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CF Dye Selection Guide

This document provides information on CFTM dyes, which are next generation fluorescent dyes. It includes a quick reference table that lists the CFTM dyes, their excitation and emission wavelengths, what dyes they can replace, and their features. The document then discusses the dyes' technical information, reactive dyes and labeling kits, dye conjugates, and related products.

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0% found this document useful (0 votes)
629 views32 pages

CF Dye Selection Guide

This document provides information on CFTM dyes, which are next generation fluorescent dyes. It includes a quick reference table that lists the CFTM dyes, their excitation and emission wavelengths, what dyes they can replace, and their features. The document then discusses the dyes' technical information, reactive dyes and labeling kits, dye conjugates, and related products.

Uploaded by

Ramona Andronesi
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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CF Dyes

Next Generation Fluorescent Dyes

Introduction to CF Dyes
Quick reference table ... p. 2
Overview of CF dyes ... p. 3
CF dyes FAQs ... p. 4

CF Dyes Technical Information


Technical profiles by CF dye color ... pp. 5-19
CF dyes for super-resolution microscopy ... pp. 20-21
Selected CF dye product references ... p. 22

Reactive Dyes and Labeling Kits


Mix-n-Stain Antibody Labeling Kits ... p. 23
Mix-n-Stain Small Ligand Labeling Kits ... p. 23
Reactive dyes ... p. 24

CF Dye Conjugates
Bioconjugates ... p. 25
Labeled nucleotides ... p. 25
Primary antibody conjugates ... p. 26
Anti-biotin, anti-GFP, and anti-tag antibodies .... p. 27
Secondary antibodies ... p. 27
Highly cross-adsorbed secondary antibodies ... pp. 28-29
F(ab)2 fragments ... p. 29
Isotype-specific secondary antibodies ... p. 29

Related Products and Accessories


EverBrite antifade mounting media, counterstains,
TrueBlack autofluorescence quencher and more ... pp. 30-31
CF Dyes Quick Reference Table
Ex Em
CF dye Page Excitation * Replacement for Features and applications
(nm) (nm)
Alexa Fluor 350, AMCA, DyLight Brightest blue fluorescent conjugates for 350 nm excitation
CF350 5 347 448 UV
350 Highly water-soluble and pH insensitive
Alexa Fluor 405, Cascade Blue,
CF405S 5 404 431 405 nm Better compatibility with common instruments
DyLight 405
BD Horizon V450, eFluor 450, More photostable than Pacific Blue dye with less green spill-over
CF405M 5 408 452 405 nm
Pacific Blue Excellent choice for super-resolution imaging by SIM**
CF405L 6 395 545 405 nm Pacific Orange 405 nm excitable orange fluorescent dye for multicolor detection
Pacific Green, BD Horizon V500, Photostable 405 nm excitable green dye
Visible spectrum

CF430 6 426 498 405 nm


Krome Orange Perfect match for the CFP filter set
CF440 6 440 515 405 nm Alexa Fluor 430 Photostable 405 nm excitable green dye
CF450 7 450 538 405 nm Unique dye Green dye with unique spectral properties
ATTO 488, Alexa Fluor 488, Less non-specific binding and less red spill-over than Alexa Fluor 488
CF488A 7 490 515 488 nm Cy2, DyLight 488, FAM, FITC, Very photostable
Fluorescein Compatible with super-resolution imaging by TIRF**

CF514 8 516 548 488 nm Alexa Fluor 514 Green dye that can be separated from CF488A by spectral unmixing

CF532 9 527 558 532 nm Alexa Fluor 532, ATTO 532 Significantly brighter than Alexa Fluor 532
CF535ST 9 535 568 532 nm Unique dye for STORM** Orange dye designed for STORM super-resolution microscopy**
532, 543, or Alexa Fluor 546,
CF543 10 541 560 Significantly brighter than Alexa Fluor 546
546 nm Tetramethylrhodamine (TAMRA)
532, 543, 546,, Alexa Fluor 555, ATTO 550, Cy3, Brighter than Cy3
CF555 10 555 565
555, or 568 nm DyLight 549, TRITC Validated in multicolor super-resolution imaging by STORM**
Optimized for the 568 nm line of the Ar-Kr mixed-gas
532, 543, 546, Alexa Fluor 568, ATTO 565,
CF568 11 562 583 Brighter and more photostable than Alexa Fluor 568
555, or 568 nm Rhodamine Red
Compatible with TIRF and multicolor STORM**
532, 543, 546, Alexa Fluor 594, ATTO 594, Yields the brightest conjugates among spectrally similar dyes
CF594 12 593 614
555, or 568 nm DyLight 594, Texas Red Extremely photostable
532, 543, 546,
CF594ST 12 593 614 Unique dye for STORM** Specifically designed for super-resolution imaging by STORM**
555, or 568 nm
CF620R 13 617 639 633 or 635 nm LightCycler Red 640 Highly fluorescent dye with unique spectral properties
Yields the brightest antibody conjugates among spectrally similar dyes
Alexa Fluor 633, Alexa Fluor 647,
CF633 14 630 650 633 or 635 nm Far more photostable than Alexa Fluor 647
Far-red

Cy5, DyLight 633


Compatible with super-resolution TIRF, FIONA, and gSHRImP**
Has the best photostability among dyes with Cy5-like spectra
633, 635, or Alexa Fluor 647, ATTO 647N, Cy5,
CF640R 15 642 662 Yields highly fluorescent protein conjugates
640 nm DyLight 649
Compatible with TIRF and FLIMP super-resolution techniques**
633, 635, or Alexa Fluor 647, ATTO 647N, Cy5, Brighter than Cy5
CF647 16 650 665
640 nm DyLight 649 Compatible with multicolor super-resolution imaging by STORM**
633, 635, or Much brighter and more photostable than Alexa Fluor 660
CF660C 17 667 685 Alexa Fluor 660
640 nm Compatible with multicolor super-resolution imaging by STORM**
633, 635, or Brighter than Alexa Fluor 660
CF660R 17 663 682 Alexa Fluor 660
640 nm The most photostable 660 nm dye
The brightest among spectrally similar 680 nm dyes
Alexa Fluor 680, Cy5.5, DyLight
CF680 18 681 698 680 or 685 nm Validated in multicolor STORM and dual-color 3D super-resolution imaging**
680, IRDye 680LT
Compatible with LI-COR Odyssey System
The most photostable 680 nm dye
Alexa Fluor 680, Cy5.5, DyLight Suitable for labeling nucleic acids and small biomolecules
CF680R 18 680 701 680 or 685 nm
680, IRDye 680LT Compatible with LI-COR Odyssey System
Compatible with STED and single molecule spectroscopy**
Exceptionally bright and stable
Alexa Fluor 750, Cy7,
CF750 19 755 777 680 or 685 nm Highly water soluble without bearing excessive charge
DyLight 750, IRDye 750
Near-infrared

Validated in super-resolution imaging by STORM**


DyLight 800, IRDye 800CW, Exceptionally bright and stable
CF770 19 770 797 785 nm
ZW800-1 Compatible with LI-COR Odyssey System
Exceptionally bright and stable
CF790 19 784 806 785 nm Alexa Fluor 790
Highly water soluble without bearing excessive charge
Spectrally similar to Indocyanine
CF800 19 797 816 785 nm Unique long wavelength near-infrared dye
green

*Visible and far-red dyes can be excited by a UV light source for epifluorescence microscopy.
**See pp. 20-21 for more information about CF dyes for super-resolution microscopy
Alexa Fluor, Cascade Blue, Pacific Blue, and Texas Red are registered trademarks of Invitrogen; ATTO dyes are products of ATTO-TEC GmbH; BD Horizon is a trademark of BD Biosciences; Cy is a registered trademark of GE Healthcare; DyLight is a registered
trademark of Thermo Fisher Scientific; eFluor is a registered trademark of eBioscience; IRDye and Odyssey are registered trademarks of LI-COR Bioscience; Krome Orange is a trademark of Beckman Coulter; LightCycler is a registered trademark of Roche Applied
Science.

2 www.biotium.com
CF Dyes Overview

Next-generation fluorescent dyes CF Dyes for Super-Resolution Microscopy

CF dyes are a series of highly water-soluble fluorescent dyes spanning the visible Recent publications comparing synthetic dyes for super-resolution imaging have
and near-infrared (IR) spectrum for labeling biomolecules, especially proteins and shown CF dyes give the best performance for multiple methods. The superior
nucleic acids. Developed by scientists at Biotium using new breakthrough chemistries, brightness, photostability, and photochemical switching properties of certain CF dyes
CF dyes rival or exceed the quality of other commercial dyes, such as Alexa Fluor are ideal for 3-D SIM, 3-D STORM, and other super-resolution and single-molecule
dyes, due to the following novel features. imaging techniques. See pp. 20-21 for more information.

Novel rhodamine chemistry Unrivaled near-infrared dyes

Rhodamine dyes are known for their excellent photostability and good fluorescence Near-IR dyes are typically much larger in size than dyes in the visible range. The
quantum yield; consequently several of the Alexa Fluor dyes bear the rhodamine large size often results in serious problems of low dye solubility, dye aggregation
core structure. Unfortunately, traditional rhodamine chemistry makes it difficult to and poor fluorescence quantum yield. To overcome the problems, many commercial
extend the fluorescence wavelength to the far-red region and even more challenging near-IR dyes, such as the near-IR Alexa Fluor dyes, DyLight dyes and IRDyes,
in the near-IR region, especially for water-soluble dyes for bioconjugation. Recently, are prepared by placing a number of negatively charged sulfonate group on the dyes.
Biotium scientists discovered a new way to prepare novel rhodamine dyes of any While sulfonation improves dye solubility and fluorescence quantum yield to some
fluorescence color from green to near-IR. The new chemistry is a key element in the degree, it creates another even more serious problem: non-specific binding of the
development of many of our CF dyes, particularly our far-red CF dyes, which are bioconjugates prepared from the dyes. For example, conjugation to a highly negatively
not only bright and water-soluble but also extremely photostable. charged dye can dramatically alter an antibodys isoelectric point (iP), which is
essential for maintaining specific antibody-antigen interaction. With this insight, Biotium
scientists devised a revolutionary new approach to near-IR dye design that results in
Excellent labeling efficiency
superior physical properties of the dyes without introducing an excessive amount of
negative charge.
Reactive dyes for bioconjugation are generally susceptible to hydrolysis, which
can cause problems for shipping, handling and storage and result in lower labeling
Biotiums near-IR CF dyes are based on the core structure of either cyanine dyes
efficiency. Heavily sulfonated dyes, such as the Alexa Fluor dyes, DyLight dyes
or rhodamine dyes. Those core structures are modified such that the intramolecular
and IRDyes are particularly hygroscopic, worsening the hydrolysis problem. For
mobility of the dyes is restricted, which leads to higher quantum yield and better
example, the percent of active Alexa Fluor 488 succinimidyl ester (SE) could be well
water solubility without adding excessive charge. As a result, near-IR CF dyes are
below 50% by the time of application (according to Life Technologies Alexa Fluor
much brighter and more photostable than any other near-IR dyes. Most importantly,
488 microscale labeling kit product information sheet, Invitrogen). In contrast, all of
antibodies labeled with near-IR CF dyes give far better signal-to-noise ratio in
Biotiums amine-reactive CF dyes have a relatively stable form of SE, which is more
immunostaining compared with antibody conjugates prepared with other commercial
resistant to hydrolysis than the SE in many of the Alexa Fluor dyes. Accordingly,
near-IR dyes.
CF dye SE products generally give consistently higher labeling efficiency, thus
providing users a better value.
Multi-color flexibility
Mix-n-Stain antibody labeling technology
Biotium currently offers 26 CF dyes with additional colors in development. The CF
dye product line includes reactive CF dyes, labeling kits, CF-labeled secondary
Biotium has developed a breakthrough antibody labeling technology with CF
antibodies and streptavidin, and many other CF-labeled biomolecules.
dyes Mix-n-Stain antibody labeling kits. With this technology, you merely need
to mix your antibody with the reaction buffer and CF dye provided in the kit, and
in 30 minutes you will have an optimally labeled CF dye-antibody conjugate ready CF dyes and Mix-n-Stain antibody labeling technology are covered
for immunostaining. The labeling technology provides unprecedented convenience by pending U.S. and international patents. We welcome inquiries about
for antibody labeling. Mix-n-Stain labeled antibodies can be used for multicolor licensing the use of our dyes, trademarks or technologies; email us at
immunostaining, allowing staining with multiple primary antibodies from the same host [email protected].
species when pre-labeled primary antibodies are not available.

Emission spectra of CF dyes


CF350
CF405S
CF405M
CF405L
CF430
CF440
CF488A
CF514
CF532
CF543
CF555
CF568
CF594
CF620R
CF633
CF640R
CF647
CF660C
CF660R
CF680
CF680R
CF750
CF770
CF790
CF800
350 450 550 650 750 850 950
Wavelength (nm)

www.biotium.com 3
Alexa Fluor is a registered trademark of Invitrogen; DyLight is a registered trademark of Thermo Fisher Scientific; IRDye is a registered trademark of Li-COR Bioscience.
CF Dyes
Frequently Asked Questions

Question Answer
What does the CF in CF dyes stand for? CF initially was an abbreviation for Cyanine-based Fluorescent dyes. These were the first patented CF dyes based on cyanine dye
structures. Since then, our CF dye patent portfolio has expanded to include four different fluorescent dye core structures that cover the
fluorescence spectrum from UV to NIR.
What are the chemical structures of CF dyes? The exact chemical structures of CF dyes are currently confidential but will be fully disclosed at a later stage when pending patents
become granted. In general terms, the structure of a CF dye may be divided into two parts: a) dye core structure (i.e. the aromatic ring
skeleton that defines the dyes color or absorption/emission wavelengths), and b) core structure-modifying elements. At present, CF dyes
bear the core structures of coumarin, pyrene, rhodamine or cyanine dyes. Blue fluorescent CF dyes are based on coumarin or pyrene dye
core structure, while green to near-IR CF dyes are based on either cyanine or rhodamine dye core structures. Core structure-modifying
elements refer to various chemical attachments to the core structure and are a key aspect of the CF dye invention that makes CF dyes
superior to other commercial dyes.
What are the quantum yields of CF dyes? The quantum yield of a fluorescent dye can vary widely depending on the dyes micro-environment if the dye is attached to a protein or
other molecule. A good way to compare the relative quantum yields of different dyes is to plot the total fluorescence of the labeled proteins
as a function of degree of labeling by the dyes, as we have done with CF dyes and other commercial dyes in the dye description pages in
this guide.
How stable are CF dyes? There are three aspects to dye stability: 1) chemical stability of the dye core structure; 2) stability of the reactive group; and 3)
photostability of the dye.
CF dyes bear the core structures of coumarin, pyrene, rhodamine or cyanine dyes, all of which are known to have excellent chemical
stability. In general, the dyes are far more stable than the antibodies or other biomolecules they label. CF dyes are also stable enough for
labeled nucleic acids to be used in PCR or nucleic acid hybridization, where high temperature is involved.
Reactive CF dyes comprise a reactive group used in bioconjugation. Among the various reactive groups, only amine-reactive
succinimidyl ester (SE) and thiol-reactive maleimide groups are susceptible to hydrolysis and therefore are moisture-sensitive. CF dye
SE products are relatively more stable than other commercial SE dyes. This is because CF SE dyes are derived from aliphatic carboxylic
groups, which results in a more stable SE form, while other commercial SE dyes usually are derived from aromatic carboxylic acid groups
that yield a less stable SE form.
Photostability refers to the dyes ability to withstand photobleaching. Photobleaching is mainly a concern when dyes are subjected
to intense illumination for an extended period of time, such as during confocal microscopy. Among the four types of core structures,
rhodamine is the most photostable, followed by cyanine, pyrene and coumarin cores. The structure-modifying groups and the way they are
attached to the dye cores are a key innovative aspect of CF dye technologies that contributes to the superior photostability of CF dyes over
that of other commercial dyes. In general, rhodamine-based CF dyes, whose wavelengths range from green to the near-IR region, offer the
best photostability, making these dyes ideal for microscopy applications.
Are CF dyes sensitive to pH? CF dyes are chemically stable within the pH range of at least 2 11. The fluorescence of most CF dyes is relatively insensitive to pH,
except for that of CF405M, CF568, CF620R, and CF633. The fluorescence of these four CF dyes becomes weaker when pH drops below
4.5.
Are CF dyes fixable? CF dyes can tolerate formaldehyde fixation. However, whether a CF dye-labeled probe is fixable will depend on the fixability of the
probe itself. Proteins with free amine groups that bind other proteins generally are formaldehyde-fixable.
What is the difference between CF405s, All three of these dyes can be excited by the 405 nm laser (or UV mercury lamp). They differ in their emission wavelengths. CF405S
CF405M, and CF405L? has the shortest blue fluorescence emission at 431 nm, while CF405M has longer wavelength blue fluorescence emission at 452 nm.
CF405L has orange fluorescence emission at 545 nm. We recommend choosing the dye that best fits your instruments detection
settings (see pp. 5-6 for more information).
For several CF dye colors, there is an R form Rhodamine-based CF dyes (designated R) generally have better photostability but weaker fluorescence than their cyanine-based
and a C form, both having similar absorption equivalents (designated C). Therefore, rhodamine-based near-IR CF dyes are a better choice for microscopy, while cyanine-based CF
and emission spectra. In such a case, which of dyes are more ideal for flow cytometry, Western blotting, and other applications where photobleaching is less of a concern. Another factor
the two CF dyes should I choose? to consider is the size of the dyes. Some of the cyanine-based near-IR CF dyes are much larger than the rhodamine-based equivalents.
For antibody labeling, either version of the CF dyes is suitable. However, for applications where the dye size may cause a steric problem,
the smaller dye may be a better choice.
How soluble are CF dyes? CF dyes are highly water soluble (>100 mg/mL). They are also very soluble in other polar solvents, such as DMSO, DMF, methanol and
ethanol. However, CF dyes are poorly soluble or insoluble in non-polar solvents.
What are the charges on CF dyes? Most CF dyes carry 1-2 negative charges while a few cyanine-based near-IR CF dyes carry 3-4 negative charges. However, the more
negatively charged CF dyes comprise unique structural features that shield the negative charges such that the biomolecules (such as
antibodies) the dyes label do not lose specificity due to the excessive negative charges.
Can CF dyes be used for STORM? Several CF dyes have been validated in super-resolution imaging by STORM, as well as other super-resolution techniques. Biotium also
offers dyes specifically designed for STORM imaging. See pp. 20-21 for more information.
What are the major applications of CF dyes? CF dyes are ideal for protein labeling because of their high water solubility, which reduces fluorescence quenching. They are also useful
for labeling oligonucleotides that require multiple copies of a dye for maximal fluorescence, such as the preparation of FISH probes, where
water soluble dyes can minimize fluorescence quenching. Finally, CF dyes make excellent polar tracers that can be used for visualizing the
morphology or long-term tracing of neurons.

4 www.biotium.com
CF350

CF350
A bright UV-excitable blue fluorescent dye

Features
Technical Summary Brighter and more photostable than AMCA
Direct replacement for Alexa Fluor 350
Abs/Em Maxima: 347/448 nm Highly water soluble and pH-insensitive
Extinction coefficient: 18,000
Molecular weight: ~ 496
Excitation source: UV
Replaces: Alexa Fluor 350, AMCA, DyLight 350

CF350
Absorption

Figure 1. Absorption and emission


spectra of CF350 goat anti-mouse Emission
conjugate in PBS.

250 300 350 400 450 500 550


Wavelength (nm)
Figure 2. HeLa cells stained with mouse anti-tubulin
antibody and CF350 goat anti-mouse IgG (cyan).

CF405S and CF405M

CF405S & CF405M


Improved brightness and photostability for the 405 nm laser line

- - -CF405S
Technical Summary CF405M
Absorption

Emission
CF405S
Abs/Em Maxima: 404/431 nm
Extinction coefficient: 33,000
Molecular weight: ~ 1,169 320 370 420 470 520
Wavelength (nm)
Excitation laser line: 405 nm
Replaces: Alexa Fluor 405, Cascade Blue, DyLight 405
Figure 1. Absorption and emission spectra of CF405S
and CF405M goat anti-mouse conjugates in PBS.
CF405M
Abs/Em Maxima: 408/452 nm
Extinction coefficient: 41,000
Molecular weight: ~ 503 Features
Excitation laser line: 405 nm CF405S: Brighter than Alexa Fluor 405
Replaces: Pacific Blue, BD Horizon V450 CF405M: More photostable than Pacific Blue, with less spill-over in
the green channel
CF405M: an excellent choice for super-resolution imaging by SIM
(see pp. 20-21)

16 100
Normalized Fluorescence

Figure 2. Intracellular staining of Jurkat Isotype Control


80 CF405M
12
Relative Fluorescence

cells was performed with mouse anti-CD3 Mouse Anti-CD3 Pacific Blue
or isotype control followed by goat anti- 60 Figure 3. Photostability of CF405M
mouse IgG conjugated to Alexa Fluor 405 8 and Pacific Blue. CF405M and Pacific
(AF405) or CF405S. Fluorescence was 40 Blue dye solutions were continuously
analyzed on a BD LSR II flow cytometer 4 exposed to mercury arc lamp microscope
with 405 nm excitation and 450/50 nm 20 excitation with a DAPI filter set. Images
emission filter. Bars represent the relative 0
were captured every 5 seconds for one
fluorescence of the geometric means of 0 minute. Fluorescence intensity was
1.5 5.4 6.4 1.6 4.8 7.2
DOL:
the cell populations. 0 15 30 45 60 normalized to time 0.
AF405 CF405S Time (s)

www.biotium.com 5
CF405L Dye
A 405 nm-excitable dye with orange fluorescence emission
CF405L

Technical Summary
CF405L
Abs/Em Maxima: 395/545 nm

Absorption

Emission
Extinction coefficient: 24,000
Molecular weight: ~1573
Excitation laser line: 405 nm
Replaces: Pacific Orange 300 400 500 600 700
Wavelength (nm)

Figure 1. Absorption and emission spectra of CF405L


goat anti-mouse conjugate in PBS.

CF430 and CF440


Photostable 405 nm-excitable dyes with green fluorescence
CF430 & CF440

Technical Summary Features


Photostable dyes suitable for microscopy
CF430 CF430 is a perfect match for the CFP filter set
Abs/Em Maxima: 426/498 nm Suitable for flow cytometry in the AmCyan channel
Extinction coefficient: 40,000 Highly water soluble and pH-insensitive
Molecular weight: ~429
Excitation laser line: 405 nm
Replaces: Pacific Green, BD Horizon V500, Krome Orange CF430
CF440
Absorption

Emission
CF440
Abs/Em Maxima: 440/515 nm
Extinction coefficient: 40,000
Molecular weight: ~716
300 400 500 600 700
Excitation laser line: 405 nm
Wavelength (nm)
Replaces: Alexa Fluor 430
Figure 1. Absorption and emission spectra of CF430 and
CF440 goat anti-mouse conjugates in PBS.

100%

80%
Relative Maen Intensity

60%

40%

CF440
20% CF430
Pacific Green
Horizon V500
0%
1 2 3 4 5 6 7 8 9 10 11 12
Scan number

Figure 2. Relative photostability of CF430 and CF440 compared to


spectrally-similar dyes. Cells were stained with biotinylated primary
antibodies followed by streptavidin conjugates of CF430, CF440, Pacific Figure 3. Flow cytometry analysis of Jurkat cells stained
Green, or BD Horizon V500. Fluorescence was imaged on a Zeiss LSM700 with isotype control (gray peak) or mouse anti-CD3 (green
confocal microscope in the FITC channel using 405 nm excitation. Images peak) followed by CF430 goat anti-mouse IgG, analyzed in
were acquired every 5 seconds for 12 consecutive scans of the same field of the AmCyan channel of a BD LSRII flow cytometer.
view using the same imaging settings for each dye. The mean fluorescence
intensity of each image was normalized to the first scan for each dye.

6 www.biotium.com
CF450

CF450
A green fluorescent dye with unique spectral properties

Technical Summary
CF450
Abs/Em Maxima: 450/538 nm

Absorption

Emission
Extinction coefficient: 40,000
Molecular weight: ~689
Excitation laser line: 405 nm
350 400 450 500 550 600 650
Wavelength (nm)

Figure 1. Absorption and emission of CF450 goat anti-


mouse conjugate in PBS.

CF488A

CF488A
A superior green fluorescent dye

Technical Summary Features


Minimally charged, for less non-specific binding than Alexa Fluor 488
Abs/Em Maxima: 490/515 nm
Narrower emission spectrum for less bleed to red
Extinction coefficient: 70,000
Very photostable
Molecular weight: ~914
Compatible with super-resolution imaging by TIRF (see pp. 20-21)
Excitation laser line: 488 nm
Highly water soluble and pH-insensitive
Replaces: Alexa Fluor 488, DyLight 488, fluorescein (aka FITC,
FAM), Cy2

CF488A
Absorption

Emission

400 450 500 550 600


Wavelength (nm)

Figure 1. Absorption and emission spectra of CF488A


goat anti-mouse conjugate in PBS.

Figure 2. HeLa cells stained with rabbit anti-COXIV and CF488A goat anti-
rabbit IgG (mitochondria, green) , mouse anti-Golgin 97 and CF555 goat
anti-mouse IgG (Golgi, red), CF405M phalloidin (actin filaments, blue), and
RedDot2 (nuclei, magenta). See p. 30 for more information on RedDot2.

www.biotium.com 7
CF514
Alternative green fluorescent dye
CF514

Technical Summary Features


Image using the same settings as FITC or CF488A
Abs/Em Maxima: 516/548 nm
Can be distinguished from CF488A in the same specimen by
Extinction coefficient: 105,000
spectral imaging and linear unmixing
Molecular weight: ~1216
Excitation laser line: 488 nm
Replaces: Alexa Fluor 514

CF488A
CF514
Absorption

Emission

350 450 550 650


Wavelength (nm)

Figure 1. Absorption and emission spectra of CF514


goat anti-mouse conjugate in PBS.

8 www.biotium.com
CF532

CF532
A bright orange fluorescent dye for the 532 nm laser

Technical Summary Features


Designed for the 532 nm laser
Abs/Em Maxima: 527/558 nm
Brighter than Alexa Fluor 532 (Fig. 2)
Extinction coefficient: 96,000
Highly water-soluble and pH-insensitive
Molecular weight: ~ 685
Excitation laser line: 532 nm
Direct replacement for: Alexa Fluor 532, Atto 532
300
2nd Ab Alone
250

Relative Fluorescence
Mouse anti-CD3
200

150
CF532
100
Absorption

Emission

50

0
DOL: 4.2 6.1 8.8 3.1 6.1 7.3
AF532 CF532
300 400 500 600 700
Wavelength (nm) Goat Anti-Mouse Conjugate

Figure 2. Flow cytometry analysis of Jurkat cells stained with Alexa


Figure 1. Absorption and emission spectra of CF532 Fluor 532 (AF532) antibody or CF532 secondary antibody conjugates.
goat anti-mouse IgG conjugate in PBS. Intracellular staining was performed with mouse anti-CD3 antibody
followed by goat anti-mouse IgG conjugates. Background was determined
by staining with secondary antibody (2nd Ab) alone. Fluorescence was
analyzed on a BD FACSCalibur flow cytometer in the FL2 channel. The
bars represent the relative fluorescence of the geometric means of the cell
populations.

CF535ST

CF535ST
An orange fluorescent dye designed for STORM super-resolution imaging

Technical Summary
CF535ST
Absorption

Abs/Em Maxima: 535/568 nm


Emission

Extinction coefficient: 95,000


Molecular weight: ~728
Excitation laser line: 532 nm
400 450 500 550 600 650 700
Wavelength (nm)
See pp. 20-21 for more information about CF dyes for super-resolution imaging.

Figure 1. Absorption and emission spectra of CF535ST


goat anti-mouse IgG conjugate in PBS.

www.biotium.com 9
CF543
An orange fluorescent dye ideal for the 543 nm laser
CF543

Technical Summary Features


Optimized for the 543 nm laser
Abs/Em Maxima: 541/560 nm
Yields the brightest conjugates among spectrally similar dyes
Extinction coefficient: 100,000
Highly water-soluble and pH-insensitive
Molecular weight: ~ 870
Excitation laser line: 532 nm, 543 nm, or 546 nm
Direct replacement for: Alexa Fluor 546, TAMRA

100

Relative Fluorescence
CF543 80
CF543
60
Absorption

Emission

AF546
40

20

0
450 500 550 600 650
2 4 6 8 10 12 14
Wavelength (nm)
Degree of Labeling (DOL)

Figure 1. Absorption and emission spectra of CF543


goat anti-mouse conjugate in PBS. Figure 2. Relative fluorescence of CF543 and Alexa Fluor 546
(AF546) goat anti-mouse conjugates as a function of the number of
dye molecules per protein (degree of labeling).

CF555
A bright and photostable orange-red dye
CF555

Technical Summary Features


Brighter than Cy3
Abs/Em Maxima: 555/565 nm
Highly water-soluble
Extinction coefficient: 150,000
Validated in multicolor STORM super-resolution imaging (see pp. 20-21)
Molecular weight: ~ 901
Excitation laser line: 532 nm or 568 nm
Direct replacement for: Alexa Fluor555, ATTO 550, Cy3,
DyLight 549, Rhodamine

CF555
Absorption

Emission

450 500 550 600 650


Wavelength (nm)

Figure 1. Absorption and emission spectra of CF555


goat anti-mouse conjugate in PBS. Figure 2. Frozen section of rat testis stained with mouse anti-tubulin
and CF488A goat anti-mouse (min x rat) (microtubules, green), CF555
Mix-n-Stain labeled mouse anti-ZO1 (tight junctions, red) and CF640R
phalloidin (actin filaments, cyan). See p. 23 for more information on
Mix-n-Stain antibody labeling kits.

10 www.biotium.com
CF568

CF568
Outshines Alexa Fluor568

Technical Summary Features


Yields much brighter antibody conjugates than Alexa Fluor 568
Abs/Em Maxima: 562/583 nm
Extremely photostable
Extinction coefficient: 100,000
Excellent choice for multi-color imaging with CF488A and CF640R
Molecular weight: ~ 714
Compatible with TIRF and multicolor STORM super-resolution imaging
Excitation laser line: 532 nm or 568 nm
(see pp. 20-21)
Direct replacement for: Alexa Fluor 568, ATTO 565,
Rhodamine Red

100
CF568

Normalized Fluorescence
80 CF568
Absorption

Emission

AF568
60

40

20
450 500 550 600 650 700
Wavelength (nm) 0
0 60 120 180 240 300
Figure 1. Absorption and emission spectra of CF568 Time (s)
goat anti-mouse conjugate in PBS.
Figure 3. Photostability of CF568 and Alexa Fluor 568 (AF568)
streptavidin conjugates. Intracellular staining of Jurkat cells
was performed using anti-CD3-biotin followed by streptavidin-
CF568 or streptavidin-AF568. Cells were continuously exposed
to mercury arc lamp microscope excitation with a Cy3 filter set.
Images were captured every 15 seconds for 5 minutes and
fluorescence intensity was normalized to time 0.

200

Isotype
Relative Fluorescence

150
CD3

100

50

0
AF568 AF568 CF568 CF568
DOL 2.9 DOL 4.2 DOL 2.2 DOL4.1
Goat Anti-Mouse Conjugate

Figure 2. Intracellular staining of Jurkat cells was performed


using mouse anti-CD3 or isotype control followed by goat
anti-mouse IgG conjugates. Fluorescence was analyzed on
a BD FACSCalibur flow cytometer in the FL2 channel. Bars
represent the relative fluorescence of the geometric means of
the cell populations.
Figure 4. MCF-7 cells stained with CF568 monoclonal anti-Ep-CAM
(clone EGP40/826) at 5 ug/mL (red). Nuclei are counterstained with
Hoechst 33342 (blue). See p. 26 for more information on primary
antibody conjugates.

www.biotium.com 11
CF594
CF594

Truly the brightest deep red dye

Technical Summary Features


Yields the brightest antibody conjugates among spectrally similar dyes.
Abs/Em Maxima: 593/614 nm
Excellent choice for multicolor imaging with green dyes like CF488A
Extinction coefficient: 115,000
Extremely photostable
Molecular weight: ~730
Also see CF594ST, a version of CF594 engineered specifically for
Excitation laser line: 532 nm, 568 nm or 594 nm STORM microcopy (pp. 20-21).
Replaces: Alexa Fluor 594, DyLight 594, Texas Red

100
CF594

Normalized Fluorescence
CF594
80
AF594
Absorption

Emission

60

40

20
475 525 575 625 675 725 0
Wavelength (nm)
0 60 120 180 240 300
Time (s)
Figure 1. Absorption and emission spectra of CF594
goat anti-mouse conjugate in PBS.
Figure 3. Photostability of CF594 and Alexa Fluor 594 (AF594)
goat anti-mouse conjugates. Intracellular staining of Jurkat
cells was performed with mouse anti-CD3 followed by CF594
or AF594 goat anti-mouse conjugates. Cells were continuously
exposed to mercury arc lamp microscope excitation with a Texas
Red filter set. Images were captured every 15 seconds for 5
min and fluorescence intensity was normalized to time 0.
100
Relative Fluorescence

80
CF594
60 AF594

40

20

0
0 2 4 6 8 10
Degree of Labeling (DOL)

Figure 2. Relative fluorescence of CF594 and Alexa Fluor


594 (AF594) goat anti-mouse conjugates as a function of the
number of dye molecules per protein (degree of labeling).

Figure 4. Glial cells in frozen section of rat brain stained with rabbit
anti-GFAP antibody and CF594 goat anti-rabbit IgG (red). Nuclei are
stained with RedDot2 (pseudocolored cyan). Mounted with Everbrite
Mounting Medium. See p. 30 for more information on RedDot2 and
EverBrite Mounting Medium.

12 www.biotium.com
CF620R

CF620R
A bright and photostable far-red dye

Technical Summary Features


Highly water-soluble
Abs/Em Maxima: 617/639 nm
Highly fluorescent and extremely photostable
Extinction coefficient: 115,000
Absorption/emission at 617/639 nm for use in FRET or multi-color detection
Molecular weight: ~ 738
Excitation laser line: 633 nm or 635 nm
Replaces: LightCycler Red 640

CF620R

Absorption

Emission
500 550 600 650 700 750
Wavelength (nm)

Figure 1. Absorption and emission spectra of CF620R


free acid in PBS.

www.biotium.com 13
CF633
CF633

The best dye for 633/635 laser lines

Technical Summary Features


Yields the brightest antibody conjugates among spectrally similar dyes
Abs/Em Maxima: 630/650 nm
Far more photostable than Alexa Fluor 647
Extinction coefficient: 100,000
Compatible with TIRF, FIONA, and gSHRImP super-resolution imaging
Molecular weight: ~820
methods (see pp. 20-21)
Excitation laser line: 633 nm or 635 nm
Replaces: Alexa Fluor 633, Alexa Fluor 647, Cy5, DyLight
633, DyLight 649

0 min. 1 min. 5 min.

CF633
Absorption

Emission

CF633

Figure 1. Absorption and emission spectra of CF633


goat anti-mouse conjugate in PBS.
500 550 600 650 700 750
Wavelength (nm)
AF647
Figure 1. Absorption and emission spectra of CF633
goat anti-mouse conjugate in PBS.

Figure 3. Relative photostability of CF633 and Alexa Fluor 647 (AF647) goat anti-mouse conjugates.
Jurkat cells were fixed, permeabilized and stained with rabbit anti-CD3 followed by CF633 or Alexa Fluor
647 goat anti-rabbit IgG conjugates. Cells were imaged using a mercury arc lamp microscope equipped
with a Cy5 filter set and CCD camera. Sequential images were captured at 0, 1, and 5 minutes.

1600
Relative Fluorescence

Isotype
1200 CD3

800

400

0
AF633 CF633 AF647 CF633
DOL 3.0 DOL 3.0 DOL 6.0 DOL 5.8
Goat Anti-Mouse Conjugate

Figure 2. Intracellular staining of Jurkat cells was performed


using mouse anti-CD3 or isotype control followed by goat anti-
mouse IgG conjugates. Fluorescence was analyzed on a BD
FACSCalibur flow cytometer in the FL4 channel. Bars represent
the relative fluorescence of the geometric means of the cell
populations.

14 www.biotium.com
CF640R

CF640R
A highly photostable far-red dye

Technical Summary Features


Best photostability among Cy5-like dyes
Abs/Em Maxima: 642/662 nm
Yields highly fluorescent protein conjugates
Extinction coefficient: 105,000
Compatible with TIRF and FLIMP super-resolution microscopy
Molecular weight: ~ 832
(see pp. 20-21)
Excitation laser line: 633 nm, 635 nm or 640 nm
Replaces Alexa Fluor 647, ATTO 647N, Cy5, DyLight 649

100

Normalized Fluorescence
CF640R 80

60
Absorption

Emission

40
CF640R
AF647
20

0
0 30 60 90 120 150 180

525 575 625 675 725 775 Time (s)


Wavelength (nm)

Figure 1. Absorption and emission spectra of CF640R Figure 3. Photostability comparison between CF640R and Alexa
goat anti-mouse conjugate in PBS. Fluor 647 (AF647). HeLa cells were stained with anti-tubulin antibody
conjugates of each dye. Cells were continuously illuminated by a
mercury arc lamp microscope and sequential images were captured at
0, 1, and 3 minutes. Mean fluorescence was normalized to time 0.

2500
2nd Ab
2000 Mouse Anti-CD3
Relative Fluorescence

1500

1000

500

0
Cy5 AF647 DOL 6.0 CF640R DOL 6.0
Goat Anti-Mouse Conjugate

Figure 2. Intracellular staining of Jurkat cells was performed using


mouse anti-CD3 or isotype control followed by goat anti-mouse IgG
conjugates. Fluorescence was analyzed on a BD FACSCalibur flow
cytometer in the FL4 channel. Bars represent the relative fluorescence
of the geometric means of the cell populations.

Figure 4. MCF-7 cells stained with CF640R monoclonal anti-Cyclin B1 (clone


CCNB1/1098) at 5 ug/mL (red). Nuclei are counterstained with Hoechst
33342 (blue) and actin filaments are stained with CF488A phalloidin (green).
See p. 26 for more information on primary antibody conjugates.

www.biotium.com 15
CF647
CF647

A highly fluorescent far-red dye

Technical Summary Features


Brighter than Cy5
Abs/Em Maxima: 650/665 nm
Highly water soluble and pH insensitive
Extinction coefficient: 240,000
Validated in multi-color super-resolution imaging by STORM (see pp. 20-21)
Molecular weight: ~ 1058
Excitation laser line: 633 nm, 635 nm or 640 nm
Replaces: Cy5, Alexa Fluor 647, DyLight 649

CF647
Absorption

Emission

550 600 650 700 750


Wavelength (nm)

Figure 1. Absorption and emission spectra of


CF647 goat anti-mouse conjugate in PBS.

Figure 3. Cultured rat hippocampal neurons microinjected with CF647


hydrazide (red) and stained with SynaptoGreen C4 (FM1-43) (green,
synaptic vesicles). Image courtesy of Professor Guosong Liu, Tsinghua
University, Beijing, China.

Figure 2. Intracellular staining of Jurkat cells with CF647


monoclonal anit-nucleollin (clone 365-2) (pink) or CF647 IgG1
isotype control (blue) at 1 ug/tube, compared to unstained
cellls (yellow). Cells were analyzed in the APC channel of a
BD LSRII flow cytometer. See p. 26 for more information on
primary antibody conjugates.

16 www.biotium.com
CF660C and CF660R

CF660C & CF660R


Superior alternatives to Alexa Fluor 660

Technical Summary CF660C Features


Much brighter and more photostable than Alexa Fluor 660
CF660C
Compatible with multicolor super-resolution imaging by STORM (see pp.
Abs/Em Maxima: 667/685 nm 20-21)
Extinction coefficient: 200,000
Molecular weight: ~ 3112
CF660R Features
Excitation laser line: 633 nm, 635 nm or 640 nm
Brighter than Alexa Fluor 660
Replaces: Alexa Fluor 660, Allophycocyanin (APC)
Unrivaled photostability among spectrally similar dyes

CF660R
Abs/Em Maxima: 663/682 nm
Extinction coefficient: 100,000
Molecular weight: ~ 888
Excitation laser line: 633 nm, 635 nm or 640 nm 100
Replaces: Alexa Fluor 660, Allophycocyanin (APC)

Relative Fluorescence
CF660C
80
CF660R
60 AF660

40
20
0
CF660C CF660R
0 2 4 6 8 10 12
Degree of Labeling (DOL)
Absorption

Emission

Figure 2. Relative fluorescence of CF660, CF660R and Alexa Fluor


660 (AF660) goat anti-mouse conjugates as a function of the number
of dye molecules per protein (degree of labeling).

550 600 650 700 750 800


Wavelength (nm)

120
Figure 1. Absorption and emission spectra of CF660C
and CF660R goat anti-mouse conjugates in PBS.
Normalized Fluorescence

100

80 CF660R
CF660C
60 AlexaFluor 660
40

20

0
0 60 120 180 240 300
Time (s)

Figure 3. Photostability of CF660C, CF660R, and Alexa Fluor 660


(AF660) goat anti-mouse conjugates. HeLa cells were stained with
mouse anti-tubulin followed by CF660C, CF660R or AF660 goat anti-
mouse IgG conjugates. Cells were continuously exposed to mercury
arc lamp microscope excitation using a Cy5 filter set. Images were
captured every 10 seconds for five minutes and fluorescence intensity
was normalized to time 0.

www.biotium.com 17
CF680 and CF680R Dyes
CF680 & CF680R

Two outstanding 680 nm-excitable dyes

CF680 Features
Technical Summary
The brightest among spectrally similar dyes
CF680 Validated in multicolor STORM and 3D super-resolution microscopy (see
Abs/Em Maxima: 681/698 nm pp. 20-21)
Extinction coefficient: 210,000 Compatible with LI-COR Odyssey
Molecular weight: ~ 3241
Excitation laser line: 680 nm or 685 nm CF680R Features
Replaces: Alexa Fluor 680, Cy5.5, IRDye 680 Unrivaled photostability among spectrally similar dyes
Compatible with STED and single molecule spectroscopy super-resolution
CF680R imaging (see pp. 20-21)
Abs/Em Maxima: 680/701 nm Molecular weight compatible with nucleic acid labeling
Extinction coefficient: 140,000 Compatible with LI-COR Odyssey
Molecular weight: ~ 912
Excitation laser line: 680 nm or 685 nm
Replaces: Alexa Fluor 680, Cy5.5, IRDye 680

30
CF680 CF680R
25 Signal to Noise
20
S/N Ratio
Absorption

Emission

15
10
5
0
DOL: 2.8 3.8 2.6 3.9 2.7 3.5 3.0 4.0
550 600 650 700 750 800
DL 680 Cy5.5 AF 680 CF680
Wavelength (nm)
Goat Anti-Mouse Conjugates
Figure 1. Absorption and emission spectra of CF680 and
CF680R goat anti-mouse conjugates in PBS. Figure 2. Intracellular staining of Jurkat cells was performed using
mouse anti-human CD3 antibody or isotype control followed by
goat anti-mouse secondary antibody conjugates. Fluorescence was
analyzed on a BD FACSCalibur flow cytometer in the FL4 channel
Bars represent the signal-to-noise ratio of CD3-positive fluorescence
to isotype control.

100
Normalized Fluorescence

80
CF680R
60 CF680
Cy5.5
AF680
40

20

0
0 60 120 180 240 300
Time (s)

Figure 3. Photostability of far red dye conjugates. Jurkat cells were


stained with mouse anti-CD3 followed by the indicated goat anti-mouse
IgG conjugates. Cells were continuously exposed to mercury arc lamp
excitation with a Cy5 filter set. Images were captured every 10 seconds
for 5 minutes and fluorescence intensity was normalized to time 0.

18 www.biotium.com
CF750, CF770, CF790, and CF800

Near-IR CF Dyes
Unrivaled Near-Infrared Dyes

Technical Summary Features

CF750 Exceptionally bright and stable

Abs/Em Maxima: 755/777 nm Ideal for in vivo imaging

Extinction coefficient: 250,000 Compatible with LI-COR Odyssey

Molecular weight: ~ 3009 Superior signal-to-noise for bioconjugates

Excitation laser line: 633 nm, 635 nm, 680 nm or 685 nm CF750 validated in STORM microscopy (see pp. 20-21)

Replaces: Alexa Fluor 750, Cy7, DyLight 750


CF770
Abs/Em Maxima: 770/797 nm
Extinction coefficient: 220,000 CF750 CF770

Molecular weight: ~ 3138

Absorption

Emission

Absorption

Emission
Excitation laser line: 785 nm
Replaces: DyLight 800, IRDye 800CW

600 650 700 750 800 850 900 600 650 700 750 800 850 900
CF790 Wavelength (nm) Wavelength(nm)

Abs/Em Maxima: 784/806 nm


Extinction coefficient: 210,000
CF790 CF800
Molecular weight: ~ 3267

Absorption
Absorption

Emission
Emission
Excitation laser line: 785 nm
Replaces: Alexa Fluor 790

600 650 700 750 800 850 900


CF800 600 650 700 750 800 850 900
Wavelength (nm)
Wavelength(nm)
Abs/Em Maxima: 797/816
Figure 1. Absorption and emission spectra of near-IR CF dye goat anti-mouse conjugates in PBS.
Extinction coefficient: 210,000
Molecular weight: ~3334
Excitation laser line: 785 nm
Spectrally similar to: Indocyanine Green A IRDye 680 LT/800 CW CF680/ CF770 B AF 790 CF 790
1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4

24h 48h 72h

Figure 3. Near-infrared western blotting with CF dyes compared to spectrally similar dyes. A. Two-fold
dilutions of HeLa cell lysate containing 2 ug, 1 ug, 0.5 ug, 0.25 ug. 0.125 ug total protein per lane
were separated by SDS-PAGE, transferred to Immobilon FL PVDF (Millipore), and probed with mouse
anti-tubulin and rabbit anti-COXIV antibodies. Secondary detection was performed with either IRDye
680LT goat anti-mouse (red) and IRDye 800CW goat anti-rabbit (green) (LI-COR; lanes 1-6) or CF680
goat anti-mouse (red) and CF770 goat anti-rabbit (green) (lanes 7-12) at the same final concentrations.
Membranes were scanned using an Odyssey infrared imaging system. Quantitation of the bands
showed approximately 1.5-2-fold higher fluorescence intensity of CF dye secondary antibodies
compared to IRDye secondary antibodies. Lanes 1 and 7 contain Odyssey Molecular Weight Marker
(LI-COR Biosciences). B. Western blots of HeLa cell lysate (lanes 2 and 4) were probed with mouse
anti-tubulin antibody followed by goat anti-mouse conjugated to Alexa Fluor 790 (AF790, left) or CF790
(right). CF790 does not introduce excessive negative charge to antibody conjugates, which can increase
non-specific binding. Lanes 1 and 3 contain Dylight 680/800 Protein Ladder (Pierce).
Figure 2. Tumors in mice were imaged using an IVIS imaging system (Caliper
Life Sciences) 24 hours, 48 hours, and 96 hours after IV injection of Avastin
conjugated to CF750. Images courtesy of Caliper Life Sciences.
IRDye, LI-COR, Odyssey, and In-Cell Western are trademarks or registered trademarks of LI-COR, Inc. in the
United States and other countries. IVIS is a registered trademark of Caliper LIfe Sciences.

www.biotium.com 19
CF Dyes for Super-Resolution Imaging
Super-Resolution Imaging

Recent publications comparing synthetic dyes for super-resolution imaging have shown CF dyes give the best performance for multiple methods. The superior brightness,
photostability, and photochemical switching properties of certain CF dyes are ideal for 3-D SIM, 3-D STORM, and other super-resolution and single molecule imaging techniques.
Biotiums CF405M has been found to be the brightest and most photostable short wavelength fluorescent dye for SIM. Six CF dyes spanning the visible red, far-red, and
near-infrared spectra have been validated for STORM, including three color imaging with CF568, CF647, and CF680. See Lehmann et al. 2015, and a full list of references
for CF dye single-molecule imaging applications on page 21. Biotium offers a wide selection of CF dye labeled secondary antibodies, other conjugates, and labeling kits; visit
www.biotium.com for our full selection of products.

Wide-field microscopy STORM CF568 Cy3b


CF647
2 mm 2 mm

CF660C

+600
500 nm 500 nm

z (nm)
CF680

-600
Figure 2. CF568 (left) produces better images than Cy3b (right) in 3-D STORM microscopy.
Fixed cells were stained with mouse anti-tubulin antibody followed by dye-conjugated anti-
mouse secondary antibodies. See Figure 1 legend for imaging conditions. Dye molecules
were photoswitched and imaged using a 560 nm laser; a 405 nm laser was used to assist dye
Figure 1. Comparison of conventional wide-field microscopy (left) with STORM (right)
reactivation to the emitting state.
using CF dye conjugates. Fixed cells were stained with mouse anti-tubulin antibody
followed by CF dye conjugated anti-mouse secondary antibody (top row: CF647,
middle row: CF660C, bottom row: CF680). For STORM, samples were sealed
in buffer that contained 5% (w/v) glucose, 100 mM cysteamine, 0.8 mg/mL glucose
oxidase, and 40 g/mL catalase, in Tris-HCl (pH 7.5). Samples were imaged on a
Nikon Ti-Eclipse w/ PFS microscope with a CFI Plan Apo Lambda 100x oil objective.
Dye molecules were photoswitched and imaged using a 647 nm laser; a 405 nm laser
was used to assist dye reactivation to the emitting state. Emission was collected with
an Andor iXon Ultra 897 EMCCD camera for a total of 100,000 frames per image at a
frame rate of 110 Hz.

STORM microscopy images courtesy of Sam Kenny and Professor Ke Xu, College of Chemistry, University of California, Berkeley.

20 www.biotium.com
CF Dyes for Super-Resolution Imaging

Super-Resolution Imaging
Super-resolution imaging techniques validated for CF dyes
CF Dye Abs/Em maxima Extinction Super resolution References
(nm) coefficient application
CF405M 408/452 41,000 SIM Markaki, Y. et al. (2013). Fluorescence In Situ Hybridization Applications for Super-Resolution 3D Structured
Illumination Microscopy. Methods Mol Biol 950, 43-64.
CF488A 490/515 70,000 TIRF Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule
Tracking Experiments Due to Non-Specific Binding. PLoS ONE 8(9): e74200.
CF535ST 535/568 95,000 STORM Collaborator communication; contact [email protected] for more information.
CF555 555/565 150,000 Multicolor Lehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy. J
STORM Biophotonics DOI 10.1002/jbio.201500119
CF568 562/583 100,000 TIRF, multicolor Lehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy. J
STORM Biophotonics DOI 10.1002/jbio.201500119
Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule
Tracking Experiments Due to Non-Specific Binding. PLoS ONE 8(9): e74200.
Zhang, M. et al. (2015). Translocation of interleukin-1 into a vesicle intermediate in autophagy-mediated
secretion. eLife 2015;10.7554/eLife.11205
CF594ST 593/614 115,000 STORM Collaborator communication; contact [email protected] for more information.
CF633 630/650 100,000 TIRF, FIONA, Bosch, P. J. et al. (2014). Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-
gSHRImP molecule tracking microscopy in live cells. Biophys J 107, 803-814.
Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule
Tracking Experiments Due to Non-Specific Binding. PLoS ONE 8(9): e74200.
Kim, H. J., and Selvin, P. R. (2013). Fluorescence Imaging with One Nanometer Accuracy. SpringerReference
Encyclopedia of Biophysics
Simonson, P. D.,Rothenberg, E., and Selvin, P. R. (2011). Single-molecule-based super-resolution images in
the presence of multiple fluorophores. Nano Lett 11, 5090-5096. DOI:10.1021/nl203560r
CF640R 642/662 105,000 TIRF, FLImP Bosch, P. J. et al. (2014). Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-
molecule tracking microscopy in live cells. Biophys J 107, 803-814.
Martin-Fernandez, M. L. et al. (2013). A 'pocket guide' to total internal reflection fluorescence. J Microsc 252,
16-22.
Zanetti-Domingues, L.C. et al. (2013). Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule
Tracking Experiments Due to Non-Specific Binding. PLoS ONE 8(9): e74200.
Needham, S.R.,et al. (2015). Determining the geometry of oligomers of the human epidermal growth factor
family on cells with <10 nm resolution. Biochem Soc Trans 43, 309314.
CF647 650/665 240,000 Multicolor Lehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy. J
STORM Biophotonics DOI 10.1002/jbio.201500119
Olivier, N. et al. (2013). Simple buffers for 3D STORM microscopy. Biomed Opt Express 4, 885-899.
CF660C 667/685 200,000 Multicolor Zhang, Z., et al. (2015). Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-
STORM resolution microscopy. Nature Methods doi:10.1038/nmeth.3528
CF680 681/698 210,000 Multicolor Frh, S.M. et al. (2015). Molecular architecture of native fibronectin fibrils. Nature Communications 6, 7275.
STORM, Lehmann, M. et al. (2015). Novel organic dyes for multicolor localization-based super-resolution microscopy. J
dual-color 3D Biophotonics DOI 10.1002/jbio.201500119
super resolution Platonova, E. et al. (2015). A Simple Method for GFP- and RFP-based Dual Color Single-Molecule Localization
microscopy Microscopy. ACS Chem. Biol.10(6),14111416.
Platonova, E. et al. (2015). Single-molecule microscopy of molecules tagged with GFP or mRFP derivatives in
mammalian cells using nanobody binders. Methods doi: http://dx.doi.org/10.1016/j.ymeth.2015.06.018
Salvador-Gallego, R. et al. (2016). Bax assembly into rings and arcs in apoptotic mitochondria is linked to
membrane pores. EMBO J. DOI 10.15252/embj.201593384
Winterflood, C.M. et al. (2015). Dual-Color 3D Superresolution Microscopy by Combined Spectral-Demixing
and Biplane Imaging. Biophys J. 109, 36.
Zhang, Z., et al. (2015). Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-
resolution microscopy. Nature Methods doi:10.1038/nmeth.3528
CF680R 680/701 140,000 STED, single- Grlitz, F. et al. (2014). A STED Microscope Designed for Routine Biomedical Applications. Progress
molecule Electromagnetics Res 147, 57-68.
spectroscopy Knig, I. et al. (2015). Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells.
Nature Methods doi:10.1038/nmeth.3475

CF750 755/777 250,000 STORM Collaborator communication; contact [email protected] for more information.

FIONA: Fluorescence Imaging with One Nanometer Accuracy; FLImP: Fluorophore localization imaging with photobleaching; SHRImP: Single-molecule high-resolution imaging with
photobleaching; SIM: Structured illumination microscopy; STED: Stimulated emission depletion; STORM: Stochastical optical reconstruction microscopy; TIRF: Total internal reflection
fluorescence

www.biotium.com 21
Selected CF Dye References
CF Dye References

CF dyes and conjugates have been cited in hundreds of publications, with new references published every day.
Visit www.biotium.com/downloads for a more comprehensive list of CF dye references by color and application.

Immunofluorescence microscopy Mix-n-Stain Antibody Labeling Kits In Cell Western


Ahmed, S. M. et al., J Cell Biol 199, 951 (2012). Ahi, Y. S. et al., J Gen Virol 94, 1325 (2013). Andriamihaja, M. et al., Free Radical Biol Med 85, 219 (2015).
Akhmetshina, A. et al., Nat Commun 3, 735 (2012). Anderson, M. S. et al., J Virol 88, 9111 (2014). Audebert, M. et al., Toxicol Appl Pharmacol 260, 58 (2012).
Al Tanoury, Z. et al., J Cell Sci 127, 521 (2014). Arul, M. et al., Cytotechnology 66, 481 (2013). Jamin, E. L. et al., PLoS One 8, e58591 (2013).
Amann, R. et al., J Virol 87, 1618 (2012). Deo, D. I. et al., Biomacromolecules 15, 2555 (2014). Khoury, L. et al., Environ Mol Mutagen 54, 737 (2013).
Azzedine, H. et al., Hum Mol Genet 22, 4224 (2013). Ersek, B. et al., J Immunol 189, 1602 (2012). Khoury, L. et al., Mutagenesis 31, 83 (2016).
Barboro, P. et al., PLoS One 8, e79212 (2013). Galletti, G. et al., Lab Chip 14, 147 (2014).
Blankenburg, S. et al., Neuropharmacol 88, 134 (2014). Gorham, J. B. et al., Food Hydrocolloids 52, 952 (2016). Near-infrared western blotting
Bosch, P. J. et al., Biophys J 107, 803 (2014). Hirtz, M. et al., Adv Mat Interfaces, n/a (2016).
Annahazi, A. et al., Am J Gastroenterol 108, 1392 (2013).
Chen, T. et al., J Am Chem Soc 135, 11595 (2013). Home, P. et al., Proc Natl Acad Sci U S A 109, 7362 (2012).
Avelar, G. M. et al., Curr Biol 24, 1234 (2014).
Fan, Y. et al., Nat Cell Biol 16, 445 (2014). Kesik, M. et al., RSC Advances 5, 83361 (2015).
Babelova, A. et al., PLoS One 8, e80328 (2013).
Felix-Ortiz, A. C. et al., Neuron 79, 658 (2013). Lim, A. K. et al., Development 140, 3819 (2013).
Dabek, M. et al., Inflamm Bowel Dis 17, 1409 (2011).
Feng, X. et al., Nat Commun 5, 4487 (2014). Lin, T.-B. et al., J Pineal Res, n/a (2016).
Gauthier, T. et al., Mol Nutr Food Res 57, 1026 (2013).
Feng, X. et al., Cell Death Differ 21, 397 (2014). Mikosik, A. et al., Immun Ageing 10, 27 (2013).
Huc, L. et al., Toxicol In Vitro 26, 709 (2012).
Gan, E. S. et al., Nat Commun 5, 5098 (2014). Miyagishima, S. Y. et al., BMC Plant Biol 14, 57 (2014).
Kohler, C. et al., BMC Microbiol 12, 210 (2012).
Hoepflinger, M. C. et al., J Exp Bot 64, 5553 (2013). Montesinos-Rongen, M. et al., J Immunol 195, 1312 (2015).
Liang, Y. et al., Nat Immunol 14, 858 (2013).
Huh, D. et al., Nat Protoc 8, 2135 (2013). Osteikoetxea, X. et al., PLoS One 10, e0121184 (2015).
Lucioli, J. et al., Toxicon 66, 31 (2013).
Inutsuka, A. et al., Neuropharmacol 85, 451 (2014). Park, K. S. et al., Nat Med 17, 1504 (2011).
Martinsen, A. et al., Cell Calcium 52, 413 (2012).
Ise, H. et al., Glycobiology 22, 788 (2012). Ruger, M. et al., BMC Microbiol 14, 56 (2014).
Moussa, L. et al., Clin Nutr 32, 51 (2012).
Jalewa, J. et al., PLoS One 9, e88003 (2014). Ruger, M. et al., Cytometry A 81, 1055 (2012).
Nebot-Vivinus, M. et al., World J Gastroenterol 20, 6832 (2014).
Kanno, T. et al., Free Radic Biol Med, (2012). Sainski, A. M. et al., J Cell Biol 207, 159 (2014).
Oliveira, A. F. et al., J Neurosci 34, 776 (2014).
Kapoor, N. et al., PLoS One 8, e53657 (2013). Tschumper, R. C. et al., Blood Cancer J 3, e112 (2013).
Olivier, I. et al., Inflamm Bowel Dis 17, 747 (2011).
Kawase, A. et al., J Nat Med 68, 395 (2013). Wienand, K. et al., PLoS One 10, e0120734 (2015).
Ottenheijm, C. A. et al., Brain 136, 1718 (2013).
Kern, F. et al., Biochem J 455, 217 (2013). Xu, Z. et al., Proc Natl Acad Sci U S A 110, 13097 (2013).
Wu, C. L. et al., PLoS One 7, e34999 (2012).
Kiyono, M. et al., Planta 235, 841 (2012). Yamamoto, S. et al., Dev Biol 393, 33 (2014).
Kohara, K. et al., Nat Neurosci 17, 269 (2014). Yamashita, A. et al., PLoS One 9, e86426 (2014).
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In vivo imaging
Lee, A. T. et al., J Neurosci 34, 11519 (2014). Zolnerciks, J. K. et al., FASEB J 28, 4335 (2014).
Li, W. et al., J Neurosci 33, 8423 (2013). Abe, S. et al., J Immunol 190, 6239 (2013).
Lim, A. K. et al., Development 140, 3819 (2013). Flow cytometry Alawieh, A. et al., J of Neuroinflamm 12, 1 (2015).
Lindberg, O. R. et al., PLoS One 7, e46380 (2012). Alfonso-Loeches, S. et al., Glia 60, 948 (2012).
Lozada, A. F. et al., J Neurosci 32, 7651 (2012). Endo, H. et al., Cell Death Dis 5, e1027 (2014). Darniot, M. et al., Antiviral Res 93, 364 (2012).
Ma, L. et al., PLoS One 7, e51777 (2012). Gielen, P. R. et al., Neuropharmacology, (2013). Fan, Q. et al., Biomed Res Int 2014, 459676 (2014).
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Ouyang, D. Y. et al., Autophagy 9, 20 (2013). Li, X. et al., Eur J Pharm Sci 52, 132 (2014). Li, X. et al., J Pharmacol Exp Ther 351, 206 (2014).
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Perez Bay, A. E. et al., EMBO J 32, 2125 (2013). Mikosik, A. et al., Immun Ageing 10, 27 (2013). Matsuo, H. et al., Int J Nanomed 7, 3341 (2012).
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Visit our website for more CF


dye references and applications

22 www.biotium.com
In-Cell Western is a registered trademark of LI-COR, Inc. in the United States and other countries.
Mix-n-Stain Antibody and Ligand Labeling Kits

Antibody Labeling Kits


Antibody labeling made simple
Mix-n-Stain Antibody Labeling Kits Mix-n-Stain Small Ligand Labeling Kits
The simplest antibody labeling protocol available For labeling small molecules on primary amines
Label your antibody with your choice of more than 20 CF dye colors, biotin, or Label 0.1 umol SNAP-Tag, CLIP-Tag, HALO-Tag or TMP tag ligands
FITC in just 30 minutes, with minimal hands-on time
Choose from 10 CF dye colors for surface targets, or 5 CF dye colors for
Label your antibody with enzymes or fluorescent proteins in a few hours intracellular targets
No post-labeling purification required
Labeling is covalent, suitable for multiplex staining CF Dye SE and VivoBrite Protein Labeling Kits
Choice of small-scale labeling sizes preserves precious primary antibodies Everything you need to label and purify 3 x 1 mg antibody or other protein using
Reactions tolerate common antibody buffer components and stabilizer proteins standard conjugation techniques
VivoBrite kits feature our superior near-infrared CF dyes for in vivo imaging

Mix-n-Stain Antibody Labeling Kits Mix-n-Stain Small Ligand Labeling Kits


SE Protein VivoBrite Antibody 1 labeling of 1 labeling of 20- 1 labeling of 50- For cell surface For intracellular
Label Ex/Em (nm) Labeling Kits Labeling Kits 5-20 ug antibody 50 ug antibody 100 ug antibody targets targets
Biotin N/A 92224 92286 92266 92244
FITC 494/519 92294 92295 92296
CF350 347/448 92210 92270 92250 92230
CF405S 404/431 92211 92271 92251 92231
CF405M 408/452 92212 92272 92252 92232 92362
CF408 408/450 92356
CF405L 395/495 92228 92303 92304 92305
CF488A 490/515 92213 92273 92253 92233 92350
CF500 500/510 92357
CF514 516/548 92231 92232 92233
CF532 527/558 92208 92289 92290 92291
CF540 540/570 92358
CF543 541/560 92209 92287 92267 92247
CF555 555/565 92214 92274 92254 92234 92364
CF568 562/583 92215 92275 92255 92235 92351
CF594 593/614 92216 92276 92256 92236 92352
CF633 630/650 92217 92277 92257 92237 92353
CF640R 642/662 92225 92278 92258 92245 92354
CF647 650/665 92218 92279 92259 92238 92359
CF650 650/670 92363
CF660C 667/685 92219 92280 92260 92239 92360
CF660R 663/682 92223 92281 92261 92243
CF680 681/698 92220 92160 92282 92262 92240 92361
CF680R 680/701 92226 92283 92263 92246 92355
CF750 755/777 92221 92161 92284 92264 92241
CF770 770/797 92222 92162 92285 92265 92242
CF790 784/806 92163 92288 92268 92248
R-PE 496,564/578 92298** 92299
*10-20 ug labeling; **25-50 ug labeling

APC 650/660 92306** 92307


Per-CP 482/678 92308** 92309
APC-CF750T 650/780 92310** 92311
HRP N/A 92300* 92301** 92302
Alk. Phos. N/A 92314** 92315
Glucose oxidase N/A 92312** 92313
digoxigenin 92328 92329 92330
DNP 92325 92326 92327

www.biotium.com 23
CF Dye Reactive Dyes
Reactive Dyes

A wide selection of colors and functional groups for dye conjugation

Reactive Alkyne Amine Aminooxy Azide BCN Hydrazide Maleimide MTS Picolyl azide SE Tyramide**
group/ 0.5 mg 1 mg 1 mg 0.5 mg 0.5 mg 1 mg 1 umol 1 mg 0.5 mg 1 umol 0.5 mg
unit size
Reacts Azides, Activated Aldehydes & Alkynes, Azides Polar tracer* Thiols Thiols Alkynes Primary HRP
with picolyl carboxylic ketones BCN amines;lysine substrate
azides acids residues
CF350 92035 92050 92151 92020 92109 92170
CF405S 92036 92055 92113 92183 92030 92110 92197
CF405M 92093 92056 92092 92114 92021 92111
CF405L 92046 92112 92198
CF430 92118 92117
CF440 92124 92123
CF450 96012 96011
CF488A 92086 92037 92051 92080 92075 92152 92022 92097 92187 92120 92171
CF500 96026
CF514 92103 92199
CF532 92180 92045 92104
CF543 92181 92044 92098 92105 92172
CF555 92087 92038 92081 92153 92023 92130 96021
CF568 92088 92039 92057 92082 92076 92154 92024 92188 92131 92173
CF570 96015 96014
CF583 96017 96016
CF594 92089 92040 92052 92083 92077 92158 92025 92099 92189 92132 92174
CF620R 92033 92106 92194
CF633 92041 92053 92156 92026 92133
CF640R 92091 92043 92058 92085 92078 92157 92034 92096 92190 92108 92175
CF647 92090 92042 92084 92136 92027 92191 92135 96022
CF650 96027
CF660C 92095 92094 92028 96001 92137
CF660R 96004 96010 92059 92182 96024 92031 92134 92195
CF680 96005 92119 92029 96003 92139
CF680R 96006 92054 92079 96025 92032 96007 92107 92196
CF750 92102 92142
CF770 92065 92192 92150
CF790 92155*
CF800 92128 92127*

* For conjugation to aldehyde or ketone groups, we recommend using CF dye aminooxy forms. * Unit size 0.25 umol

** Visit www.biotium.com to see our Tyramide Amplification Kits, containing CF dye tyramide and HRP secondary antibodies.

Dont see what youre looking for?


We regularly add new CF dye products to our catalog according to customer demand. Be sure to check our website for updates. If you are looking for a CF
dye product not listed in our catalog, please let us know. We may be able to add it as a new product, or perform a custom synthesis for you.

Visit www.biotium.com to see our full selection of reactive biotin reagents and traditional reactive dyes, as well as sets of size- and charge-matched dyes.

24 www.biotium.com
CF Dye Bioconjugates

Bioconjugates
Bioconjugate applications
Conjugate Application

Annexin V Phosphatidyl serine probe; apoptosis marker


Figure 1. Frozen section of rat skeletal muscle stained
a-Bungarotoxin Acetylcholine receptor probe; neuromuscular junction stain with CF633 a-bungarotoxin (magenta) to detect nicotinic
Bovine serum albumin (BSA) Fluid-phase endocytosis tracer; in vivo blood flow tracer acetylcholine receptors at the neuromuscular junction.
Nuclei are stained with DAPI (blue).
Cholera Toxin Subunit B GM1 receptor probe; lipid raft, endocytic vesicle, neuronal tracing
Concanavalin A (Con A) Lectin; binds -D-mannosyl and -D-glucosyl groups, stains yeast cell wall
Dextran, anionic, fixable:
Fluid-phase endocytosis tracer
MW 10K, 40K, 150K, 250K
Phalloidin Filamentous actin probe
Peanut agglutinin (PNA) Lectin; specific for terminal b-galactose
Streptavidin Detection of biotinylated probes
Transferrin (human) Recycling endosome tracer
Lectin, binds N-acetyl-D-glucosamine and sialic acid; Figure 2. S. cerevisiae yeast stained with CF488A WGA
Wheat germ agglutinin (WGA) and CF594 ConA. ConA (red) stains the cell wall, while
bacterial Gram stain, stains yeast bud scars
WGA (green) preferentially stains bud scars.

CF dye bioconjugates
a- Cholera Dextran
Conjugate Annexin V Bungarotoxin BSA Toxin B Con A 10,000 MW Phalloidin PNA Streptavidin Transferrin WGA
CF350 29012 29015 00049 29031 29021
CF405S 00002 29075 29032 29027
CF405M 29009 29074 00034 29033 29028
CF405L 29056
CF430 00054 29065
CF440 00055 29066
CF488A 29005 00005 20289 00070 29016 80110 00042 29060 29034 00081 29022
CF532 00074 00051 29030 29064
CF543 00026 00075 80111 00043 29043 00082
CF555 29004 00018 80112 00040 29038 29076
CF568 29010 00006 00071 80113 00044 29061 29035 00083 29077
CF594 29011 00007 20290 00072 29017 80114 00045 29062 29036 00084 29023
CF620R 00076
CF633 29008 00009 00077 29018 00046 29037 29024
CF640R 29014 00004 20291 00073 29019 80115 00050 29063 29041 00085 29026
CF647 29003 00041 29039
CF660C 00052
CF660R 29069 00078 00047 29040
CF680 29007 20292 29020 80118 00053 29029
CF680R 29070 00003 00079 80116 00048 29042 00086 29025
CF750 29006 80119 00087
CF770 29046 29058 80120 29059
CF790 29047 80121
Visit www.biotium.com to see our selection of apoptosis staining kits, bacterial Gram stain kits, and phalloidin conjugates of biotin and traditional dyes.

Nucleotide conjugates for probe synthesis and TUNEL assay


CF405S CF488A CF532 CF543 CF555 CF568 CF594 CF640R CF647 CF660R CF680R
dCTP 40067 40057 40058 40027 40055 40056 40066 40028 40068
ddCTP 40031
UTP 40032
dUTP 40004 40008 40002 40005 40006 40007 40003
Visit www.biotium.com to see our CF dye TUNEL staining kits, plus a selection of nucleotide conjugates of biotin, traditional dyes, and amino-allyl nucleotides.

www.biotium.com 25
Primary antibody conjugates
Primary Antibodies

Our collection of monoclonal primary antibodies is constantly growing, visit www.biotium.com to see the most up-to-date offerings. Available in the following formats:
Purified: 200 ug/mL in PBS with 0.05% BSA & 0.05% azide, 100 uL (20 ug) or 500 uL (100 ug) unit size
Purified, BSA-free: 1 mg/ml in PBS with 0.05% azide, ready-to-use for Mix-n-Stain labeling (see p. 23) or other conjugation, 50 uL (50 ug) unit size
Conjugates: Your choice of 12 CF dye colors for microscopy, flow cytometry, or near-infrared western blot, plus R-PE, APC, and PerCP;
100 ug/mL in PBS with 0.05% BSA & 0.05% azide, 100 uL (10 ug) or 500 uL (50 ug) unit size

A CD27 Complement C4d HCG-beta MHC II Prostate Specific Antigen


A, Forssman CD28 Creatine Phosphokinase HCG-intact Milk Fat Globulin Proximal Nephrogenic
ACTH CD282 / TLR2 Cyclin A2 Helicobacter pylori MiTF Antigen
Adenosine Monophosphate CD284 / TLR4 Cyclin B1 Heparan Sulphate Proteoglycan Mitochondria pS2
Deaminase 3 CD30 Cyclin D1 Hepatocyte Specific Antigen Mitochondrial Marker PSA
AFP CD31 / PECAM-1 Cytochrome C HepPar-1 Moesin PTEN
Alkaline Phosphatase CD32 Cytokeratin 10 HER-2 / CD340 MRP-14 PTH
AMACR / p504S CD33 Cytokeratin 10/13 HIF1? MUC18 / Mucin 18 / CD146 PTH / Parathyroid
Androgen Receptor CD34 Cytokeratin 14 Histiocytoma Marker MUC2 Hormone
Arginase 1 CD35 / CR1 Cytokeratin 17 Histone H1 MUC5AC
CD36 Cytokeratin 18 HLA-Aw32 & HLA-A25 Mucin 1 / EMA / Episialin / R
CD37 Cytokeratin 19 HLA-B CD227 Rabies
B CD38 Cytokeratin 5/8 HLA-DRB Mucin 3
Bax Retinol Binding Protein-1
CD3e Cytokeratin 6 HSP27 Mucin 5AC
BCL-10 CD4 Cytokeratin 7 HSP60 Mucin 6
bcl-2 CD41a Cytokeratin 8 Human Nuclear Antigen Muscle Specific Actin
S
bcl-6 S100
CD43 Cytokeratin 8/18 Human Nucleolar Antigen Myeloid-Associated
bcl-x S100A9
CD44 Standard Cytokeratin, Acidic Human Papillomavirus 16 Differentiation Marker
Beta Catenin SHBG
CD45 / LCA Cytokeratin, Basic MyoD1
Beta-2 Microglobulin Small Cell Lung Cancer
CD45RA Cytokeratin, HMW I Myogenin
Biotin Smooth Muscle Actin
CD45RB Cytokeratin, LMW IDH1 Myosin, Smooth Muscle Heavy
Blood Group A SOX10
CD45RO Cytokeratin, multi IgA Immunoglobulin Chain
Blood Group Antigen A SUMO-1
CD46 Cytokeratin, pan IgA Secretory Component
Blood Group Antigen B SUMO-2
CD47 IGF-1
Bovine Serum Albumin CD48
N SUMO-2/3
BrdU D IgG Napsin-A
CD5 IgG Immunoglobulin
Bromodeoxyuridine DOG-1 Neurofilament
CD50
Double Stranded DNA IgM Immunoglobulin Neurofilament, phospho
T
CD53 IL-6 TAG-72 / CA72.4
NGFR
C CD54 Insulin NKX2.2
Tenascin
CA19-9 CD54 / ICAM-1 E Interferon alpha 1 Testosterone
E-Cadherin / CD324 Nuclear Antigen
Caldesmon, HMW CD55 Interferon alpha-2 TGFalpha
EGFR Nuclear Membrane
Calgranulin B CD56 / NCAM Interferon gamma TGF-beta
EMI1 Nuclear Membrane Marker
Calponin-1 CD57 / B3GAT1 Involucrin Thomsen-Friedenreich Ag.
Eosinophil Peroxidase Nucleolar / Nucleoli
Calprotectin CD59 IPO-38 Thymidylate Synthase
Ep-CAM / CD326 Nucleolin
Carbonic Anhydrase IX CD6 Isotype control, mouse IgG1, k Thyroglobulin
Erythrocyte Specific NuMA
Carcinoembryonic Antigen CD61 Isotype control, mouse IgG2a, k TIMP3
CD10 CD63 Estrogen Receptor TNF alpha
Isotype control, mouse IgG2b, k
CD100 CD66 Estrogen Receptor beta 1 O Topoisomerase I, MT
CD104 CD66, pan ODC-1 TOX3
CD68
K TRAcP
CD106 / VCAM1 F Kappa Light Chain
CD117 CD7 Fascin-1 Ksp-Cadherin / CDH16
P Transgelin / SM22-alpha
CD11a CD70 FGF23 p21 / WAF1 Transglutaminase II
Ku-Holo
CD11b CD71 Fibronectin p24-HIV TRIM29
CD11c CD74 FOXP3 p27 / KIP1 TRP1
CD13 CD79a FSH beta
L p34 / cdk1 TTF-1 / NKX2.1
CD14 CD8 Lambda Light Chain p40 Tyrosinase
CD146 / Mucin 18 CD84 Laminin p53
CD86
G LEC Chemokine p55;50 EBV-Early Antigen
CD147 GFAP Lewis A
U
CD15 / FUT4 / Lewis x CD8A p57 / KIP2 UACA / Nucling
GITR / Tnfrsf18 Lewis B
CD16 CD8B p57Kip2 UGT1A9
GLG1 Liver Canuliculi
CD16 / Fc-gamma Receptor III CD90 PAX6 UPK3A
Glucose Regulated Protein 94 Lung Specific Antigen
CD171 / L1CAM CD90 / Thy1 PAX7
Glycophorin A / CD235a Luteinizing Hormone beta
CD176 / T-F Ag CD95 PCNA
CD98
Glypican-3
PD1 / PDCD1 / CD279
V
CD18 GM-CSF VEGF-A
CD19 CD99
GnRH-Receptor
M pgp9.5
VEGFR1 / Flt-1
CD195 / CCR-5 Cdc20 Macrophage Specific Antigen Phosphotyrosine
Golgi Complex VEGFR2 / Flk-1
CD1a CDw17 MAGE A1 PLAP
gp100 / Melanosome Vimentin
CD1b CDw60 Major Vault Protein Plasma Cell Marker
Granulocyte Marker
CD2 CDw75 MALT-1 PLGF
GCSF W
CD20 CELA3B MAP3K1 Pmel17 / gp100 / SILV
Granzyme B von Willebrand Factor
CD21 Chromogranin A MART-1 / Melan-A Podocalyxin
CD22 CMV-p65 MCAM / MUC18 / Mucin 18 / CD146 Progesterone WT1
CD25 c-Myb H Melanoma Marker Progesterone Receptor
CD26 c-Myc HCG-alpha MHC I Prolactin Receptor Z
ZAP70

26 www.biotium.com
CF Dye Anti-Tag and Secondary Antibody Conjugates

Secondary Antibodies
Anti-GFP, anti-hapten, and anti-epitope tag antibody conjugates
In PBS, 50% glycerol, 2 mg/ml BSA, 0.05% sodium azide

Goat anti- Mouse monoclonal Mouse monoclonal Mouse monoclonal Mouse monoclonal Rabbit anti- Rabbit anti-
GST anti-biotin anti-fluorescein anti-GFP anti-6X His tag HA tag RFP
Concentration/ 1 mg/mL 2 mg/mL 2 mg/mL 1 mg/mL 1 mg/mL 1 mg/mL 1 mg/mL
Unit size 0.1 mL 50 uL or 0.25 mL 50 uL or 0.25 mL 0.1 mL 0.1 mL 50 uL 0.1 mL
CF405S 20203
CF405M 20214
CF488A 20424 20204 20210 20215 20228 20238 20421
CF594 20425 20205 20211 20216 20229 20239 20422
CF633 20206 20212 20217
CF640R 20426 20207 20213 20218 20237 20237 20423
CF647
CF680 20219 20359
CF770 20367 20220 20360

Secondary antibodies, whole IgG (H+L), not highly cross-adsorbed


2 mg/mL in PBS, 50% glycerol, 2 mg/ml BSA, 0.05% sodium azide, or preservative-free lyophilized form
Unit size: 0.5 mL, 50 uL, or 1 mg (lyophilized)

Chicken Chicken Chicken Goat anti- Goat anti- Goat anti- Goat anti- Llama anti- Llama anti- Rabbit anti- Rabbit Rabbit anti-
anti-goat anti-mouse anti-rabbit Guinea pig mouse rabbit swine mouse rabbit chicken anti-goat guinea pig
CF350 20364 20331 20332 20198 20140 20141
CF405S 20080 20082
CF405M 20180 20181
CF405L 20408 20409
CF488A 20225 20208 20209 20017 20010 20012 20028 20454 20449 20079 20021
CF514 20386 20387
CF532 20365 20366
CF543 20333 20334 20335 20317 20306 20309 20324 20312 20315 20336
CF555 20036 20030 20033 20236 20031
CF568 20337 20338 20339 20108 20100 20102 20091 20455 20450 20107
CF594 20226 20221 20223 20118 20110 20112 20160 20456 20451 20164 20117
CF633 20227 20222 20224 20129 20120 20122 20138 20165 20128
CF640R 20085 20197 20202 20089 20457 20452
CF647 20041 20040 20043 20286 20458 20453
CF660C 20050 20053
CF660R 20054 20055
CF680 20068 20243
CF750 20070 20073
CF770 20244
CF790 20378

Dont see what youre looking for?


We regularly add new CF dye conjugates to our catalog according to customer demand. Be sure to check our website for updates. If you are looking for a CF
dye product not listed in our catalog, please let us know. We may be able to add it as a new product, or perform a custom conjugation for you.

Visit www.biotium.com to see our full selection of secondary antibodies, including conjugates of biotin, HRP, R-PE, and APC.

www.biotium.com 27
CF Dye Secondary Antibody Conjugates
Secondary Antibodies

Highly cross-adsorbed for multiple labeling

Drop-n-Stain secondary antibodies, whole IgG (H+L), highly cross-adsorbed


5 mL solution in convenient dropper bottle format for quick and easy immunofluorence staining.

Donkey anti-mouse Donkey anti-rabbit Goat anti-mouse Goat anti-rabbit


Min x react Bv, Ch, Gt, GP, Hs, Hu, Bv, Ch, Gt, GP, Hs, Hu, Bv, Hs, Hu, Rb,Sw Hu, Ms, Rt
Rb, Sh, SHm Ms, Rt, Sh, SHm
CF488A 20952 20950 20956 20954
CF543 20967 20966 20969 20968
CF594 20953 20951 20957 20955
CF640R 20963 20962 20965 20964

Secondary antibodies, whole IgG (H+L), highly cross-adsorbed


2 mg/mL in PBS. 50% glycerol, 2 mg/ml BSA, 0.05% sodium azide, or preservative-free lyophilized form
CF350-CF660R unit sizes: 0.5 mL, 50 uL, or 1 mg (lyophilized); CF680-CF790 available in 0.25 mL or 50 uL sizes

Bovine anti- Donkey anti- Donkey anti- Donkey anti- Donkey anti- Donkey anti- Donkey anti- Donkey anti- Donkey anti-
goat chicken goat guinea pig human mouse rabbit rat sheep
Min x react Bv, Ch, GP, Hs, Bv, Gt, GP, Hs, Ch, GP, Hs, Bv, Ch, Gt, Hs, Bv, Ch, GP, Gt, Bv, Ch, Gt, GP, Bv, Ch, Gt, GP, Bv, Ch, GP, Gt, Ch, GP, Hs,
Hu, Ms, Rb, Rt, Hu, Ms, Rb, Rt, Hu, Ms, Rb, Rt, Hu, Ms, Rb, Hs, Ms, Rb, Rt, Hs, Hu, Rb, Sh, Hs, Hu, Ms, Sh, Hs, Hu, Ms, Hu, Ms, Rb, Rt,
SHm Sh, SHm SHm Sh, SHm Sh, SHm SHm SHm Rb, Sh, SHm SHm
CF350 20275 20142 20350 20351 20361 20148
CF405S 20356 20420 20419
CF405M 20376
CF430 20461 20462
CF488A 20293 20166 20016 20169 20074 20014 20015 20027 20024
CF543 20313 20310 20314 20316 20318 20305 20308 20320 20322
CF555 20039 20276 20037 20038 20234
CF568 20294 20106 20377 20105 20098 20092 20095
CF594 20295 20167 20116 20170 20075 20115 20152 20159 20156
CF633 20296 20168 20127 20171 20076 20124 20125 20137 20134
CF640R 20297 20179 20177 20178 20199 20083
CF647 20048 20046 20047 20284
CF660C 20051 20372
CF660R 20388 20389 20390
CF680 20060 20241 20278 20418 20417 20062
CF680R 20196 20194 20195
CF750 20362 20298
CF770 20277 20242
CF790 20345 20279 20363 20344

Bv: bovine; Ch: chicken; Gt: goat; GP: guinea pig; Hs: horse; Hu: human; Ms: mouse; Rb: rabbit; Sh: sheep; SHm: Syrian hamster; Sw: swine; Rt: rat

See more highly cross-adsorbed secondaries on the next page

Dont see what youre looking for?


We regularly add new CF dye conjugates to our catalog according to customer demand. Be sure to check our website for updates. If you are looking for a CF
dye product not listed in our catalog, please let us know. We may be able to add it as a new product, or perform a custom conjugation for you.

Visit www.biotium.com to see our full selection of secondary antibodies, including conjugates of biotin, HRP, R-PE, and APC.

28 www.biotium.com
CF Dye Secondary Antibody Conjugates

Secondary Antibodies
Highly cross-adsorbed, F(ab)2 fragments, and isotype-specific secondary antibodies

Secondary antibodies, whole IgG (H+L) , highly cross-adsorbed (continued from p. 28)
2 mg/mL in PBS. 50% glycerol, 2 mg/ml BSA, 0.05% sodium azide, or preservative-free lyophilized form
CF350-CF660R unit sizes: 0.5 mL, 50 uL, or 1 mg (lyophilized); CF680-CF790 available in 0.25 mL or 50 uL sizes

Goat anti- Goat anti- Goat anti- Goat anti-mouse Goat anti- Goat anti- Rabbit anti- Rabbit anti- Rabbit anti- Rabbit anti-
chicken human mouse (min x rat) rabbit rat human mouse rat sheep
Bv, Gt, GP, Hs, Bv, Hs, Ms Bv, Hs, Hu, Bv, Ch, Gt, GP Hu, Ms, Rt Bv, Hs, Hu, Ms Hu Hu Hu
Hu, Ms, Rb, Rb, Sw Hs Hu Rb Rt, Rb
Rt, Sh, SHm Sh, SHm
CF350 20143 20144 20147 20149
CF405S
CF405M 20375 20182 20340 20373 20374
CF430 20459 20460
CF488A 20020 20022 20018 20302 20019 20023 20071 20026 20025 20172
CF543 20311 20319 20299 20328 20300 20321 20307 20323
CF555 20034 20320 20231 20232 20233 20235
CF568 20104 20097 20101 20301 20103 20096 20093 20094
CF594 20114 20154 20111 20303 20113 20155 20072 20158 20157 20173
CF633 20126 20132 20121 20341 20123 20133 20066 20136 20135 20174
CF640R 20084 20081 20175 20304 20176 20088 20200 20201
CF647 20044 20280 20281 20282 20283 20285
CF660C 20371 20052 20356 20369 20370
CF660R
CF680 20287 20065 20067 20069 20061
CF680R 20192 20193
CF750 20463
CF770 20288 20077 20078 20383
CF790 20342 20343

Bv: bovine; Ch: chicken; Gt: goat; GP: guinea pig; Hs: horse; Hu: human; Ms: mouse; Rb: rabbit; Sh: sheep; SHm: Syrian hamster; Sw: swine; Rt: rat

Secondary antibodies, Goat anti-mouse Goat anti-human


F(ab)2 fragments isotype-specific antibodies isotype-specfic antibodies
2 mg/mL, unit size: 0.25 mL or 50 uL Highly cross-adsorbed for multiple labeling (min X Bv, Hu, Rb) 2 mg/mL, unit size: 0.25 mL or 50 uL
2 mg/mL, unit size: 0.25 mL or 50 uL
Goat anti- Goat anti- Goat anti- Goat anti- Goat anti- Goat anti- Goat anti-
mouse, F(ab)2 rabbit, F(ab)2 mouse IgG1 mouse IgG2a mouse IgG2b human IgA human IgM
(alpha chain) (mu chain)
CF350 20145 20146 CF350 20245 20255 20265
CF488A 20428 20347
CF488A 20011 20013 CF405S 20380 20381 20382
CF594 20429 20348
CF543 20329 20330 CF488A 20246 20256 20266
CF640R 20349
CF555 20032 20035 CF543 20325 20356 20327
CF633 20427
CF568 20109 20099 CF555 20247 20257 20267
CF647 20346
CF594 20119 20153 CF568 20248 20258 20268
CF680 20384
CF633 20130 20131 CF594 20249 20259 20269
CF770 20385
CF640R 20086 20087 CF633 20250 20260 20270
CF647 20042 20045 CF640R 20251 20261 20271
CF680 20063 20064 CF647 20252 20262 20272
CF680 20253 20263 20273
CF770 20254 20264 20274

www.biotium.com 29
Related Products and Accessories
Accessories

Buffers, mounting media, counterstains and more

RedDot1 and RedDot2


Far-Red Nuclear Stains
RedDot1
Replaces Draq5 for live cell nuclear staining
Cell normalization for In Cell Western
Cell cycle analysis by flow cytometry
RedDot2
Replaces Draq7 for dead cell staining and fixed cell staining
More specific than Draq7 for fixed cell nuclear counterstaining Figure 1. HeLa cells stained with rabbit anti-COX IV and CF488A goat anti-
rabbit (mitochondria, green), and mouse anti-Golgin 97 and CF555 goat
anti-mouse (Golgi, cyan) Actin filaments are stained with CF405 phalloidin
(blue) and nuclei are stained with RedDot2 (red).

FITC Photostability, Wet-Set Mounting Media Cy5 Photostability, Wet-Set Mounting Media
EverBrite Mounting Media 120 120

Superior antifade protection

Normalized Fluorescence
Normalized Fluorescence
100 100

Compatible with CF dyes and other dyes 80 80

Compatible with cyanine-based dyes (Cy dyes, Alexa Fluor 647 60 60


and DyLight 649), unlike VectaShield 40 40
EverBrite
Available in wet-set or hardset formulations 20
EverBrite
Vectashield 20 Vectashield
SlowFade Gold SlowFade Gold
With or without DAPI 0
PBS
0
PBS
0 20 40 60 80 100 120 0 20 40 60 80 100 120
Time (s) Time (s)

FITC Photostability, Hardset Mounting Media Cy5 Photostability, Hardset Mounting Media
120 120
Normalized Fluorescence

Normalized Fluorescence
100 100

80 80

60 60

40 40
EverBrite HS EverBrite HS
20 Vectashield HS 20 Vectashield HS
Prolong Gold Prolong Gold
PBS PBS
0 0
0 20 40 60 80 100 120 0 20 40 60 80 100 120
Time (sec) Time (sec)

CoverGrip Coverslip Sealant Figure 2. Photostability of HeLa cell immunofluorescence staining in various mounting media.
Designed specifically for sealing coverslip edges A major advantage of EverBrite mounting medium is that, unlike Vectashield, it does not
decrease the fluorescence of cyanine-based fluorophores. Fluorescence values for Cy5 in
Wont mix with aqueous mounting medium like nail polish can Vectashield media are normalized to PBS time 0 to illustrate the drop in fluorescence of
cyanine dyes caused by Vectashield.
Made with natural Limonene solvent
15 mL brush bottle, or 100 mL refill

SuperHT Pap Pens


Create hydrophobic barriers on glass slides to separate specimens
and conserve antibodies
Insoluble in aqueous buffers, detergents, alcohol, or acetone,
removable with xylene
Stable at temperatures up to 120oC
SuperHT Mini Pap Pen: 2.5 mm tip, ~400 applications
SuperHT Pap Pen: 4 mM tip, ~800 applications

Figure 3. CoverGrip Coverslip Sealant brush


bottle and refill bottle. Figure 4. SuperHT Pap Pens.
30 www.biotium.com
Related Products and Accessories

Related Products
TrueBlack Lipofuscin Autofluorescence AccuEasy Flow Cytometry Kit
Quencher Stain and harvest adherent cells for flow cytometry
Eliminates autofluorescence from lipofuscin in human and aged Prevents loss of surface marker staining upon cell detachment
animal tissue sections
Increases sensitivity of cell surface marker detection compared to
Reduces autofluorescence from other sources, such as red blood conventional methods
cells and collagen/elastin
Less red/far-red background compared to Sudan Black B
Can be used to treat tissue sections before or after antibody staining A VEGFR1 B Tie1
8 40

6 30

Signal:Noise
Signal:Noise
4 20

2 10

0 0
Conventional AccuEasy Conventional AccuEasy
Staining Method Staining Method

C Tf R
150

120

Signal:Noise
90

60

30

0
Conventional AccuEasy
Staining Method

Figure 1. The AccuEasy staining method improves signal to noise ratio in flow cytometry analysis of cell
surface markers on adherent cells compared conventional methods. A. Indirect immunofluorescence
staining of EA.hy926 human endothelial cells with mouse monoclonal antibody against VEGF Receptor
1 (VEGFR1) or isotype control and PE conjugated anti-mouse IgG. B. Staining of EA.hy926 cells with
mouse monoclonal antibody against Tie1 or isotype antibody control and PE conjugated anti-mouse
IgG. C. Direct immunofluorescence staining of HeLa cells with Mix-n-Stain CF488A labeled mouse
Figure 3. Lipofuscin autofluorescence in human cerebral cortex sections. Top row: monoclonal antibody against transferrin receptor (TfR), or isotype control.
lipofuscin appears as highly fluorescent granules throughout the tissue section
in all three fluorescent channels. Middle row: Sudan Black B masks lipofuscin
autofluorescence, but causes high background in the red and far-red channels.
Bottom row: TrueBlack quenches lipofuscin with minimal increase in fluorescence
background (bottom row).

Mini Cell Scrapers


Accessory Products For harvesting cells from 96-, 48-, or 24-well plates
0.5 cm wide and 6 cm long polystyrene scrapers
Catalog No. Product Name
Sterile and disposable
23001 EverBrite Mounting Medium
23002 EverBrite Mounting Medium with DAPI
23003 EverBrite Hardset Mounting Medium
23004 EverBrite Hardset Mounting Medium with DAPI
23005 CoverGrip Coverslip Sealant
23007 TrueBlack Lipofuscin Autofluorescence Quencher, 20X in DMF
Figure 2. Mini Cell Scraper shown
40060 RedDot1 Far Red Nuclear Counterstain, 200X in H2O
above next to a 48-well plate for scale.
40061 RedDot2 Far Red Nuclear Counterstain, 200X in DMSO
30069 AccuEasy Flow Cytometry Kit
22003 Mini Cell Scrapers
22005 Mini Super HT Pap Pen
22006 Super HT Pap Pen
23006 Flow Cytometry Fixation/Permeabilization Kit
22015 Fixation Buffer
22016 Permeabilization Buffer Visit www.biotium.com to find more buffers,
22017 Permeabilization and Blocking Buffer (5X) counterstains, and accessories.
22010 10X Fish Gelatin Blocking Agent

www.biotium.com 31
Biotium, Inc.

Toll Free: 800-304-5357


Phone: 510-265-1027
Fax: 510-265-1352

General Inquiries
[email protected]

Quotes and Ordering


[email protected]

Technical Support
[email protected]

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