Custom PCR & FISH Probes

High-quality custom PCR probes and fluorescent DNA probes for qPCR, dPCR and DNA-FISH applications. Microsynth offers fast production, stringent quality control and a broad portfolio of fluorophores, quenchers and probe formats for sensitive detection and multiplex workflows.

Applications

Our probes support a wide range of molecular biology and imaging applications:

qPCR and real-time PCR
Digital PCR and ddPCR
Allelic discrimination
Multiplex assay development
Molecular diagnostics
Fluorescence in situ hybridization (FISH)

Why Choose Microsynth Probes?

High Quality
Microsynth probe manufacturing includes thorough purification, stringent quality control and mass verification to ensure reliable assay performance.

Fast Production Times
Fast production times, typically within 3–5 working days for PCR probe products.

Broad Probe Portfolio
Microsynth offers a wide range of probe formats including dual-labeled probes, double-quenched probes, LNA probes, MGB probes and molecular beacons.

Expert Support
Expert technical support from experienced scientists for probe design, optimization and multiplex assay development.

Probe Types at Microsynth

Dual-Labeled Probes
Dual-labeled hydrolysis probes increase specificity in quantitative PCR. During amplification, probe cleavage separates fluorophore and quencher, generating a measurable fluorescence signal.

Double-Quenched Probes
Double-quenched probes reduce background fluorescence by incorporating an additional internal quencher. This improves signal-to-noise ratio and is particularly beneficial for longer probes and demanding qPCR or dPCR applications.

LNA Probes
LNA-containing probes provide increased thermal stability and improved hybridization specificity. Each incorporated LNA base typically increases melting temperature (Tm) by approximately 2–4 °C.

MGB Probes
MGB probes form highly stable duplexes with single-stranded DNA targets, enabling shorter probes with enhanced selectivity and reduced background fluorescence.

Molecular Beacons
Molecular beacons are stem-loop probes that emit fluorescence upon hybridization to their target sequence, enabling highly specific detection.

DNA-FISH Probes
Microsynth offers DNA-FISH probes for fluorescence in situ hybridization and imaging applications. Multiplex analysis is possible as multiple fluorescent dyes are available.

Fluorophores, Quenchers & Advanced Design Options

Microsynth supports a broad variety of fluorophore and quencher combinations for custom PCR probes and fluorescent DNA probes. Probe performance can be tailored using LNA, MGB and other modifications to optimize melting temperature, specificity and signal strength.

For DNA-FISH probes, multiple fluorescent labels can be incorporated to enable single-color and multiplex imaging applications. Depending on the design, two to four of the same dyes can be included within a single oligonucleotide.

This flexibility supports:

Standard qPCR assays
Challenging low-background assays
Digital PCR workflows
Multiplex detection
Fluorescence microscopy and imaging

Quality Control & Manufacturing Standards

Microsynth probe production is designed to support demanding research and diagnostic workflows.

Quality assurance includes:

Purification by HPLC or PAGE
Online trityl monitoring
MALDI-TOF mass spectrometry
EN ISO 13485:2016 certified production processes
Optional support for assay development, validation and testing

This ensures batch-to-batch consistency and reliable experimental performance.

Synthesis Scales & Purification

Notes

Synthesis scale refers to the initial amount of 3′ bases used during synthesis
Guaranteed yields are given in OD260 and calculated for a 20-mer oligonucleotide
Actual yield may vary depending on sequence composition (e.g. GC content)
PAGE purified oligos typically result in lower yields

Dual-Labeled Probes

Minimum Yields for Dual-Labeled Probes from Microsynth

5‘ Label	3‘ Label	0.04 µmol scale	0.2 µmol scale	1.0 µmol scale
FAM HEX YYE TET VIC	BHQ-1 TAMRA Dabcyl	1 OD 5 nmol	2 OD 10 nmol	12 OD 60 nmol
AlexaFluor Dyes ATTO Dyes JOE	BHQ-1	0.75 OD 3.75 nmol	1.5 OD 7.5 nmol	8 OD 40 nmol
HEX	BHQ-2	1 OD 5 nmol	2 OD 10 nmol	12 OD 60 nmol
AlexaFluor Dyes ATTO Dyes California Red Cy Dyes Dyomic Dyes NED ROX TAMRA Texas Red	BHQ-2	0.75 OD 3.75 nmol	1.5 OD 7.5 nmol	8 OD 40 nmol

Double-Quenched Probes

Minimum Yields for Double-Quenched Probes from Microsynth

5‘ Dye	3‘ Quencher	Internal Quencher	0.04 µmol scale	0.2 µmol scale	1.0 µmol scale
FAM	BHQ-1 or TAMRA	iQ530	1 OD 5 nmol	2 OD 10 nmol	8 OD 40 nmol
Yakima Yellow	BHQ-1	iQ530	1 OD 5 nmol	2 OD 10 nmol	8 OD 40 nmol
HEX	BHQ-2	iQ530	1 OD 5 nmol	2 OD 10 nmol	8 OD 40 nmol
ROX	BHQ-2	iQ530	0.75 OD 3.75 nmol	1.5 OD 7.5 nmol	8 OD 40 nmol
CalRed	BHQ-2	iQ530	0.75 OD 3.75 nmol	1.5 OD 7.5 nmol	8 OD 40 nmol
Cy5	BHQ-2	iQ530	0.75 OD 3.75 nmol	1.5 OD 7.5 nmol	8 OD 40 nmol
A647N	BHQ-2	iQ530	0.75 OD 3.75 nmol	1.5 OD 7.5 nmol	8 OD 40 nmol

LNA Probes

Minimum Yields for LNA Probes from Microsynth

		0.04 µmol scale	0.2 µmol scale	1.0 µmol scale
LNA probes		0.5 OD 2.5 nmol	1 OD 5 nmol	6 OD 30 nmol

MGB Probes

Minimum Yields for MGB Probes from Microsynth

5‘ Label	3‘ Label	Channel (Typical)	0.04 µmol scale	0.2 µmol scale	1.0 µmol scale
FAM	MGB-Q530	Green	1 OD 5 nmol	2 OD 10 nmol	10 OD 50 nmol
JOE / HEX / Yakima Yellow	MGB-Q530	Yellow
California Red	MGB-Q530	Red
Atto647N	MGB-Q530	Deep Red

FISH Probes

Minimum Yields for FISH Probes from Microsynth

Dye	Channel (Typical)	0.2 µmol scale / HPLC
Atto 488	Blue	0.6 OD 3 nmol
Atto 550	Green
Atto 590	Orange
Atto 647N	Deep Red
Dyomic781	Near Infrared

Two to four of the same dyes are possible within a single oligonucleotide.

How to Order

Enter the Microsynth webshop
Select DNA in the DNA/RNA Synthesis section
Choose Normal Entry or Upload Entry
Enter your sequence and select the required modifications, probe format and purification
Follow the ordering instructions in the webshop

For specialized probe designs, multiplex concepts or DNA-FISH projects, our team is happy to support you.