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qPCR Probes-
Singleplex to High‑plex panels with fast turnaround!

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Custom qPCR Probes

Hydrolysis (TaqMan®‑style) • MGB • LNA‑enhanced • Multiplex

Overview Probe Types Design Guidelines Multiplexing FAQ Contact
ISO 9001:2015 / ISO 13485:2016 45+ Years of Expertise U.S.A. Facilities-Texas GLP/GMP-Aligned

Overview

qPCR probes deliver real‑time, sequence‑specific fluorescence for accurate quantitation. Compared to intercalating dyes, probe‑based assays provide higher specificity, lower background, and robust multiplexing. Bio‑Synthesis designs, manufactures, and QC‑tests custom hydrolysis, MGB, and LNA‑enhanced probes from RUO to GMP.

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At-a-Glance

  • Hydrolysis (TaqMan®‑style) probes with BHQ‑1/2/3 or MGB‑NFQ quenchers
  • MGB and LNA options for shorter, high‑Tm designs and SNP assays
  • Validated dye sets for 2–6+ color multiplex
  • HPLC purification and MS identity confirmation standard
  • Flexible scales: 200 pmol up to multi‑mg (RUO → GMP)

How Hydrolysis Probes Work

Dual‑labeled probes carry a 5′ reporter and a 3′ quencher. During extension, the polymerase’s 5′→3′ exonuclease activity cleaves the probe, physically separating dye and quencher. The resulting fluorescence is proportional to the accumulating amplicon, enabling precise Cq determination.

  • Probe length: 18–30 nt; target Tm ≈ 8–10 °C > primer Tm
  • Placement: within amplicon; avoid extreme 5′/3′ ends
  • Avoid: long homopolymers; G at 5′ reporter end; strong hairpins

Probe Types

Hydrolysis (TaqMan®‑style)

Standard dual‑labeled probes for most assays; broad dye/quencher compatibility and strong performance across cyclers.

  • BHQ‑1/2/3 or TAMRA quenchers
  • General purpose; easy multiplexing

MGB & LNA‑Enhanced

MGB raises Tm to enable shorter probes; LNA increases affinity/specificity in AT‑rich or structured regions and for SNP discrimination.

  • MGB‑NFQ for tight quenching and short designs
  • LNA mix‑ins at difficult positions

Design Guidelines

Core Rules

  • Probe Tm 8–10 °C higher than primers; GC 40–60%
  • Avoid 4+ identical bases; minimize secondary structure
  • Prefer A/T at 5′ reporter end; avoid 5′‑G when possible

Placement

  • Design within 60% central region of amplicon
  • Avoid crossing known SNPs unless intended
  • Keep probe‑primer spacing ≥ 2–3 nt

Dye/Quencher Selection

Channel Reporter Quencher Notes
Green FAM / AF488 BHQ‑1 General purpose
Yellow‑Orange HEX / VIC / JOE / TAMRA BHQ‑1 Multiplex friendly
Red Texas Red / ROX BHQ‑2 Robust on most cyclers
Far‑red Cy5 / AF647 BHQ‑3 Low background, long‑wave
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Multiplex Optimization

  • Channel planning: choose spectrally separated dyes; balance brightness
  • Primer/probe balancing: titrate concentrations to equalize Cq
  • Controls: include single‑labeled and NTC controls to diagnose crosstalk

Share your instrument model and filter sets—we’ll propose dye combinations and concentrations for clean, balanced multiplex runs.

QC & Deliverables

Deliverable Details
Purification Analytical + preparative HPLC as required
Identity Mass spectrometry (MS)
Format Lyophilized or in buffer; tubes or plates
Docs COA, HPLC trace, MS data; plate maps for panels

How to Order

  1. Send target sequence(s), amplicon length, and assay purpose.
  2. Select dye/quencher and any MGB/LNA options.
  3. Specify scale, purification, and documentation requirements.
  4. Share cycler model and filter sets for multiplex planning.

Specs Checklist

  • Target gene(s) and reference sequences
  • Sample type (cells, tissue, viral RNA/DNA)
  • Plex level and instrument channels
  • Shipping/buffer preferences

FAQ

Hydrolysis vs intercalating dye assays?
Hydrolysis probes generate fluorescence only when the correct target is amplified, improving specificity and multiplex compatibility compared to intercalating dyes that report total dsDNA.
When to choose MGB or LNA?
Use MGB for shorter probes with high Tm or SNP discrimination; use LNA to boost affinity/specificity at difficult positions or in AT‑rich regions.
Can you design multiplex panels?
Yes. Provide instrument filters and target list; we’ll propose dye sets, concentrations, and plate maps.
More FAQ'sAll FAQ's

Start a qPCR Probe Project

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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.
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