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Fluorescent & Hybridization Probes

From qPCR to MERFISH—Probes Built for Precision, Sensitivity & Scale

Choose from dual-labeled qPCR probes, molecular beacons, FRET designs, MGB and Affinity-Enhanced chemistries, PNA FISH, branched DNA (bDNA) amplifiers, and complete MERFISH encoding/readout sets. We provide fast design support, RUO → GMP-like manufacturing, and full QC.

Speak to a Scientist Explore Probe Types
RUO → GMP-like documentation
Dye-balanced multiplexing
Microgram → multi-gram scale

Overview

We manufacture custom probes for qPCR, ISH/FISH, and spatial transcriptomics. Every project can be tuned for Tm, length, mismatch discrimination, dye/quencher pairing, and signal-to-noise. Options include dark quenchers, ratiometric FRET, minor groove binders (MGB), LNA/BNA/cEt upgrades, PNA backbones, disulfide-cleavable linkers for release, and dye balancing for multi-round imaging.

At-a-glance Cards Design Considerations qPCR (Hydrolysis) Molecular Beacons FRET MGB Affinity-Enhanced PNA FISH bDNA MERFISH FAQ

Probe Types — At a Glance

Nine core offerings, presented as quick-scan cards. Click in to jump to details.

qPCR • TaqMan®-style
Dual-Labeled qPCR (Hydrolysis) Probes

5′-reporter / 3′-quencher probes for hydrolysis assays with high S/N, fast cycling and robust multiplexing.
Learn more

Design Choices
qPCR Probe Options

Reporter/quencher libraries, internal quenchers, short-amplicon tuning, and multiplex kits.
See options

Minor Groove Binder
MGB (MBG) Probes

MGB tail elevates Tm for short probes, improving SNP specificity in qPCR.
Why MGB

Hairpin • Wash-Free
Molecular Beacons

Stem-loop probes that fluoresce only upon hybridization—great for multiplex & live-cell.
Beacon guide

Ratiometric
FRET Probes

Donor–acceptor pairs for distance-dependent, drift-resistant readouts - ideal for low-copy transcripts in tissue
FRET formats

MERFISH • High-plex
MERFISH Encoding & Readout Probes

Error-robust barcodes and dye-balanced readouts for 10–10,000+ targets.
MERFISH details

Signal Amplification
bDNA Amplifier Probes

Branched DNA trees deliver high brightness at low background.
Amplifier sets

High Specificity
PNA FISH Probes

Peptide-nucleic acid backbones enable strong, salt-tolerant binding for rapid ID.
PNA in FISH

LNA • BNA • cEt
Affinity-Enhanced Probes

Locked/bridged nucleic acids and 2′-mods shorten length and heighten discrimination.
Upgrade paths

Technology & Design Considerations
  • Tm & specificity: Adjust with MGB or LNA/BNA/cEt for short probes and SNP discrimination.
  • Signal strategy: Hydrolysis (qPCR), hairpin switching (beacons), or ratiometric readouts (FRET).
  • Backbone choice: DNA/RNA for routine use; PNA for salt-tolerant, high-affinity FISH; LNA mixes for tighter binding.
  • Imaging workflows: Dye compatibility, photostability, and batch-to-batch uniformity for multi-round sets (MERFISH, cyclic FISH).
  • Amplification: bDNA trees raise brightness while limiting background—ideal for low-copy targets.
  • Scale & QC: HPLC or PAGE purification, MS verification, endotoxin testing (as requested), and ISO-aligned batch records.
Popular Dye/Quencher Choices

FAM • HEX • VIC • TET • ROX • Cy3 • Cy5 • ATTO dyes • Quenchers: BHQ-1/2/3, IAbRQSp/3IABkFQ, QSY series. Ask about dye balancing for multiplex panels.

Tip: For short SNP assays, pair MGB or LNA with a dark quencher for sharp ΔRn.

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FAQ

Keyword-rich answers for quick evaluation and better search visibility.

What’s the difference between dual-labeled qPCR probes and molecular beacons?
Dual-labeled hydrolysis probes are cleaved during extension to release fluorescence; molecular beacons are hairpins that turn on only upon target binding without cleavage. Hydrolysis offers fast cycling and high S/N; beacons excel at wash-free imaging and multiplexing.
When should I choose an MGB or Affinity-Enhanced (LNA/BNA/cEt) probe?
Use MGB or LNA/BNA/cEt to raise Tm for short sequences or SNP assays. These upgrades heighten mismatch penalties, improving specificity in short amplicons or high-GC contexts.
Why use PNA FISH probes?
PNA backbones bind strongly and are less sensitive to ionic strength, enabling rapid hybridization and short, specific probes for microbial ID and resistant alleles.
How do bDNA amplifier probes improve sensitivity?
bDNA preamplifier/amplifier trees recruit multiple labeled probes per target, increasing brightness while maintaining low background—ideal for low-copy transcripts in tissue sections.
What’s special about MERFISH readout probes?
MERFISH relies on error-robust barcoding and balanced dye loads across imaging rounds. We supply encoding backbones and dye-matched readouts with consistent lot-to-lot performance (<10% CV).
Which dye/quencher pairs are best for multiplex qPCR?
Choose spectrally separated dyes (e.g., FAM, HEX/VIC, ROX, Cy5) with dark quenchers (BHQ-1/2/3, IBFQ/QSY). We can balance dye loads to minimize bleed-through across channels.

Why Choose BioSynthesis

Trusted by biotech leaders worldwide for over 45 years of delivering high quality, fast and scalable synthetic biology solutions.

Greetings Researchers,

Please be advised that any information, guidelines, writeups, and oral/video/graphic content on our website are intended solely as general guidelines.
It is the researcher's sole responsibility to conduct thorough research on the designs of the products intended for their experiments before submitting
their designs to Biosynthesis for review of production feasibility.
Thank you for your understanding.

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