ProbesOnline, May 2009

In This Issue


Cell Proliferation and Cytotoxicity AssaysCyQUANT® Direct Cell Proliferation Assay

Cell Identification for High-Content Screening PlatformsHCS NuclearMask™ and CellMask™ Stains

Measuring Cell Viability Status After FixationLIVE/DEAD® Fixable Yellow Dead Cell Stain Kit

Live-Cell Imaging and Fixed-Cell AnalysesOrganelle Lights™ Reagents

New Products for Cell &Tissue Analysis
See all of this month's New Products for Cell & Tissue Analysis


Quantitate Mitochondrial Membrane Potential with Greater AccuracyOrganelle Lights™ Fluorescent Proteins Meet Classic Molecular Probes® Organelle Stains


what it is
The CyQUANT® Direct assay is a fluorescence-based cell proliferation and cytotoxicity assay that is well suited for high-throughput screening applications.

what it offers

  • Convenience—no washes, cell lysis, or temperature equilibrations required
  • Accuracy—cytotoxicity data compare well to metabolism-based assays
  • Robust results—readout is independent of metabolic state

how it works
The CyQUANT® Direct assay is based on a cell-permeant DNA-binding dye in combination with a masking dye. The masking dye blocks staining of dead cells and cells with compromised cell membranes so that only viable cells fluoresce. Because DNA content is highly regulated, cell number estimates using the CyQUANT® Direct assay are very accurate.

Learn More at

CyQUANT Direct Assay Protocol

CyQUANT® Direct assay protocol. The CyQUANT® Direct assay is designed for use with multi-well plates (96-, 384-, or 1,536-well formats), making it ideal for high-throughput screening applications. The reagent is added directly to cells in complete medium and incubated for 30 to 60 min. Samples are read from the bottom on standard fluorescence plate readers set for green fluorescence (e.g., fluo-4 and GFP).
Product Quantity Cat. no.  
CyQUANT® Direct Cell Proliferation Assay, 10-plate size 1 kit C35011 Order Now
CyQUANT® Direct Cell Proliferation Assay, 100-plate size 1 kit C35012 Order Now

what they are
Molecular Probes® HCS CellMask™ and NuclearMask™ stains provide reliable cell delineation for image-based high-content screening (HCS) assays, with a choice of fluorescent colors ranging from blue to deep red.

what they offer

  • Proven performance—validated for image segmentation on HCS platforms
  • Selection—covers the fluorescence spectrum for true multiplexing flexibility
  • User-friendly protocol—simple and robust method

how they work
HCS CellMask™ stains label the whole cell, including cytoplasm and nucleus, and are applied to cells immediately after fixation and permeabilization or after antibody labeling. The versatile HCS NuclearMask™ stains measure DNA content in addition to enabling robust cell demarcation of live and formaldehyde-fixed cells.

To learn more about CellMask™ and NuclearMask™ reagents and other tools for high-content imaging and analysis, visit

HCS NuclearMask™ and CellMask™ Stains

Comparison of fluorescence bleed-through into adjacent detection channels using either HCS CellMask™ Orange stain (Invitrogen) or Whole Cell Stain Orange (Thermo Scientific). 
See larger image for more details.
Product Quantity Cat. no.  
HCS CellMask™ Red stain 1 set H32712 Order Now
HCS CellMask™ Orange stain 1 set H32713 Order Now
HCS CellMask™ Green stain 1 set H32714 Order Now
HCS CellMask™ Blue stain 1 set H32720 Order Now
HCS CellMask™ Deep Red stain 1 set H32721 Order Now
HCS NuclearMask™ Blue stain 65 μL H10325 Order Now
HCS NuclearMask™ Red stain 125 μL H10326 Order Now

what it is
LIVE/DEAD® cell viability assays are used to differentially stain live and dead cells in a variety of mammalian cell types. These cells can then be fixed with formaldehyde for subsequent analysis by flow cytometry. The LIVE/DEAD® Fixable Yellow dye is excited with a 405 nm violet laser and has an emission maximum of ~570 nm. These spectral properties allow you to transfer your dead-cell discrimination assays to the violet laser, thus freeing up the commonly used 488 nm laser for bright fluorochromes on antibodies directed against challenging antigens.

what it offers

  • Post-fixation measurement of viability
  • Accurate intracellular staining
  • Ideal for multicolor experiments

how it works
LIVE/DEAD® Fixable Dead Cell Stain Kits are based on the reaction of a fluorescent reactive dye with amines on cellular proteins. With viable cells, only cell surface proteins are available to react with the dye, resulting in faint staining. In contrast, the dye can penetrate the interior of dead cells, resulting in at least a 50-fold increase in fluorescence compared to live cells. Because the dye reacts covalently with proteins, the staining pattern is completely preserved following sample fixation with formaldehyde, under conditions that inactivate pathogens.

LIVE/DEAD® Fixable Yellow Dead Cell Stain Kit

LIVE/DEAD® Fixable Yellow dead-cell staining in Jurkat cells. The LIVE/DEAD® Fixable Yellow Dead Cell Stain Kit (Cat. no. L34959) was used to differentially stain a mixture of live (left peak) and heat-treated (right peak) Jurkat cells. Following the staining reaction, cells were fixed in 3.7% formaldehyde and analyzed by flow cytometry with 405 nm excitation and ~575 nm emission.
Product Quantity Cat. no.  
LIVE/DEAD® Fixable Yellow Dead Cell Stain Kit 1 kit L34959 Order Now

what they are
Molecular Probes® Organelle Lights™ reagents are prepackaged and ready-to-use fluorescent protein constructs fused with signal peptides for accurate and specific targeting to subcellular compartments and structures. The collection of Organelle Lights™ reagents has recently expanded to include new colors for staining lysosomes, mitochondria, endoplasmic reticulum (ER), and endosomes.

what they offer

  • Ready-to-use reagents—no potentially harmful cell treatments required
  • Simple method—optimize transduction conditions only once per cell type
  • Versatility—multiplex with other stains in live or fixed cells

how they work
Organelle Lights™ reagents consist of suspensions of baculovirus carrying an expression construct with a fluorescent protein fused to either a cellular protein or a localization peptide. Simply add the virus suspension to your cells, incubate overnight, and you’re ready for imaging. Organelle Lights™ reagents can label a broad range of mammalian cell types, including primary and stem cells, without the need for lipids or dye-loading protocols that can perturb cell growth and viability.

Learn more about Organelle Lights™ reagents and other tools based on powerful BacMam technology.

Organelle Lights™ ER-RFP

Live-cell imaging with Organelle Lights™ ER-RFP. 
HeLa cells were transduced with Organelle Lights™ ER-RFP (Cat. no. O36230). The next day, cells were co-stained with 50 nM MitoTracker® Deep Red 633 (Cat. no. M22426) and 1 µg/mL Hoechst 33342 (stains nuclei; Cat. no. H3570). Imaging was performed on live cells using a DeltaVision® Core microscope and standard DAPI/TRITC/Cy®5 dye filter sets.
Product Quantity Cat. no.  
Organelle Lights™ Lysosomes-GFP 1 kit O36228 Order Now
Organelle Lights™ Mito-RFP 1 kit O36229 Order Now
Organelle Lights™ ER-RFP 1 kit O36230 Order Now
Organelle Lights™ Endosomes-RFP 1 kit O36231 Order Now


Distinguish Artifacts from True Functional Changes
The use of fluorescent dyes, such as tetramethylrhodamine, methyl or ethyl ester (TMRM or TMRE) to report changes in mitochondrial membrane potential is well established. However, it is often important to determine if an apparent change in the signal from a potentiometric dye is due to a change in mitochondrial function or to an artifact resulting from a change in mitochondrial mass, shape, or movement. For more accurate measurement of mitochondrial membrane potential, these membrane potential–sensitive dyes can be combined with probes for mitochondrial morphology (such as Organelle Lights™ Mitochondria GFP) to measure changes in potential that are independent of mitochondrial mass or movement.

Ratiometric Imaging of Mitochondrial Membrane Potential
Ratiometric imaging of mitochondrial membrane potential can be achieved by first transducing cells with an Organelle Lights™ mitochondria-targeted reagent, and subsequently loading cells with a fluorescent dye that is readily sequestered by active mitochondria. For example, colocalization of green-fluorescent Organelle Lights™ Mito-GFP and red-fluorescent TMRM can be used to generate a pseudoratiometric measurement of mitochondrial membrane potential (see figure). This approach enables the observation of “flickers” in mitochondrial membrane potential that cannot be attributed to movement of mitochondria between focal planes or to a change in mitochondrial mass. A similar approach can be used to monitor mitochondrial calcium with the rhod-2 AM dye or mitochondrial superoxide production with MitoSOX™ Red indicator. 


Dynamic imaging of mitochondrial membrane potential. Mitochondria of HeLa cells were labeled with Organelle Lights™ Mitochondria GFP (Cat. no. O36210) (A1), and loaded with 50 nM TMRM (Cat. no. T668) for 10 minutes at 37°C (A2). Colocalization of TMRM and GFP can be clearly seen (A3), confirming the specific accumulation of TMRM in mitochondria. (B) Images were acquired at 5 second intervals for 90 seconds. Polarized mitochondria display both red and green fluorescence; those that have depolarized lose red TMRM fluorescence but retain GFP fluorescence and therefore appear green (B4, and quantified in C). Over time, mitochondrial membrane potential is lost in one mitochondrion (denoted by the arrow in B1) whereas surrounding mitochondria remain polarized. The recovery of membrane potential in this single mitochondrion can be seen in the subsequent image. GFP and TMRM were imaged using standard FITC and TRITC filters, respectively, on a DeltaVision® Core microscope with a 40x lens.

Product Quantity Cat. no.  
tetramethylrhodamine, methyl ester, perchlorate (TMRM) 25 mg T668 Order Now
tetramethylrhodamine, ethyl ester, perchlorate (TMRE) 25 mg T669 Order Now
Organelle Lights™ Mito-GFP 1 kit O36210 Order Now
Organelle Lights™ Mito-OFP 1 kit O36222 Order Now
Organelle Lights™ Mito-RFP 1 kit O36229 Order Now
rhod-2, AM dye 1 mg R1244 Order Now
MitoSOX™ Red mitochondrial superoxide indicator 10 x 50 µg M36008 Order Now



Click-iT® EdU Enables Rapid and Sensitive Assessment of Unscheduled DNA Synthesis

A rapid non-radioactive technique for measurement of repair synthesis in primary human fibroblasts by incorporation of ethynyl deoxyuridine (EdU). Limsirichaikul, S. et al. (2009) Nucleic Acids Res 37:e31.

How can we rapidly and reliably assess nucleotide excision repair deficiencies?
Xeroderma pigmentosum (XP), a genetic disorder of the nucleotide excision repair (NER) system, predisposes its sufferers to photosensitivity and UV-induced skin damage. Diagnosis of XP typically entails determining the level of damage-induced, non–S-phase, gap-filling DNA repair activity (termed "unscheduled DNA synthesis", or UDS). While UDS can be sensitively and accurately assayed by monitoring the incorporation of 3H thymidine, this methodology is extremely time- and labor-intensive, and incurs the problems associated with handling radioactive materials. Immunofluorescence assays based on BrdU incorporation are substantially faster, but sensitivity is also greatly reduced as compared to 3H thymidine.

In this study, Limsirichaikul and colleagues compared these two assays to one based on incorporation of Click-iT® EdU, a reactive thymidine analog that enables fluorescence detection by conjugation to an azide-containing fluorophore ("click" chemistry).

Using UVC-irradiated primary human fibroblasts and detection with Alexa Fluor® 488 azide, the group reported comparable sensitivity with Click-iT® EdU to that observed with conventional 3H thymidine autoradiography. Furthermore, the total time required to perform the EdU assay—about half a day—was dramatically less than that required for the 3H thymidine–based assay and even modestly faster than the BrdU-based assay. The Click-iT® EdU assay was also shown to be compatible with immunostaining and latex-bead labeling, allowing for the incorporation of internal controls that are crucial to rigorous lab testing. The group suggests that Click-iT® EdU–based assays could become the standard tool for the diagnosis of XP.


Product Quantity Cat. no.  
Alexa Fluor® 594 goat anti-mouse IgG 0.5 mL A11005 pHrodo, SE
Alexa Fluor® 488 goat anti-mouse IgG 0.5 mL A11001 pHrodo S. aureus BioParticles
Alexa Fluor® 594 goat anti-rabbit IgG 0.5 mL A11012 pHrodo E. coli BioParticles

Click-iT® EdU Alexa Fluor® 488 Imaging Kit

1 kit C10083 pHrodo Phagocytosis Particle Labeling Kit

Free Online Technical Webinars Free online technical webinars
You are invited to join us for a series of biweekly technical webinars from the comfort of your desk. The webinars will initially focus on imaging-related applications, but we welcome your feedback for additional topics throughout the course of the year. Upcoming topics will be announced each month via email.

Presentations will last approximately 45 minutes, followed by 15 minutes for live Q&A.
Webinars Date Time
Labeling Molecules with Fluorescent Dyes
May 26, 2009 10:00 a.m. PT
Mitochondrial Biology
June 9, 2009 10:00 a.m. PT

Missed our previous webinars? Find our recorded webinars here!

Organelle Lights™ & Cellular Lights™ Reagents   The juxtaposition of actin microfilaments and peroxisomes in subplasmalemmal regions visualized using Organelle Lights™ and Cellular Lights™ reagents. Human osteosarcoma cells were transduced with YFP targeted to peroxisomes (green), Cellular Lights™ Actin RFP (pink, Cat. no. C10127), and Cellular Lights™ Plasma Membrane CFP (blue, Cat. no. O36216) and imaged 14 hr later using CFP/YFP/RFP filters on a DeltaVision® Core microscope.

Product Quantity Cat. no.  
Cellular Lights™ Plasma membrane CFP 1 kit O36216 Order Now
Cellular Lights™ Actin RFP 1 kit C10127 Order Now

Mitochondrial Stains—Visualizing Cellular Stress

Mitochondrial structure and function are key indicators of cellular stress, and mitochondrial defects have been implicated in several neurodegenerative diseases, including Alzheimer’s disease. Recent evidence suggests that the balance between mitochondrial fission and fusion is disrupted in response to several factors implicated in Alzheimer's disease. In addition, factors related to stroke, such as oxidative and nitrosative stress, and calcium dysregulation, can disrupt this balance. All of these effects may be mediated by a key motor protein surrounding mitochondria, dynamin-related protein-1 (Science 324:102 (2009)) or the GTPase mitofusin 2 (Curr Opin Cell Biol 18:453 (2006)) . These findings show that morphological visualization of mitochondria in live or fixed cells can be used as an effective model to understand inducers of these and other neurological pathologies.

Mitochondrial staining can be achieved using:

  • Organelle Lights™ Reagents—fluorescent proteins targeted to mitochondria and delivered with efficient BacMam technology
  • MitoTracker® Probes—dyes that accumulate in all mitochondria in live cells and are retained after fixation
  • Potential-Sensitive Probes—dyes that only accumulate in healthy, hyperpolarized mitochondria, shifting their fluorescence properties with depolarization (e.g., JC-1 and JC-9)
  • Primary Antibodies—extensive collection of antibodies targeting oxidative phosphorylation pathways and more

Organelle Lights™ Endosomes-RFP  

Live-cell imaging with Organelle Lights™ Endosomes-RFP and Mito-GFP in HeLa cells.
HeLa cells were transduced with Organelle Lights™ Endosomes-RFP (Cat. no. O36231) and Organelle Lights™ Mito-RFP (Cat. no. O36229) and co-stained with 1 mg/mL Hoechst 33342 (Cat. no. H3570). Imaging was performed on live cells using a DeltaVision® Core microscope and standard DAPI/FITC/TRITC filter sets.


Fluorescence Imaging Accessories

New Web Resource for Fluorescence Imaging Accessories
Our new web page dedicated to imaging accessories makes it easier than ever to find imaging tools to help you get the most from your fluorescence imaging experiments—from microscope reference standards to sample preparation systems.

Visit the Imaging Accessories web page.


Antibody Labeling

Less Sample, More Flexibility for Antibody Labeling
APEX antibody labeling kits—the newest addition to the Molecular Probes® antibody labeling kits family—offer a simple, convenient, and fast method of directly labeling as little as 10–20 µg of IgG antibody.

Visit to learn more.


Flow Cytometer Violet Laser

Put Your Flow Cytometer’s Violet Laser to Work
Invitrogen is the recognized leader in providing world-class fluorescent reagents and antibody conjugates designed specifically for use on the violet laser. From immunophenotyping to dead-cell discrimination to cell cycle analysis, our portfolio unlocks the full multicolor potential of violet laser–equipped flow cytometers.

Visit to learn more.



Countess™ Automated Cell Counter  
What your colleagues are saying about the Countess™ Automated Cell Counter
The Countess™ Automated Cell Counter uses trypan blue staining combined with a sophisticated image analysis algorithm to enable accurate cell and viability counts in just 30 seconds. The algorithm also measures the average size of live, dead, and total cells to give you all the data you need from your cell cultures without using a hemocytometer. Here’s what researchers are saying about how the Countess™ Automated Cell Counter has benefited their research:


“The Countess makes tissue culture work much easier and more productive. I wish I had one years ago!” –John McGrath, Dana-Farber Cancer Institute
“The Countess has worked out well for our lab. The Countess cell counts agree with our manual cell counts, and the Countess is much faster.” –Danielle Krebs, UBC Life Sciences Centre
“We found the Countess very helpful for our migration assays. Instead of spending hours counting cells to get results, we are able to quickly quantify our data! A definite time saver and well worth the cost!” –Holly, University of Rochester
“The Countess saves us hours of time during experimentally intense work days. We also appreciate the consistency of counts even with different users.” –Sarah, University of Illinois

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