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Fluorophores Modifications

Freedom™ Dyes

Freedom™ Dyes are fluorophores with no licensing restrictions from IDT or third party companies. Therefore, they are free to use for commercial or diagnostic applications. Freedom dyes include IDT proprietary fluorophores that are available for commonly used dye wavelengths. The numerical value in the name represents the emission wavelength of the dye when attached to an oligo.

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.

View product details for 6-FAM (NHS Ester):

5' 3'

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.

View product details for 6-FAM (Fluorescein):

5' 3'

Fluorescein dT


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

View product details for Fluorescein dT:

5' Internal 3'

Cy3™


View product details for Cy3™:

5' Internal 3'

TAMRA™


This modification is attached to the oligo through a dT base. Incorporation of this modification will add a dT nucleotide at the 3’ end of your oligo.

View product details for TAMRA™:

3'

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.

View product details for JOE (NHS Ester):

5' 3'

Cy5™


View product details for Cy5™:

5' Internal 3'

TAMRA (NHS Ester)


The internal and 3' version 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.

View product details for TAMRA (NHS Ester):

5' Internal 3'

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.

View product details for MAX (NHS Ester):

5' 3'

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.

View product details for TET™:

5'

Cy5.5™


View product details for Cy5.5™:

5' 3'

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®.

View product details for ROX (NHS Ester):

5' 3'

TYE™ 563


A bright fluorescent dye that can be used in microarray applications. TYE 563 can be used as a direct substitute for Cy3®.

View product details for TYE™ 563:

5' 3'

Yakima Yellow®


Yakima Yellow® was developed by Epoch Biosciences as an alternative to VIC. qPCR amplification curves exhibit lower background fluorescence when this dye is combined with ZEN™ and IBFQ quenchers as a double-quenched probe. Yakima Yellow is not pH sensitive and has the same fluorescence at pH 7 as it does at pH 9. This dye is not compatible with TAMRA. Yakima Yellow® is a trademark of ELITechGroup

View product details for Yakima Yellow®:

5'

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.

View product details for HEX:

5'

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.

View product details for TEX 615:

5' 3'

TYE™ 665


A bright fluorescent dye that can be used in microarray applicaitons. TYE 665 can be used as a direct substitute for Cy5®.

View product details for TYE™ 665:

5' 3'

TYE 705


A bright fluorescent dye that can be used in microarray applications. TYE 705 can be used as a direct substitute for Cy5.5®.

View product details for TYE 705:

5'

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.

View product details for SUN:

5'

ATTOTM Dyes

ATTOTM dyes are a group of bright fluorophores that are excellent alternatives to a broad range of dyes. The dyes can be used in a multitude of applications, such as fluorescence in situ hybridization (FISH), fluorescence resonance energy transfer (FRET), DNA Sequencing, and qPCR experiments.

ATTO™ 425 (NHS Ester)


Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 425 (NHS Ester):

5'

ATTO™ 488 (NHS Ester)


ATTO™ 488 can be used as a substitute for Alexa Fluor® 488. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 488 (NHS Ester):

5' 3'

ATTO™ 532 (NHS Ester)


ATTO™ 532 can be used as a substitute for VIC®. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 532 (NHS Ester):

5' 3'

ATTO™ 550 (NHS Ester)


ATTO™ 550 can be used as a substitute for NED® and Alexa Fluor® 555. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 550 (NHS Ester):

5' 3'

ATTO™ 565 (NHS Ester)


ATTO™ 565 can be used as a substitute for PET™. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 565 (NHS Ester):

5' 3'

ATTO™ Rho101 (NHS Ester)


ATTO™ Rho101 can be used as a substitute for ROX™. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ Rho101 (NHS Ester):

5' 3'

ATTO™ 590 (NHS Ester)


ATTO™ 590 can be used as a substitute for Alexa Fluor® 594. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 590 (NHS Ester):

5' 3'

ATTO™ 633 (NHS Ester)


ATTO™ 633 is a red wavelength dye. ATTO™ 633 exhibits strong absorption, high fluorescence quantum yield, and good stability in a pH range of 2-10. ATTO™ 633 can be used as a substitute for LIZ®. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 633 (NHS Ester):

5' 3'

ATTO™ 647N (NHS Ester)


ATTO™ 647N is a red wavelength dye. ATTO™ 647N exhibits strong absorption, high fluorescence quantum yield, and good pH and photo-stability. ATTO™ 647N can be used as a substitute for Alexa Fluor® 647. Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 647N (NHS Ester):

5' 3'

ATTO™ 700 (NHS Ester)


Dye calibration may be required for each commercial detection instrument.

View product details for ATTO™ 700 (NHS Ester):

5'

Alexa Fluor® Dyes

Alexa® Dyes have high quantum yield and are relatively photostabile. They are conjugated post-synthesis to an amino-modified oligo as NHS Esters. They are available in a wide spectral range from blue to deep red.

Alexa Fluor® 488 (NHS Ester)


View product details for Alexa Fluor® 488 (NHS Ester):

5' 3'

Alexa Fluor® 532 (NHS Ester)


View product details for Alexa Fluor® 532 (NHS Ester):

5' 3'

Alexa Fluor® 546 (NHS Ester)


View product details for Alexa Fluor® 546 (NHS Ester):

5' 3'

Alexa Fluor® 594 (NHS Ester)


View product details for Alexa Fluor® 594 (NHS Ester):

5' 3'

Alexa Fluor® 647 (NHS Ester)


View product details for Alexa Fluor® 647 (NHS Ester):

5' 3'

Alexa Fluor® 660 (NHS Ester)


View product details for Alexa Fluor® 660 (NHS Ester):

5' 3'

Alexa Fluor® 750 (NHS Ester)


View product details for Alexa Fluor® 750 (NHS Ester):

5' 3'

LI-COR IRDyes®

IRDyes® can be attached at the 5'-end of an oligonucleotide. These near-infrared dyes are made by LI-COR Biosciences and are intended for use in biochemical applications and DNA sequencing.

5' IRDye® 700


View product details for 5' IRDye® 700:

5'

5' IRDye® 800


View product details for 5' IRDye® 800:

5'

5' IRDye® 800CW (NHS Ester)


IRDye® 800CW is an NHS-ester and can be attached at the 5'-end of an oligonucleotide via conjugation to a primary amine. This infrared dye is made by LI-COR Biosciences and is more hydrophillic than any of the other infrared dyes available. Combined with excellent tissue penetration seen in the 800 nm wavelength sprectra, it is ideal for in vivo fluorescence imaging applications.

View product details for 5' IRDye® 800CW (NHS Ester):

5'

Rhodamine Dyes

A variety of fluorophores from the rhodamine family are offered that range from green (Rhodamine Green, Em 531 nm) through red (ROX, Em 608 nm) emission. Compared to the fluorescein family of dyes, rhodamine dyes are relatively resistant to photobleaching and can be used over a wider pH range.

Rhodamine Green™-X (NHS Ester)


View product details for Rhodamine Green™-X (NHS Ester):

5' 3'

Rhodamine Red™ (NHS Ester)


View product details for Rhodamine Red™ (NHS Ester):

5' 3'

5-TAMRA™ (Azide)


The 5-isomer of TAMRA™ has a similar spectral property to 6-TAMRA™. 5-TAMRA™ is attached to an oligo through the copper (I) catalyzed alkyne-azide click reaction. The internal version of this modification is attached to the oligo through a dT base. Incorporation of the internal version will add a dT nucleotide at that position. To avoid adding an extra nucleotide, replace an existing T nucleotide in your sequence with the required modification.

View product details for 5-TAMRA™ (Azide):

5' Internal

Additional

6-FAM (Azide)


This form of FAM is attached to the oligonucleotide using click chemistry. The internal version of this modification is attached to the oligo through a dT base. A dT nucleotide will be added at the position of the modification. To avoid adding an extra nucleotide, replace an existing T nucleotide in your sequence with the required modification.

View product details for 6-FAM (Azide):

5' Internal

Alexa Fluor 405


View product details for Alexa Fluor 405:

5'

Fluorescein


Texas Red®-X (NHS Ester)


Texas Red®-X is a commonly used red wavelength fluorescent dye. It is available only as an NHS ester and must be attached to an amino-modified oligonucleotide.

View product details for Texas Red®-X (NHS Ester):

5' 3'

Lightcycler® 640 (NHS Ester)


Lightcycler® 640 (NHS Ester) is only available as an NHS Ester and must be attached to an amino-modified oligonucleotide. It is a red dye which spectrally lies between Texas Red® (NHS Ester) and Cy5™. It is commonly used as a FRET reporter along with a 6-FAM™ donor in assays run on the Roche Lightcycler® real-time PCR platform.

View product details for Lightcycler® 640 (NHS Ester):

5' 3'

Dy 750 (NHS Ester)


View product details for Dy 750 (NHS Ester):

5'