Fluorescent Dyes - Select The Best Label For Your Assay!

5'
Int
3'

Multicolour detection
FRET
In-situ hybridisation / FISH
Fluorescence microscopy

The general characteristics of Alexa Fluor dyes from Molecular Probes are:

• Bright photo stable fluorescence
• Good water solubility
• pH insensitive between pH 4 - 10
• High quantum yield
• Long fluorescence life time

5'
Int
3'

FRET
Multicolor detections
Imaging applications
In-situ hybridisation / FISH
Fluorescence microscopy

DY-415 is part of the Dyomics fluorescent dyes produced by Dyomics GmbH. Dyomics dyes are characterised by:

• High extinction coefficients
• High fluorescence quantum yield
• Large Stoke-Shift
• High stability to photo-bleaching

5'
Int
3'

Multicolour detection
Imaging applications
In-situ hybridisation / FISH
Fluorescence microscopy

ATTO 425 is a novel fluorescent label produced by ATTO-TEC GmbH. Characteristic features of the labels are

• High fluorescence quantum yield
• Large stokes shift
• High photo stability and
• Low molecular weight

5'
Int
3'

FRET
Multicolour detection
Imaging applications
In-situ hybridisation / FISH
Fluorescence microscopy

ATTO 465 is a novel fluorescent label produced by ATTO-TEC GmbH.

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High thermal and photo-stability

In aqueous solution the dye shows a large stokes shift of 55 nm.

ATTO 465 is moderately hydrophilic.

The fluorescence can be excited efficiently in the range 420-465 nm.

5'
Int
3'

FRET
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Bodipy FL is part of the Bodipy family produced by Molecular Probes.

The characteristics of these modifications are

• Less susceptible to photo-bleaching
• Offer high signal intensity

CY2
DY-495
ATTO 495

5'
Int
3'

Multicolor detection
FRET
Fluorescence microscopy
In-situ hybridisation/FISH

These are the characteristics of Alexa Fluor 488 from Molecular Probes:

• Spectra almost identical to those of Fluoresceine
• Fluorescence lifetime of ~4.1 nanoseconds
• Strong absorption, with an extinction coefficient at 71,000 cm-1M-1
• Great photo stability
• pH-insensitive between pH 4 and 10

5'

6-FAM (6-carboxyfluorescein) is the most commonly used fluorescent dye for various of applications.

It has the same spectral characteristics than Fluoresceine and FITC and high quantum yields.

FAM is compatible with most fluorescence detection systems and is typically used in the pH range 7.5-8.5.

5'
Int
3'

Multicolor detection
FRET
Fluorescence microscopy
In-situ hybridisation / FISH

FITC is the abbreviation of fluoresceine isothiocyanate.

The fluorescence of this molecule is very high and can be labelled at any position of an oligonucleotide.

It is a derivate of fluoresceine with an isothiocyanate group.

It has the same absorption spectra like Fluoresceine and FAM.

3'

Real-time PCR, FRET
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Fluoresceine is offered compared to FITC and FAM for the 3’ labeling of an oligo.

It blocks the terminal OH-group of the oligomer.

It is known as a dye with

• Instability against photo bleaching and
• Its natural background fluorescence at 480-530nm

Therefore this dye is displaced with more stable dyes like Oregon Green™ for applications such as FISH.

3’ Fluoresceine is used as the preferred donor dye in FRET systems or as an alternative to Digoxigenin and Biotin in immunological detection systems.

472.71

DY-495
ATTO 495

Fluorescein-dT is offered compared to Fluoresceine, FITC and FAM for labelling an oligo internally. This is done via the deoxy-group of the Thymidin base (-dT) and can therefore be used as modified primer.

Fluorescein-dT is known as a dye with

• Instability against photo bleaching and
• Natural background fluorescence at 480-530nm

Therefore this dye is displaced with more stable dyes like Oregon Green dyes for most of applications such as FISH.

It can be used as alternative to Digoxigenin and Biotin-dT in immunological detection systems.

5'
Int
3'

Real-time PCR, qPCR, FRET
In-situ hybridisation
FISH microscopy

ATTO 488 is a novel fluorescent label produced by ATTO-TEC GmbH.

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High photo-stability
• Excellent water solubility
• Very little triplet formation

The fluorescence is excited most efficiently
in the range 480-515 nm.

For instance the 488 nm line of the Argon-Ion laser is very suitable for excitation.

5'
Int
3'

Laser scanning microscopy
Flow cytrometry
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Oregon Green dyes are produced by Molecular Probes.

Oregon Green 488 matches closely to the absorption spectra of fluoresceine but

• With improved photo stability and
• High fluorescence quantum yield

5'
Int
3'

Laser scanning microscopy
Flow cytrometry
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Oregon Green dyes are produced by Molecular Probes.

Oregon Green 514 matches closely to the absorption spectra of fluoresceine but

• With improved photo stability and
• Less sensitivity to pH

5'
Int
3'

Laser scanning microscopy
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Rhodamine Green from Molecular Probes are characterised by

• A high extinction coefficient
• A high quantum yield and
• Its photo-stability

The interaction between this modification and the oligo is reduced by a C7-Aminolink.

5'

DNA sequencing / fragment length analysis
Real-time PCR, qPCR, FRET
Microsatellite analysis
SNP detection / genotyping

TET is the abbreviation of 5-Tetrachloro-Fluorescein, a phosphoramidite from Applied Biosystem.

TET is an extremely stable dye. Its use is limited due to the close emission spectrum to FAM.

TET is commonly used as 5’ fluorophore for Dual Labeled Probes and Molecular Beacons or as 5' labelled primer for different approaches on ABI instruments.

5'
Int
3'

Real-time PCR, qPCR, FRET
In-situ hybridisation
FISH microscopy

ATTO 520 is a novel fluorescent label produced by ATTO-TEC GmbH  related to the well-known dye Rhodamine 6G. Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High thermal and photo-stability

The dye is moderately hydrophilic.

The fluorescence is excited most efficiently in the range 510 - 535 nm. A suitable source of excitation is an Argon-Ion laser using the 514 nm line.

5'
INT
3'

DNA sequencing
Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation / FISH microscopy
Gene expression profiling
SNP detection / genotyping

6-JOE is a 6-carboxy-4',5'-dichloro-2',7'-dimethoxyfluoresceine.

As NHS ester the dye can be coupled to amino-modified oligonucleotides at any position.
As 5´-modification the dye is employed as cyclohexyl-linked amidite.

6-JOE has similar absorption and emission spectra to those of Rhodamine 6G.

JOE is one of the traditional fluorophores used in automated DNA sequencing and as reporter dye for multiplex Real-Time qPCR.

5'

DNA sequencing
Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation
FISH microscopy

Yakima Yellow is an exclusive dye made and sold under license from Epoch Biosciences, Inc. It offers researchers the best alternative to VIC of Applied Biosystems.

Yakima Yellow is ideally suited to be used as a matched fluorophore in any
detection system that involves FRET.

Yakima Yellow labeled oligonucleotides are for resarch purpose only, and may not be used for commercial, clinical, diagnostic or any other use.

5'
INT
3'

FRET
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Bodipy 530/550 is part of the Bodipy family produced by Molecular Probes.

The characteristics of these modifications are

• Less susceptible to photo-bleaching and
• Offer high signal intensity

5'
INT
3'

Real-time PCR, qPCR, FRET
In-situ hybridisation
Flow cytometry
FISH microscopy

ATTO 532 is a novel fluorescent label produced by ATTO-TEC GmbH related to the well-known dye Rhodamine 6G. The characteristics of this modification are:

• strong absorption
• high fluorescence quantum yield
• high photostability
• excellent water solubility.

5'

DNA sequencing / fragment length analysis
Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation / FISH microscopy
SNP detection / genotyping

HEX is the abbreviation of hexachloro-fluoresceine, a phosphoramidite from Applied Biosystem.

HEX is commonly used as 5’ fluorophore for Dual Labeled Probes, Molecular Beacons or as 5' labeled primer for different approaches on ABI instruments.

The phosphoramidite is already relatively unstable in the production.

HEX labeled primers are very hydrophobe, affecting PCR efficiency.

Thus, HEX is being substituted by Yakima Yellow for various of applications, already.

5'
INT
3'

Multicolour detection
FRET
Fluorescence microscopy
In-situ hybridisation / FISH

These are the specifications of Alexa Fluor 555 from Molecular Probes:

• Spectra is similar to Tetramethylrhodamine (TRITC, TMR TAMRA) and Cy3
• Optical filters designed for Cy3 dye also work with Alexa Fluor 555 as well
• It is more photo stable than Cy3
• It has a better stability to photo bleaching than Alexa Fluor 546

544

5'
INT
3'

FRET
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Bodipy TMR-X is part of the Bodipy family produced by Molecular Probes.

The characteristics of these modifications are

• Less susceptible to photo-bleaching and
• Offer high signal intensity

5', 3', intern

Microarray experiments
Real-time PCR, qPCR, FRET
In-situ hybridisation
FISH microscopy
DNA Sequencing

Cyanine3 is a fluorescent dye of the cyanine family.

It is characterised by

• Excellent spectroscopic performance
• High quantum yields
• High extinction coefficient
• Good stability of fluorescence signal against changes in pH in various buffer conditions

The fluorescence lies in the deep yellow range.

5'
Int
3'

Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation
FISH microscopy

ATTO 550 is a novel fluorescent label produced by ATTO-TEC GmbH related to the dyes Rhodamine 6G and Rhodamine B.

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High thermal and photo-stability

The dye is moderately hydrophilic.

The fluorescence is excited most efficiently in the range 540 - 565 nm.

5'
3'

DNA sequencing / fragment length analysis
Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation / FISH microscopy
SNP detection / genotyping

TAMRA is an abbreviation for carboxy-tetramethyl-rhodamine from Applied Biosystems.

It can be used as fluorescent dye labelled on the 5’ end of the oligo, preferably used for fluorescence microscopy or for dye primer sequencing on ABI analyzers, but mostly used as 3’ quencher for short waved reporter dyes.

5'
Int
3'

Multicolour detection
FRET
Fluorescence microscopy
In-situ hybridisation / FISH

Rhodamine Red from Molecular Probes is a useful second label in combination with other fluorescent dyes.

It is characterised by

• A high extinction coefficient
• A high quantum yield and
• Higher photo-stability to Rhodamine B

5'
Int
3'

Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation
FISH microscopy

ATTO 565 is a novel fluorescent label produced by ATTO-TEC GmbH belonging to the class of Rhodamine dyes.

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High thermal and photo-stability

The dye is moderately hydrophilic.

The fluorescence is excited most efficiently in the range 545-575 nm.

5'
Int
3'

Real-time PCR, qPCR

ATTO RHO12 is a new rhodamine dye which belongs to the ATTO family from ATTO-TEC GmbH. 

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High photo-stability 

The dye is moderately hydrophilic.

The fluorescence is excited most efficiently in the range of 550 - 580 nm.

5'
Int
3'

DNA sequencing / fragment length analysis
Real-time PCR, qPCR, FRET
Microsatellite analysis
Gene expression profiling
SNP detection / genotyping

ROX is the abbreviation for Carboxy-X-Rhodamine from Applied Biosystems. This ester is a red fluorescent dye that is coupled through an amino linker to the oligo, hence, ROX can not be combined with other ester based linkers.

ROX is a member of the Rhodamine family.

Compared to the fluoresceine family of dyes, Rhodamine dyes are more resistant to photo bleaching and stable over a wider pH range.

The relatively long wavelength emission maximum for ROX makes it an attractive choice in multiplex detection systems.
Its spectral properties are similar to Texas Red

5'
Int
3'

Real-time PCR, qPCR, FRET
Microsatellite analysis
Gene expression profiling
SNP detection / genotyping

Texas Red is a commonly used red fluorescent dye from Molecular Probes. Its spectral properties are similar to ROX.

TexasRed is only available as NHS ester and  requires the attachment to an amino-modified oligonucleotide. It cannot be combined with other ester based linkers.

Texas Red is commonly used as a third dye in specific experiments such as multiplex PCR due to their limited spectral overlap with other fluorescent dyes.

It is also used as 5' reporter in FRET systems or just as alternative for ROX.

5'

Microarray experiments
Real-time PCR, qPCR, FRET
In-situ hybridisation
FISH microscopy
Multicolour detection

Cyanine3.5 is a fluorescent dye of the cyanine phosphoramidite family.

It is characterised by

• High extinction coefficient,
• Good pH stability in various buffer conditions
• Absorbance in the orange range

5'
Int
3'

FRET, real-time PCR, qPCR
SNP detection
Allelic discrimination
End point detection

LightCycler Red 610 is an NHS ester supplied and patented by Roche Diagnostics GmbH. It is used for labelling the 5’-end for LightCycler probes to be used in LightCycler instruments.

In addition, the 3’-end of the probe has to be blocked with C3 spacer or phosphate to avoid elongation during PCR.

5'
Int
3'

Multicolour detection
Imaging applications
In-situ hybridisation / FISH
Fluorescence microscopy

ATTO 594 is a novel fluorescent label produced by ATTO-TEC GmbH belonging to the class of Rhodamine dyes. Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High thermal and photo-stability and
• Excellent water solubility

5'
Int
3'

Microarray experiments
FISH microscopy
Gel electrophoresis

DY-480 XL is a part of the so called Megastoke family produced by Dyomics GmbH. Megastoke dyes exhibit a
large Stokes-Shift. These dyes are compatible with the use of qPCR probes on LightCycler real-time PCR machines.

Additionally Megastoke dyes are also characterised by

• High extinction coefficients
• High fluorescence quantum yields
• High stability to photo-bleaching

5'
Int
3'

Real-time PCR, qPCR, FRET
Multicolour detection
Imaging applications
In-situ hybridisation / FISH
Fluorescence microscopy

DY-610 is part of the Dyomics fluorescent dyes produced by Dyomics GmbH.

Dyomics dyes are characterised by

• High extinction coefficients
• High fluorescence quantum yields
• Large Stoke-Shift
• High stability to photo-bleaching

5'
Int
3'

Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation
FISH microscopy

ATTO 610 belongs to a new generation of fluorescent labels from ATTO-TEC GmbH for the red spectral region.

Characteristic features of this label are

• Strong absorption
• High fluorescence quantum yield
• High thermal and photo-stability

ATTO 610 is moderately hydrophilic. The dye is very stable in pH-values up to pH 8.5. It slowly degrades at higher pH.

The fluorescence is excited most efficiently in the range 595-625 nm.

5'
Int
3'

FRET, real-time PCR
SNP detection
Allelic discrimination
End point detection

LightCycler Red 640 is an NHS ester supplied and patented by Roche Diagnostics GmbH. It is used for labeling the 5’-end for LightCycler probes to be used in LightCycler instruments.

In addition, the 3’-end of the probe has to be blocked with C3 spacer or phosphate to avoid elongation during PCR.

5'
Int
3'

FRET
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Bodipy 630/650 is part of the Bodipy family produced by Molecular Probes.

These are the characteristics of Bodipy 630/650:

• Less susceptible to photo-bleaching and
• High signal intensity

5'
Int
3'

Real-time PCR, qPCR, FRET
Microsatellite analysis
In-situ hybridisation
FISH microscopy

ATTO 633 belongs to a new generation of fluorescent labels from ATTO-TEC GmbH for the red spectral region.

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• High thermal and photo-stability

Absorption and fluorescence are independent of pH, at least in the range of pH 2 to 11.

ATTO 633 is moderately hydrophilic.

Its fluorescence is excited most efficiently in the range 610-645 nm.

A suitable excitation source is the 633 nm line of the He:Ne laser or a diode-laser emitting at 635 nm.

5'
Int
3'

Multicolour detection
FRET
Fluorescence microscopy
In-situ hybridisation / FISH

The specifications from Alexa Fluor 647 from Molecular Probes are

• Spectra are virtually identical to those of the Cy5
• Photo stability and fluorescence typically exceeds that of Cy5
• Reasonable water solubility

5'
Int
3'

FRET
Immunological detection
In-situ hybridisation
Fluorescence microscopy

Bodipy 650/665 is part of the Bodipy family produced by Molecular Probes.

The characteristics of these modifications are

• Less susceptible to photo-bleaching
• A high signal intensity

5', 3', intern

Real-time PCR, qPCR, FRET
Microarray experiments
In-situ hybridisation
FISH microscopy
DNA sequencing

Cyanine5 is a fluorescent dye of the cyanine family.
It is characterised by

• Excellent spectroscopic performance
• High extinction coefficient
• Good stability of fluorescence signal against pH changes in various buffer conditions

5'
Int
3'

Real-time PCR, qPCR, FRET
Multicolour detection
Imaging applications
In-situ hybridisation / FISH
Fluorescence microscopy

DY-649 is part of the Dyomics fluorescent dyes produced by Dyomics GmbH.

Dyomics dyes are characterised by

• High extinction coefficients
• High fluorescence quantum yields
• Large Stoke-Shift
• High stability to photo-bleaching

Alexa Fluor 690
TYE 705

5'

Microarray experiments
Real-time PCR, qPCR, FRET
In-situ hybridisation
FISH microscopy

Cyanine5.5 is a fluorescent dye of the cyanine phosphoramidite family.

It is characterised by

• High extinction coefficient
• Good pH stability in various buffer conditions
• Absorbance in the orange range

Cyanine5.5 is an alternative modification in multi-colour experiments.

Alexa Fluor 680
Alexa Fluor 700

5'
Int
3'

Real-time PCR, qPCR, FRET
Microarray experiments
In-situ hybridisation
FISH microscopy

ATTO 680 belongs to a new generation of fluorescent labels produced by ATTO-TEC GmbH.

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• Good water solubility, and
• High thermal and photo-stability

The fluorescence is excited most efficiently in the range 645-695 nm.

A suitable excitation source for the dye is the krypton-ion laser using the 676 nm line or a diode-laser emitting at 670 nm.

5'
INT
3'

DNA sequencing
AFLP analysis
TILLING
Microsatellite analysis

DY-682 is part of the Dyomics fluorescent dyes produced by Dyomics GmbH.

Dyomics dyes are characterised by

• High extinction coefficients
• High fluorescence quantum yields
• Large Stoke-Shift
• High stability to photo-bleaching

5'
INT
3'

DNA sequencing
AFLP analysis
TILLING
Microsatellite analysis

ATTO 700 belongs to a new generation of fluorescent labels produced by ATTO-TEC GmbH.

Characteristic features of the label are

• Strong absorption
• High fluorescence quantum yield
• Good water solubility and
• High thermal and photo-stability

ATTO 700 is a strong electron acceptor.

The fluorescence is excited most efficiently in the range 670-715 nm.

Cy7
Alexa Fluor 740

5'
Int
3'

Real-time PCR, qPCR, FRET
Microarray experiments
In-situ hybridisation
FISH microscopy

ATTO 740 belongs to a new generation of fluorescent labels produced by ATTO-TEC GmbH for the near infrared spectral region.

Characteristic features of the dye are

• Strong absorption
• Good fluorescence
• Excellent thermal and photo-stability

ATTO 740 is a pH sensitive product. While practically stable up to pH 7.4 (PBS-buffer), it slowly degrades at higher pH.

The fluorescence is excited most efficiently in the range 720 - 755 nm.

5'
INT
3'

DNA sequencing
AFLP analysis
TILLING
Microsatellite analysis

DY-782 is part of the Dyomics fluorescent dyes produced by Dyomics GmbH.

Dyomics dyes are characterised by

• High extinction coefficients
• High fluorescence quantum yields
• Large Stoke-Shift
• High stability to photo-bleaching