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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.

Overview

ISO 9001:2015 / ISO 13485:2016 45+ Years of Expertise U.S.A. Facilities-Texas GLP/GMP-Aligned RUO → GMP-like documentation Dye-balanced multiplexing Microgram → multi-gram scale

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.

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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Why Choose Bio-Synthesis

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