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Nuclear Blue™ DCS1
The cell nucleus is a membrane-bound organelle that contains most of the cell's genetic material (DNA) in the form of chromosomes. The main components of the nucleus include the nuclear envelope, a double membrane that encloses the entire organelle and isolates its contents from the cytoplasm, and the nuclear matrix, a network within the nucleus that adds mechanical support. Its primary functions include controlling gene expression, regulating DNA replication, and preserving the integrity of the DNA it houses.

Visualizing the cell nucleus either by fluorescence microscopy or flow cytometry is frequently done using high-affinity nucleic acid dyes. Before binding to DNA or RNA, the intrinsic fluorescence of these dyes are minimal, and once bound, its fluorescence intensity enhances significantly. Nucleic acid dyes are available in membrane-permeant and impermeant formats for live and dead cell analysis and quantification and in various wavelengths to support multiplex and colocalization studies with other fluorescent probes.



Membrane Permeant Nucleic Acid Dyes

Membrane permeant nucleic acid dyes can be used to label both live cells with healthy intact cell membranes and cells with compromised membranes such as dead, fixed, or permeabilized cells. The overall toxicity of these dyes is relatively low with minimal effect on cell functionality, allowing for live cells to be tracked during stages of development and cellular processes such as mitosis and meiosis or as a suitable counterstain in live cells. Examples of cell-permeant nucleic acid dyes include Hoechst dyes and AAT Bioquest's Nuclear Violet™ LCS1, Nuclear Green™ LCS1, Nuclear Orange™ LCS1, and Nuclear Red™ LCS1/LCS2 dyes.

Hoechst 33342
Nuclear Violet™ LCS1
Nuclear Green™ LCS1
Nuclear Red™ LCS1

Membrane Permeant Nucelic acid dyes


Table 1. Membrane permeant nucleic acid stains for labeling the nucleus in live, dead and fixed cell.

Product name
Cell Permeability
Live/Fixed Cells
Ex/Em (nm)
Filter Set
Unit Size
Cat No.
Hoechst 33342 *20 mM solution in water*Membrane permeantLive and fixed cells352/454DAPI5 mL17535
DAPI *10 mM solution in water*Membrane permeantLive and fixed cells359/457DAPI2 mL17507
Nuclear Violet™ LCS1Membrane permeantLive and fixed cells400/458DAPI0.5 mL17543
Nuclear YellowMembrane permeantLive and fixed cells368/501FITC25 mg17539
CYTO-13 *5 mM DMSO solution*Membrane permeantLive and fixed cells486/511FITC0.5 mL17553
CYTO-13Membrane permeantLive and fixed cells486/511FITC5 mg17554
Nuclear Green™ LCS1Membrane permeantLive and fixed cells501/526FITC0.5 mL17540
Nuclear Orange™ LCS1Membrane permeantLive and fixed cells512/554TRITC0.5 mL17541
Hexidium Iodide *CAS 211566-66-4*Membrane permeantLive and fixed cells518/600Texas Red5 mg17562
Nuclear Red™ LCS1Membrane permeantLive and fixed cells622/645Cy50.5 mL17542


Membrane Impermeant Nucleic Acid Dyes

Membrane impermeant nucleic acid dyes are used to label the nuclei of cells with compromised plasma membranes. These include dead, fixed, or permeabilized cells. Since cell-impermeant nucleic acid dyes cannot label live cells. They are frequently used in cell viability studies as a dead cell indicator or as a nuclear counterstain in colocalization or immunolabeling applications. Examples of cell-impermeant nucleic acid dyes include DAPI, propidium iodide (PI), 7-aminoactinomycin D (7-AAD), Nuclear Blue™ DCS1, Nuclear Green™ DCS1, Nuclear Orange™ DCS1, and Nuclear Red™ DCS1. Cyanine dimer dyes - DiTO™, DiYO™, and TWO-PRO™ - also display exceptional sensitivity for nucleic acids, including double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA. These symmetric dimmers of cyanine dyes exhibit a 100 to 1000-fold fluorescence enhancement upon nucleic acid binding, and their molar extinction coefficients are an order magnitude greater than ethidium homodimers.

Nuclear Blue™ DCS1
Nuclear Green™ DCS1
Nuclear Red™ DCS1

Membrane Impermeant Nucleic Acid Dyes


Table 2. Membrane impermeant nucleic acid stains for labeling the nucleus in dead and fixed cells.

Product name
Cell Permeability
Live/Fixed Cells
Ex/Em (nm)
Filter Set
Unit Size
Cat No.
Nuclear Blue™ DCS1Membrane impermeantDead and fixed cells344/465DAPI0.5 mL17548
DiYO™-1 [equivalent to YOYO®-1]Membrane impermeantDead and fixed cells491/508FITC1 mg17575
Nuclear Green™ DCS1Membrane impermeantDead and fixed cells501/526FITC0.5 mL17550
DiTO™-1 [equivalent to TOTO®-1]Membrane impermeantDead and fixed cells514/531FITC0.2 mL17575
TWO-PRO™ 1 [equivalent to TO-PRO®-1]Membrane impermeantDead and fixed cells515/531FITC0.2 mL17571
Nuclear Orange™ DCS1Membrane impermeantDead and fixed cells512/554TRITC0.5 mL17551
Propidium Iodide *CAS 25535-16-4*Membrane impermeantDead and fixed cells537/618Texas Red5 g17516
Propidium Iodide *10 mM aqueous solution*Membrane impermeantDead and fixed cells537/618Texas Red1 mL17517
DiYO™-3 [equivalent to YO-YO®-3]Membrane impermeantDead and fixed cells612/631Cy50.2 mL17580
7-AAD [7-Aminoactinomycin D] *CAS 7240-37-1*Membrane impermeantDead and fixed cells549/648Cy51 mg17501


Product ordering information


Table 3. Ordering Info for Nuclear Labeling Products

Product Name
Unit Size
7-AAD [7-Aminoactinomycin D] *CAS 7240-37-1*1 mg17501
Acridine orange 100 mg17502
Acridine orange *10 mg/mL solution in water* 10 mL17503
Actinomycin D 5 mg17505
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *10 mM solution in water*2 mL17507
DAPI Dilactate25 mg17509
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *CAS 28718-90-3*10 mg17510
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *CAS 28718-90-3*100 mg17511
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *CAS 28718-90-3*25 mg17513
Hoechst 33258 *CAS 23491-45-4*100 mg17520