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In situ hybridisation

Fluorescent probes

Fluorescent probes

Each oligonucleotide labeled with fluorescent dyes is purified using a special HPLC procedure. Excess of dye as well as partial- and unmodified oligonucleotide is completely separated during this process. Quality control with Maldi mass spectrometry guarantees the identity of the oligonucleotide probes.

Depending on the experimental requirements several probe formats are available:


The classic probes with one fluorescent dye at the 5´-end of the oligonucleotide.

Fam, Cyanine 3, Cyanine 5, Atto-dyes, Dyomics-dyes      
Synthesis scale S M L
Guaranteed yield > 2 OD > 5 OD > 15 OD



A nearly twofold increase in sensitivity may be achieved in in situ hybridization experiments (DOPE-FISH) by using double labelled probes. The dopeProbes are labeled with an identical fluorophore at the 5´- and 3´-end of the oligonucleotide.

1. Double Labeling of Oligonucleotide Probes for Fluorescence in Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility. Stoecker K, Dorninger C, Daims H, Wagner M; Appl. Environ. Microbiol. (2010), 76, 922-926.

3',5'-Fam, Cyanine 3, Cyanine 5, Tamra                               
Synthesis scale S M L
Guaranteed yield > 1 OD > 3 OD > 6 OD



Highest sensitivity due to 4 labels per oligonucleotide. The special probe-design in which the dyes are coupled to the oligonucleotide backbone, prevents "self-quenching effects". The signal intensity of the hybridized probe nearly increases linear with the number of fluorophores  per oligo; that means that tetraProbes may be two times  brighter than dopeProbes and four times brighter than  monoProbes under identical conditions.

e.g. Fam, Atto 488                                                                     
Synthesis scale S M L
Guaranteed yield > 1 OD > 3 OD > 6 OD



Horseradish peroxidase labelled oligonucleotides

Oligonucleotides labelled with horseradish peroxidase (HRP), a 45 kDa large enzyme, are gaining more and more importance as probes for fluorescence in situ hybridisation (FISH) for detection of microorganisms. The combination of HRP probes and the tyramide signal amplification system (TSA) leads to 10- 20-fold increased signal intensities in comparison to fluorescein monolabelled probes. This "Catalysed Reporter Deposition - Fluorescent in situ hybridisation" (CARD-FISH) method represents an excellent tool for quantitative detection of microorganisms. has a long standing experience in synthesis and purification of high quality hrpProbes. 

Synthesis procedure:

In a first step, an oligonucleotide, usually 18 - 25 bases long, is modified with an aminolink at the 5’-end. This primary amino function is coupled to a reactive bi-functional crosslinking reagent, resulting in an activated oligonucleotide, which can react in a further step with a free amino function of the horseradish peroxidase molecule. Thus, a stable covalent coupling is achieved. The appropriate choice of reaction conditions and excess of reagents leads to 1:1 connection between oligonucleotide and HRP.

Purification and isolation of the HRP oligonucleotide is best achieved by using polyacrylamide gel electrophoresis (PAGE). offers three synthesis scales of HRP oligos:

Synthesis scale S M L
Guaranteed yield > 1 OD > 2 OD > 4 OD

Other scales and final yields on request. For larger numbers of HRP-oligonucleotides per order please inquire for special offers.

smFISH - OligoPool 48

Oligonucleotides for single molecule in situ hybridisation (smFISH)

In gene expression analysis in tissue, in situ RNA detection is becoming increasingly important. But to detect a specific RNA with just a few copies in the cell, extremely sensitive methods are needed. 1

In the so-called single molecule fluorescence in situ hybridisation (smFISH), single RNA molecules in fixed cells are detected using 48 short, single labelled oligonucleotide probes. Each probe is thereby marked with a fluorophore at its 3´-ending. By binding of all or many complementary oligo probes to different regions of the target, the desired mRNA is visible as a small fluorescent dot in the microscope. 2

Since smFISH probes are also capable to bind to partially degraded RNA, the method is additionally suitable for fixed cells or embedded tissues. The large number of probes in the set ensures a high degree of sensitivity and specificity, so the likelihood of false-positive results is minimised. 3 If in individual cases a non-specific “off-target” binding occurs, only a weak fluorescence will be generated that is below the detection limit of specific mRNA binding. The use of different fluorescent dyes with clearly distinct emission spectra enables detection of several individual mRNA molecules in one cell. These so-called multiplex-imaging assays can create single cell gene expression profiles. 

For detection of specific RNA in a cell, offers a complete set of 24 or 48 single-labelled oligo probes. Each oligo pool is purified by HPLC and controlled by Maldi mass spectrometry. 

Modification              ABS [nm]                 EM [nm]                 Price category
Fam 494 520 1
Atto 488 501 523 2
Cyanine 3 550 570 1
Atto 550 554 579 2
Atto 565 563 592 2
Cyanine 3.5 588 604 1
Atto 594 601 627 2
Atto 647N 646 664 2
Cyanine 5 649 670 1
HRP     3


                     Price category*                OligoPool 24                 OligoPool 48
1 395,00 EUR / 299,00 GBP 459,00 EUR / 339,00 GBP
2 495,00 EUR / 390,00 GBP 595,00 EUR / 490,00 GBP
3 1290,00 EUR / 1161,00 GBP 1890,00 EUR / 1701,00 GBP

Our excel order form for requests or orders can be download here.

For further information, please contact our customer support team at any time. We will be happy to support you.
Tel 0731-70 396 0   I

* The prices are valid for an oligo pool with 24 or 48 oligonucleotide probes (18-25 bases) in scale S (guaranteed yield > 1 OD, 5 nmol pooled oligo) including HPLC purification and Maldi quality control. Prices are only valid for electronic orders ( online order form). VAT and shipping may apply. Upon request, we also offer oligonucleotide pools with 36 or 96 oligo probes. Additional conditions are according to our current price list. 


1. Imaging individual mRNA molecules using multiple singly labeled probes. Ray A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S; Nature Methods (2008), Vol.5 No.10, 877-879.

2. Single Molecule Imaging of RNA in Situ. Batish M, Raj A, Tyagi S; Methods in Molecular Biology (2011), vol.714, DOI 10.1007/978-1-61779-005-8_1.

3. Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules. Kwon S; BMB Reports – Manuscript Draft, BMB-13-016 (2013), 65-72.


Links for probe design


For the design and application of probes in the field of in situ hybridisation we suggest the following links: 

Arb-Silva (
The SILVA rRNA database is a project of Max Planck Institute for Marine Microbiology, Bremen. SILVA database is the world´s largest collection for ribosomal RNA sequences for all three domains of life (Bacteria, Archaea and Eukarya) and thus it is one of the first addresses for taxonomic and phylogenetic questions. In addition to specially developed software for aligning, handling and analysis of sequence data, the website offers a comprehensive labor and troubleshooting collection for fluorescence in situ hybridisation.

Ribocon (
Ribocon provides useful bioinformatic services and solutions for industry and academies in the area of environmental, clinical and molecular microbiology. Especially with microbial diversity analysis, phylogenetic studies and in the design of custom probes, Ribocon team is highly experienced.

probeBase (
The online server probeBase is maintained by the Department of Microbial Ecology at the University of Vienna. The online resource enables the targeted search of FISH and microarray probes and PCR primers by name, sequence or target organism. In addition, a detailed documentation of the probes is available.

Protocols (
The Department of Microbiology at the Technical University of Munich presents a collection of informative laboratory protocols and helpful links.