Stellaris® FISH Probes, Custom Assay with CAL Fluor® Orange 560 Dye

Custom Stellaris® RNA FISH Probe Set labeled with CAL Fluor® Orange 560 dye to detect your RNA of interest.

Product Description

Stellaris RNA FISH is a RNA visualization method that allows simultaneous detection, localization, and quantification of individual RNA molecules at the cellular level in fixed samples using fluorescence microscopy.

A set of Stellaris RNA FISH Probes is comprised of a pool of up to 48 unique probes, each labelled with a fluorophore, that collectively bind along an RNA target transcript to produce a diffraction limited spot.

Before considering designing a Stellaris RNA FISH Customized Probe Set, please also check out our Stellaris RNA FISH DesignReady Probe Sets for a large selection of professionally designed targets.

Stellaris Buffers are the perfect accompaniment to your experiment, allowing for even more robust RNA detection and analysis through reduced background signal. 

CAL Fluor Orange 560 Dye

The CAL Fluor Orange 560 modification adds a fluorescent CAL Fluor Orange 560 dye to the end of an oligonucleotide. CAL Fluor Orange 560 fluoresces in the orange region of the visible spectrum. It is used as a replacement for the VIC, HEX and JOE dyes.

Special Notes and Considerations: The CAL Fluor Orange 560 dye is not commonly used for Stellaris RNA FISH probes, though it is a viable option and has been successfully used and published. As a result, we have limited experience with the particular characteristics of this dye when attached to RNA FISH probe sets.

Anti-fade Recommendations: We generally recommend Vectashield by Vector Labs (H-1000) and Prolong® Diamond Anti-fade Mountant by ThermoFisher Scientific (P36961) for all of our dyes, but no compatibility tests have been performed with this dye.

How long will my sample last after mounting?: No longevity studies have been performed on this dye. We recommend imaging immediately after mounting.

Absorption and Emission Spectra for CAL Fluor Orange 560 Dye

Properties:

• Name: CAL Fluor Orange 560
• Formula: C₃₉H₅₀N₅O₇
• Absorption maximum (lambda max): 538 nm
• Extinction coefficient at lambda max: 87,800 M^-1cm^-1
• Extinction coefficient at 260 nm: 18,800 M^-1cm^-1
• Fluorescence maximum: 559 nm

Design considerations

Please read the tech article titled, “Designing Stellaris RNA FISH Probes” before designing your custom assay.

You can also use Chroma’s Spectra Viewer to check your microscope’s dye filter set compatibility. Use the Stellaris Dyes and Modifications page to select the right dye for your microscope and multiplexing recommendations.

Note I: Due to the variable autofluorescence in the green channel inherent to some cells and tissues, it is not recommended to use FAM for some Stellaris RNA FISH assays. We recommend testing your sample for green channel autofluorescence before ordering FAM labeled sets or ordering an alternative dye that is compatible with your experiment.

Note II: The success rate of Custom Probe Sets depend on many variables, such as imaging platform, operator use of optics, target sequence, transcript number, subcellular localization of transcript, number of probes in the set, space between probes, masking level, sample identity whether cultured cells or fresh or frozen tissue, preparation and handling of sample, and customer's design of probe sets with or without the Stellaris Probe Designer. The customer is responsible for designing a probe set that is compatible with all of the variables mentioned above unique to their platform technologies and model system, and therefore we cannot guarantee the success of Customer Probe Sets, or troubleshoot the designs.

Please contact us by email, phone or using this form for further advise and details.