BHQ-2-dT | CAS 1415097-34-5

Name: BHQ-2-dT
Brand: BOC Sciences
Rating: 5 (1 reviews)

Catalog Number	A20-0012
Category	Black Hole Quencher (BHQ)
Molecular Formula	C73H87N12O15P
Molecular Weight	1403.53

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Product Introduction

BHQ-2-dT plays a critical role in propelling PCR probes and hybridization assays to new heights of detection, this modified nucleoside serves as a beacon for identifying viral pathogens, genetic diseases, and cancer biomarkers. With its distinctive fluorescent abilities, molecular matching is taken to the next level of precision and accuracy, boosting sensitivity like never before.

Chemical Information
Product Specification
Application

Chemical Information

Synonyms	HCQ-2-dT Phosphoramidite; BHQ-2-dT CE Phosphoramidite; 5'-Dimethoxytrityloxy-5-[(N-4''-carboxyethyl-4''-(N-ethyl)-4'-(4-Nitro-phenyldiazo)-2'-methoxy-5'-methoxy-azobenzene)-aminohexyl-3-acrylimido]-2'-deoxyUridine-3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite; BHQ-2-dT Phosphoramidite; BHQ-2-dT Amidite
Purity	≥95%
IUPAC Name	2-[4-[[2,5-dimethoxy-4-[(4-nitrophenyl)diazenyl]phenyl]diazenyl]-N-ethylanilino]ethyl N-[6-[[(E)-3-[1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]prop-2-enoyl]amino]hexyl]carbamate
SMILES	N#CCCOP(OC1CC(OC1COC(C=2C=CC=CC2)(C3=CC=C(OC)C=C3)C4=CC=C(OC)C=C4)N5C=C(C=CC(=O)NCCCCCCNC(=O)OCCN(C6=CC=C(N=NC7=CC(OC)=C(N=NC8=CC=C(C=C8)N(=O)=O)C=C7OC)C=C6)CC)C(=O)NC5=O)N(C(C)C)C(C)C
InChI	InChI=1S/C73H87N12O15P/c1-10-82(58-30-26-56(27-31-58)78-80-62-45-65(95-9)63(46-64(62)94-8)81-79-57-28-32-59(33-29-57)85(90)91)42-44-96-72(89)76-41-17-12-11-16-40-75-68(86)38-21-52-48-83(71(88)77-70(52)87)69-47-66(100-101(98-43-18-39-74)84(50(2)3)51(4)5)67(99-69)49-97-73(53-19-14-13-15-20-53,54-22-34-60(92-6)35-23-54)55-24-36-61(93-7)37-25-55/h13-15,19-38,45-46,48,50-51,66-67,69H,10-12,16-18,40-44,47,49H2,1-9H3,(H,75,86)(H,76,89)(H,77,87,88)/t66-,67+,69+,101?/m0/s1
InChIKey	QCQIEDGINBSSOG-GOQRVKJUSA-N
Solubility	Soluble in Anhydrous Acetonitrile/Dichloromethane 1:3 (v/v)
Appearance	Blue Solid

Product Specification

Storage

Store at -20 °C

Application

BHQ-2-dT is a fluorescence quencher oligonucleotide building block designed for incorporation into DNA-based fluorescent assays. It combines the BHQ-2 quencher scaffold with a deoxythymidine (dT) handle, enabling straightforward placement of quenching functionality within probes where distance-dependent suppression of fluorophore emission is required. This reagent is commonly used to control background fluorescence in nucleic acid hybridization formats and related fluorescence readouts.

1. Molecular Beacon Quenching

BHQ-2-dT is used in molecular beacon probe design to suppress fluorescence in the unhybridized state and enable target-dependent fluorescence recovery upon hybridization. Researchers incorporate the quencher at a defined position within the beacon stem or loop to tune the proximity between the fluorophore and quencher, supporting robust signal-on behavior in fluorescence microscopy and plate-based nucleic acid assays. This format is widely used in nucleic acid detection workflows where probe conformational changes regulate the optical output.

2. Real-Time PCR Probe Suppression

BHQ-2-dT serves as a quencher component for fluorescence-based real-time PCR and related amplification assays that rely on oligonucleotide reporters. By integrating the quencher into the probe sequence (through the dT handle), assay developers can position the quencher near the reporter dye to minimize background emission prior to target-dependent processing. The result is a fluorescence readout that is governed by probe cleavage or separation, supporting controlled signal generation during nucleic acid amplification experiments.

3. Oligonucleotide Hybridization Probes

BHQ-2-dT is applied in fluorescence hybridization probes for monitoring nucleic acid binding events, including probe-based genotyping and sequence-specific detection platforms. Incorporating the quencher within the oligonucleotide allows researchers to manage residual fluorescence from the reporter dye and reduce nonspecific signal arising from incomplete separation or transient interactions. This quencher building block is therefore used when precise quencher placement within DNA probes is important for reliable fluorescence reporting in nucleic acid analysis workflows.

4. FRET-Based Nucleic Acid Assays

BHQ-2-dT is also used in FRET-style nucleic acid assay architectures where a fluorophore-quencher pair provides distance-dependent signal control. Probe designers incorporate the quencher into DNA constructs to regulate energy transfer efficiency and thereby modulate emission output in response to hybridization or conformational changes. This approach is particularly useful for fluorescence readouts that benefit from engineered intramolecular spacing within oligonucleotide probes.