BHQ-3 amine | CAS 1661064-89-6

Name: BHQ-3 amine
Brand: BOC Sciences
Rating: 5 (1 reviews)

Catalog Number	A20-0004
Category	Black Hole Quencher (BHQ)
Molecular Formula	C32H36N7+
Molecular Weight	518.69

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Product Introduction

BHQ-3 amine is a dark quencher commonly used in the range 550-650 nm and is most effective in quenching fluorophores such as TAMRA, ROX, Cyanine-3, Cy3, Cy3.5™ and Red 640.

Chemical Information
Application

Chemical Information

Related CAS	871240-94-7 (BHQ-3 NHS) 1338332-66-3 (BHQ-3 acid)
Synonyms	Black Hole Quencher-3 amine; 3-((4-((3-Aminopropyl)(methyl)amino)phenyl)diazenyl)-7-(diethylamino)-5-phenylphenazin-5-ium
Purity	95% by HPLC
IUPAC Name	N'-[4-[[8-(diethylamino)-10-phenylphenazin-10-ium-2-yl]diazenyl]phenyl]-N'-methylpropane-1,3-diamine
SMILES	CCN(CC)C1=CC2=[N+](C3=C(C=CC(=C3)N=NC4=CC=C(C=C4)N(C)CCCN)N=C2C=C1)C5=CC=CC=C5
InChI	InChI=1S/C32H36N7/c1-4-38(5-2)28-17-19-30-32(23-28)39(27-10-7-6-8-11-27)31-22-25(14-18-29(31)34-30)36-35-24-12-15-26(16-13-24)37(3)21-9-20-33/h6-8,10-19,22-23H,4-5,9,20-21,33H2,1-3H3/q+1
InChIKey	NECUSXWMLLFPOX-UHFFFAOYSA-N

Application

BHQ-3 amine is an amine-functionalized fluorescence quencher designed for constructing fluorescence signal-suppression systems in bioconjugation workflows. As a quencher reagent, it is commonly used to reduce background fluorescence and enable distance-dependent quenching in labeled oligonucleotides and FRET-like assay formats, where the quencher is chemically linked through its reactive amine handle. This functionality supports reagent development for nucleic acid assays, molecular beacons, and other fluorescence readouts that require controlled on/off signaling.

1. Molecular Beacon Probes

BHQ-3 amine is used to build molecular beacon oligonucleotides for fluorescence-based nucleic acid detection, where quencher placement suppresses donor emission until hybridization-driven conformational changes separate the fluorophore and quencher. Researchers in genomics and assay development teams incorporate the amine handle for conjugation to labeled strands or for coupling into custom beacon architectures used in plate-based fluorescence measurements and real-time monitoring workflows.

2. FRET Signal Suppression Assays

BHQ-3 amine supports FRET assay development in chemical biology and screening formats by providing a convenient quencher attachment point for donor-acceptor proximity control. In donor-quencher labeled constructs, the amine-functional quencher enables stable conjugate preparation for monitoring binding or reaction progress through fluorescence recovery or emission changes, including assay designs that rely on robust background suppression during incubation and washing steps.

3. Oligonucleotide Conjugation Platforms

BHQ-3 amine is frequently used as a building block for quencher-functional oligonucleotide conjugates, including custom probe sets where the quencher must be positioned reproducibly within a sequence context. Molecular biology groups and diagnostic reagent developers use the amine functionality to couple BHQ-3 into oligo workflows that support multiplexing strategies, standardized probe libraries, and fluorescence readouts compatible with common microplate and fluorescence imaging instrumentation.

4. Quencher-Labeled Bioconjugates

BHQ-3 amine also serves as a quencher component for broader bioconjugation projects that require fluorescence turn-off behavior in labeled biomolecule constructs. Chemical biology teams use the amine handle to integrate the quencher into peptide or polymer conjugates used as signal-control reagents in fluorescence assays, where quencher placement helps manage background during incubation and enables readout through fluorophore dequenching under experimentally defined conditions.