Freedom™ Dyes

Freedom fluorescein dyes

Yakima Yellow is registered trademark of EliTech group; JOE is a trademark of ThermoFisher.

6-FAM (Fluorescein): A single isomer derivative of fluorescein. FAM is the most commonly used fluorescent dye attachment for oligonucleotides and is compatible with most fluorescence detection equipment. It becomes protonated and has decreased fluorescence below pH 7; it is typically used in the pH range 7.5–8.5. FAM can be attached to 5' or 3' end of oligos.

6-FAM (NHS Ester): A post-deprotection reaction is used to attach this fluorophore to the oligonucleotide. This is commonly used to modify RNA oligos with FAM.

Fluorescein dT: Fluorescein is attached to position 5 of the thymine ring by a 6-carbon spacer arm.

SUN: A VIC^® (ThermoFisher Scientific) equivalent (emission maximum of 554 nm) that is recommended for use in multiplexed assays when added to the 5' end of a dual-labeled 5' nuclease probe for qPCR.

HEX: Hexachlorofluorescein is a chemical relative of fluorescein that is commonly used for multiplexed assays with FAM and TET. HEX can be added only to the 5' end of an oligonucleotide.

JOE (NHS Ester): JOE (6-carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein) is available only as an NHS ester and must be attached to an amino-modified oligonucleotide. JOE is frequently used in multiplex reactions with FAM.

MAX (NHS Ester): Most often used to multiplex with FAM. It can be used as a VIC substitute because its spectral profile is nearly identical to VIC. Importantly, MAX is efficiently excited by either a 488 nm laser or a broad emission light source; therefore, it can be used with most commercial detection platforms.

TET: Tetrachlorofluorescein is a chemical relative of fluorescein that is commonly used for multiplexed assays with FAM and HEX. TET can be added only to the 5' end of an oligonucleotide.

Freedom Cy dyes

Cy 3: A standard orange-fluorescent label for nucleic acids used in imaging, flow cytometry, and genomic applications.

Cy 5: A standard far red-fluorescent label for nucleic acids used in imaging, flow cytometry, and genomic applications.

Cy 5.5: Used as a fluorescent label in 5' nuclease probes for qPCR, Scorpion^® primers (Premier Biosoft), and Molecular Beacons. Cy 5.5 can also be used to label DNA oligos for use as hybridization probes in other applications, such as fluorescent in situ hybridization (FISH).

Freedom rhodamine dyes

TEX 615 is a trademark of ThermoFisher, and Texas Red is a registered trademark of Molecular Probes, Inc. 

ROX (NHS Ester): ROX (carboxy-X-rhodamine) is available only as an NHS ester; therefore, it must be attached to an amino-modified oligonucleotide. It has spectral properties similar to Texas Red.

TAMRA: This phosphoramidite modification is only available at the 3' end of an oligonucleotide. This was used as a quencher in first generation real-time PCR.

TAMRA (NHS Ester): The internal and 3' versions of this modification are attached to the oligonucleotide through a dT base; therefore, a dT nucleotide will be added at the position of these modifications. To avoid adding an extra nucleotide, replace an existing T nucleotide in your sequence with the required modification.

TEX 615: A red wavelength dye commonly used in multiplex reactions with FAM or in fluorescence-activated cell sorting (FACS) and microscopy applications using the rhodamine filter. TEX 615 can be used as a direct substitute for Texas Red or CAL Fluor 610.

Freedom ATTO Dyes

Alexa Fluor fluorophores are registered trademarks of Molecular Probes, Inc., VIC and LIZ are registered trademarks of ThermoFisher; PET is a trademark of ThermoFisher.

ATTO™ dyes are patented fluorescent markers that feature strong absorption and sensitivity, enhanced photostability, and high fluorescence quantum yield. ATTO dyes are perfect substitutes for dyes such as ROX, VIC, LIZ, and Alexa Fluor dyes. The dyes offer alternatives for applications including fluorescence in situ hybridization (FISH), fluorescence resonance energy transfer (FRET), and dual-labeled probes used in real-time PCR experiments. For real-time PCR applications, dye calibration will be needed for each real-time PCR instrument.

Other Freedom Dyes

TYE™ dyes are proprietary fluorophores from IDT that are available for commonly used dye wavelengths. The numerical value in the name of these dyes represents the emission wavelength when attached to an oligo.

TYE 563: A bright fluorescent dye that can be used in microarray applications. TYE 563 can be used as a direct substitute for Cy 3.

TYE 665: A bright fluorescent dye that can be used in microarray applications. TYE 665 can be used as a direct substitute for Cy 5.

TYE 705: A bright fluorescent dye that can be used in microarray applications. TYE 705 can be used as a direct substitute for Cy 5.5.

TYE Fluorophores are licensed from ThermoFisher

Additional fluorophores (which may include licensing restrictions) are available. Click here to see our full catalog of fluorophore modifications.

Technical reports

Frequently asked questions