabling clean readouts in fluorescence microplate assays and real-time fluorescence monitoring workflows. This positioning control is particularly valuable when optimizing beacon design for different probe lengths and hybridization architectures.

2. Real-Time PCR Probe Design

Eclipse® Quencher Phosphoramidite supports fluorescence-based qPCR and related nucleic acid amplification assay development by enabling quencher placement within sequence-specific oligonucleotide probes. In probe-based chemistries where a reporter fluorophore is held near a quencher until an event during amplification separates or alters their effective proximity, the phosphoramidite format allows consistent construction of probe sets for assay screening and multiplexing development. Molecular biology teams use the reagent to streamline probe synthesis for instrument-compatible fluorescence detection schemes.

3. FRET-Based Oligonucleotide Constructs

Eclipse® Quencher Phosphoramidite is used in FRET-oriented oligonucleotide designs where a quencher is positioned to tune fluorescence output through proximity effects between donor and acceptor components. Fluorescence technology groups and molecular imaging developers incorporate the quencher into custom nucleic acid scaffolds to create distance-sensitive reporters for hybridization studies, binding kinetics experiments, and assay development requiring controlled background suppression. Defined incorporation supports reproducible construct architecture across probe libraries.

4. Nucleic Acid Hybridization Probes

Eclipse® Quencher Phosphoramidite is applied to hybridization probe development for fluorescence readouts in research workflows that require low background from unbound probe. By embedding the quencher within the oligonucleotide, teams can engineer probes that remain quenched in solution and exhibit fluorescence changes upon target association, supporting endpoint fluorescence measurements and imaging-compatible nucleic acid analyses. This approach is commonly used in assay prototyping where probe placement and architecture strongly influence signal behavior.