5'-BBQ-650^®-CE Phosphoramidite | CAS 1027512-25-9

Name: 5'-BBQ-650®-CE Phosphoramidite
Brand: BOC Sciences
Rating: 5 (1 reviews)

Catalog Number	A20-0036
Category	Other Quencher
Molecular Formula	C41H55N8O7P
Molecular Weight	802.90

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Product Introduction

5'-BBQ-650®-CE Phosphoramidite is a highly complex and exceedingly versatile chemical reagent that boasts an impressive array of applications in the realms of oligonucleotide synthesis, bioimaging, diagnostics, gene expression and genetic disorders. Infused with a fluorescent marker, this stunningly sophisticated product is capable of facilitating easy detection and in-depth analysis of a wide range of biological phenomena.

Chemical Information
Product Specification
Application

Chemical Information

Synonyms	5'-BBQ-650 CEP; 9-[4-Nitro-2',5'-dimethoxy-azobenz-4'-yl)-diazo]-julolidine-8]-O-hexyl-[2-cyanoethyl-(N,N-diisopropyl)]-phosphoramidite; 5'-BBQ-650 CE-Phosphoramidite; Phosphoramidous acid, N,N-bis(1-methylethyl)-, 2-cyanoethyl 6-[[9-[2-[2,5-dimethoxy-4-[2-(4-nitrophenyl)diazenyl]phenyl]diazenyl]-2,3,6,7-tetrahydro-1H,5H-benzo[ij]quinolizin-8-yl]oxy]hexyl ester; 2-Cyanoethyl 6-[[9-[2-[2,5-dimethoxy-4-[2-(4-nitrophenyl)diazenyl]phenyl]diazenyl]-2,3,6,7-tetrahydro-1H,5H-benzo[ij]quinolizin-8-yl]oxy]hexyl N,N-bis(1-methylethyl)phosphoramidite
IUPAC Name	3-[6-[[7-[[2,5-dimethoxy-4-[(4-nitrophenyl)diazenyl]phenyl]diazenyl]-1-azatricyclo[7.3.1.05,13]trideca-5(13),6,8-trien-6-yl]oxy]hexoxy-[di(propan-2-yl)amino]phosphanyl]oxypropanenitrile
SMILES	CC(C)N(C(C)C)P(OCCCCCCOC1=C(C=C2CCCN3C2=C1CCC3)N=NC4=C(C=C(C(=C4)OC)N=NC5=CC=C(C=C5)[N+](=O)[O-])OC)OCCC#N
InChI	InChI=1S/C41H55N8O7P/c1-29(2)48(30(3)4)57(56-25-13-20-42)55-24-10-8-7-9-23-54-41-34-15-12-22-47-21-11-14-31(40(34)47)26-37(41)46-45-36-28-38(52-5)35(27-39(36)53-6)44-43-32-16-18-33(19-17-32)49(50)51/h16-19,26-30H,7-15,21-25H2,1-6H3
InChIKey	QDVVHDWLKVWLFU-UHFFFAOYSA-N

Product Specification

Storage

Store at -20°C

Application

5'-BBQ-650®-CE Phosphoramidite is a fluorescence quencher phosphoramidite designed for incorporation into oligonucleotides during solid-phase DNA/RNA synthesis. Its long-wavelength absorption profile supports quenching in red-emitting fluorescence systems, enabling distance-dependent suppression of fluorophore signals in nucleic acid probe formats. Researchers use this quencher building block to construct molecular beacons, hybridization probes, and related fluorescence-controlled assays where background reduction and target-dependent fluorescence recovery are required.

1. Molecular Beacons Construction

5'-BBQ-650®-CE Phosphoramidite is used to build molecular beacons for fluorescence readouts in nucleic acid hybridization studies. In these designs, the quencher is positioned within the oligonucleotide so that fluorophore emission is suppressed in the unhybridized state and restored upon target binding, supporting real-time monitoring of nucleic acid interactions in solution or instrument-based fluorescence workflows. This quencher phosphoramidite format is particularly convenient for researchers who want to specify quencher placement directly in the oligo sequence during synthesis rather than relying on post-synthetic conjugation.

2. Real-Time PCR Probe Design

5'-BBQ-650®-CE Phosphoramidite supports the development of fluorescence quenching architectures used in qPCR and related nucleic acid amplification assays. Probe designs that employ a fluorophore/quencher pair benefit from controlled signal suppression until amplification-dependent strand displacement or hybridization events occur, which helps streamline assay workflows that rely on continuous fluorescence monitoring. Oligonucleotide chemists and assay developers commonly choose quencher phosphoramidite building blocks to integrate the quencher at defined positions for consistent probe performance across synthesis lots.

3. Oligonucleotide Hybridization Assays

5'-BBQ-650®-CE Phosphoramidite is applied in fluorescence hybridization probes used for detecting complementary nucleic acid sequences in research assays and analytical method development. By integrating the quencher into the probe strand, teams can engineer probe architectures that minimize off-target fluorescence from unbound probes while enabling a measurable fluorescence change when target duplex formation occurs. This approach is frequently used in nucleic acid profiling, workflow development for diagnostic reagent research, and multiplex assay prototyping where probe geometry and quencher placement are critical to assay behavior.

4. FRET-Based Nucleic Acid Sensors

5'-BBQ-650®-CE Phosphoramidite is leveraged in FRET-style nucleic acid sensor constructs that require an efficient quencher partner for a red-emitting donor fluorophore. Researchers incorporate the quencher into oligonucleotide scaffolds to create proximity-dependent fluorescence control, enabling signal modulation tied to hybridization, strand displacement, or conformational changes. In fluorescence instrumentation workflows such as plate-based readers and gel-free optical assays, this quencher building block helps teams design nucleic acid sensors with defined fluorophore-quencher spacing encoded directly in the synthesized sequence.