Freedom™ Dyes

Freedom™ Dyes are fluorophores with no patent 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 of these IDT proprietary (TYE) dyes represents the emission wavelength of the dye when attached to an oligonucleotide.

Additional fluorophore dyes are available from IDT. Click here for a list of all available dyes.

Freedom™ Fluorescein Dyes

Dye 5' Internal 3' Excitation
(nm)
Emission
(nm)
Alternative
6-FAM (Fluorescein) details details 495 520 N/A
6-FAM (NHS Ester) details

details
496 516 N/A
Fluorescein dT details
details
details
495 520 N/A
HEX details


538 555 N/A
JOE (NHS Ester) details

details
529 555 MAX (NHS Ester)
MAX details

details
524 557 JOE (NHS Ester)
TET details


522 539 N/A

Freedom™ Cy Dyes

Dye 5' Internal 3' Excitation
(nm)
Emission
(nm)
Alternative
Cy3 details
details
details
550 564 TYE 563
Cy5 details
details
details
648 668 TYE 665
Cy5.5 details
details
685 706 TYE 705

Freedom™ Rhodamine Dyes

Dye 5' Internal 3' Excitation
(nm)
Emission
(nm)
Alternative
ROX details details 588 608 ATTO™ Rh101 (NHS Ester)
TAMRA
details
559 583 N/A
TAMRA™ (NHS Ester) details
details
details
559 583 N/A
TEX 615 details

details
596 613 Texas Red®-X (NHS Ester)

Freedom™ ATTO™ Dyes

Dye 5' Internal 3' Excitation
(nm)
Emission
(nm)
Alternative
ATTO™ 488 details

details
502 522 Alexa Fluor® 488
ATTO™ 532 details
details
534 554 VIC®
ATTO™ 550 details

details
560 575 Alexa Fluor® 555
ATTO™ 565 details
details
570 591 PET™
ATTO™ Rho101 details

details
592 609 ROX
ATTO™ 590 details
details
602 624 Alexa Fluor® 594
ATTO™ 633 details

details
635 653 LIZ®
ATTO™ 647N details
details
649 662 Alexa Fluor® 647

Other Freedom™ Dyes

Dye 5' Internal 3' Excitation
(nm)
Emission
(nm)
Alternative
TYE™ 563 details details 549 563 Cy® 3
TYE™ 665 details

details
645 665 Cy® 5
TYE™ 705 details


686 704 Cy® 5.5

Freedom™ Fluorescein Dyes

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.

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

Cy3: A standard orange-fluorescent label for nucleic acids used in imaging, flow cytometry, and genomic applications.

Cy5: A standard far red-fluorescent label for nucleic acids used in imaging, flow cytometry, and genomic applications.

Cy5.5:
 Used as a fluorescent label in qPCR 5' nuclease probes, Scorpion
® primers, and Molecular Beacons. Cy5.5 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

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 phosporamidite 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.

Other Freedom™ Dyes

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

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

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®.

Fluorescein Dyes

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.

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.