Schematic of cell structure with expanded view of the nucleus

The nucleus of the cell is a membrane-bound organelle that includes the nuclear envelope, nucleolus, and nuclear matrix, and is the site of gene expression. The nucleus can be selectively visualized by staining nuclear proteins or directly staining nucleic acids. Here we describe a wide selection of nuclear stains that are available with a choice of wavelengths for multiplexing and colocalization in either live or fixed cells.

Cell-permeant nucleic acid stains make it possible to stain live cells or tissues with minimal processing. They reveal the natural location of cells in tissues and provide a means to follow nuclear changes throughout cellular processes, from mitosis to apoptosis. Cell-impermeant nucleic acid stains, used with fixed cells or tissues, are also used as dead-cell indicators providing a means to follow cellular processes, from apoptosis to viability.

See nucleus stains selection guide

Nucleus introduction

The nucleus (plural: nuclei) is found in eukaryotic cells. While most cells have a single nucleus, some cell types do not have a nucleus while others have many nuclei. A cell’s nucleus is a membrane-bound organelle that consists of the nuclear envelope, a double membrane that surrounds and isolates the nuclear contents, and the nuclear matrix which acts like the cytoskeleton and provides support [1,2].

The nucleus contains the cell’s genetic material (chromosomes) and is the primary site of gene expression and DNA replication during cell cycle. The nucleus also contains various proteins such as histones, which form chromosomes.

Within the nucleus is a sub-compartment known as the nucleolus, which is responsible for synthesizing ribosomal RNA (rRNA) and subsequently assembling ribosomes.

Selection guide for nucleus stains

ReadyProbes reagents provide the easiest fluorescent staining method for nucleic acids in live or fixed cells. These are ready-to-use solutions in convenient dropper bottles, formulated for room temperature storage.
Learn more about ReadyProbes reagents

 
Readout
Fluorescent staining of nucleic acids
Target
 Membrane-permeable dyes targeting RNA and DNA
Membrane impermeable dye targeting RNA and DNA
 
Common filter set
DAPI
Cy5
DAPI
Labels
Hoechst 33342
NucRed Live
DAPI
Ex/Em (nm)
360/460
638/686
360/460
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Live cells
Yes
Yes
No
Fixed cells
No
No
Yes
Fixable
Yes
No
No
Platform
Imaging 
Imaging 
Imaging 
ProtocolMicroscopy protocolMicroscopy protocolMicroscopy protocol
Format
6 x dropper bottles
6 x dropper bottles
6 x dropper bottles
Cat. No.

SYTO dyes are live cell, cell-permeant nucleic acid stains that exhibit bright fluorescence upon binding to nucleic acids. Hoechst dyes are blue-fluorescent nucleic acid stains that have multiple applications including distinguishing condensed pycnotic nuclei in apoptotic cells and for cell-cycle studies in combination with BrdU.
Learn more about SYTO nucleic acid stains

 Hoechst 33342SYTO 9 Green Nucleic Acid StainSYTO 82 Orange Nucleic Acid StainSYTO 59 Red Nucleic Acid Stain SYTO Deep Red Nucleic Acid Stain
ReadoutFluorescent staining of nucleic acids
TargetPreferentially binds AT regions of dsDNACell-permeant dyes targeting DNA and RNA
Common filter setUV / DAPIFITCTRITCTexas RedCy5
LabelsHoechst 33342SYTO 9SYTO 82SYTO 59SYTO Deep Red
Ex/Em (nm)350/461483/503541/560622/645652/669
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYes
Live cellsYesYesYesYesYes
Fixed cellsNoNoNoYesNo
FixableYesYesYesYesYes
PlatformImagingImagingImagingImagingImaging
ProtocolImaging protocolImaging protocolImaging protocol
Format10 mL100 μL250 µL100 µL1 vial
Cat. No.H3570S34854S11363S11341S34900

SYTO RNASelect Green Fluorescent Cell Stain is a cell-permeant nucleic acid stain that is selective for RNA. Although virtually nonfluorescent in the absence of nucleic acids, the SYTO RNASelect stain exhibits bright green fluorescence when bound to RNA, but only a weak fluorescent signal when bound to DNA.

Learn more about SYTO RNASelect

SYTOX dyes are cell-impermeant nucleic acid stains making them useful dead-cell stains. DAPI is a classic nuclear and chromosome counterstain for identifying nuclei and observing chromosome-banding patterns. Upon binding the minor groove of double-stranded DNA, its fluorescence is ~20-fold greater than the unbound state.
Learn more about SYTOX nucleic acid stains

 DAPISYTOX Blue Nucleic Acid StainSYTOX Green Nucleic Acid StainSYTOX Orange Nucleic Acid StainSYTOX Deep Red Nucleic Acid StainTO-PRO
ReadoutFluorescent staining of nucleic acids
TargetBinds double-stranded DNA
Common filter setDAPIViolet/DAPIFITCRFP/TRITCCy5Cy5
LabelsDAPISYTOX BlueSYTOX GreenSYTOX OrangeSYTOX Deep RedTO-PRO-3
Ex/Em (nm)360/460444/480483/503547/570660/682642/661
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYesYes
Live cellsSemi-permeantNoNoNoNoNo
Fixed cellsYesYesYesYesYesYes
FixableYesYesYesYesYesNo
PlatformImagingImagingImagingImagingImagingImaging
ProtocolImaging protocolImaging protocol
Format1 mL250 μL250 µL250 µL5 x 50 µL1 mL
Cat. No.62248S11348S7020S11368S11381T3605

SelectFX Nuclear Labeling Kit includes four spectrally distinct fluorescent dyes for staining nuclei in fixed cells: blue fluorescent DAPI, green-fluorescent SYTOX Green stain, red-fluorescent 7-aminoactinomycin D (7-AAD), and far red-fluorescent TO-PRO-3 dye.

CellLight fluorescent fusion proteins label histone proteins and can multiplexed with other fluorescent probes in live cells or after fixation.
Learn more about nuclear CellLight reagents

 
Readout
 Expression of fluorescent fusion protein
Expression of fluorescent fusion protein
Target
 Labels histone proteins within the chromosome
 Localizes fluorescent protein in the nucleus
Common filter set
FITC
TRITC
DAPI
FITC
TRITC
Labels
GFP
RFP
CFP
GFP
RFP
Ex/Em (nm)
488/520
555/584
435/485
488/520
555/584
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Yes
Yes
Live cells
Yes
Yes
Yes
Yes
Yes
Fixed cells
No
No
No
No
No
Fixable
Yes
Yes
Yes
Yes
Yes
Platform
 Imaging
 Imaging
Imaging 
Imaging 
 Imaging
Format
1 mL
1 mL
1 mL
1 mL
1 mL
Cat. No.

HCS NuclearMask stains can be used to measure DNA content and perform cell demarcation on high-content imaging and analysis (HCS) platforms. These stains can be applied to live or fixed cells—able to survive standard formaldehyde-based fixation and detergent-based permeabilized methods. HCS NuclearMask stains are available in a choice of colors for multiplexing flexibility with other functional and structural probes.
Learn more about HCS reagents

 
Readout
Stains nucleus for demarcation
Common filter set
DAPI
Texas Red
Cy5
Ex/Em (nm)
350⁄451
622⁄645
638⁄686
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Live cells
Yes
Yes
Yes
Fixed cells
Yes
Yes
No
Fixable
Yes
Yes
Yes
Platform
HCS
HCS
HCS
Protocol
HCS protocolHCS protocol
HCS protocol
Format
65 µL
125 µL
400 µL
Cat. No.

ReadyProbes reagents provide the easiest fluorescent staining method for nucleic acids in live or fixed cells. These are ready-to-use solutions in convenient dropper bottles, formulated for room temperature storage.
Learn more about ReadyProbes reagents

 
Readout
Fluorescent staining of nucleic acids
Target
 Membrane-permeable dyes targeting RNA and DNA
Membrane impermeable dye targeting RNA and DNA
 
Common filter set
DAPI
Cy5
DAPI
Labels
Hoechst 33342
NucRed Live
DAPI
Ex/Em (nm)
360/460
638/686
360/460
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Live cells
Yes
Yes
No
Fixed cells
No
No
Yes
Fixable
Yes
No
No
Platform
Imaging 
Imaging 
Imaging 
ProtocolMicroscopy protocolMicroscopy protocolMicroscopy protocol
Format
6 x dropper bottles
6 x dropper bottles
6 x dropper bottles
Cat. No.

SYTO dyes are live cell, cell-permeant nucleic acid stains that exhibit bright fluorescence upon binding to nucleic acids. Hoechst dyes are blue-fluorescent nucleic acid stains that have multiple applications including distinguishing condensed pycnotic nuclei in apoptotic cells and for cell-cycle studies in combination with BrdU.
Learn more about SYTO nucleic acid stains

 Hoechst 33342SYTO 9 Green Nucleic Acid StainSYTO 82 Orange Nucleic Acid StainSYTO 59 Red Nucleic Acid Stain SYTO Deep Red Nucleic Acid Stain
ReadoutFluorescent staining of nucleic acids
TargetPreferentially binds AT regions of dsDNACell-permeant dyes targeting DNA and RNA
Common filter setUV / DAPIFITCTRITCTexas RedCy5
LabelsHoechst 33342SYTO 9SYTO 82SYTO 59SYTO Deep Red
Ex/Em (nm)350/461483/503541/560622/645652/669
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYes
Live cellsYesYesYesYesYes
Fixed cellsNoNoNoYesNo
FixableYesYesYesYesYes
PlatformImagingImagingImagingImagingImaging
ProtocolImaging protocolImaging protocolImaging protocol
Format10 mL100 μL250 µL100 µL1 vial
Cat. No.H3570S34854S11363S11341S34900

SYTO RNASelect Green Fluorescent Cell Stain is a cell-permeant nucleic acid stain that is selective for RNA. Although virtually nonfluorescent in the absence of nucleic acids, the SYTO RNASelect stain exhibits bright green fluorescence when bound to RNA, but only a weak fluorescent signal when bound to DNA.

Learn more about SYTO RNASelect

SYTOX dyes are cell-impermeant nucleic acid stains making them useful dead-cell stains. DAPI is a classic nuclear and chromosome counterstain for identifying nuclei and observing chromosome-banding patterns. Upon binding the minor groove of double-stranded DNA, its fluorescence is ~20-fold greater than the unbound state.
Learn more about SYTOX nucleic acid stains

 DAPISYTOX Blue Nucleic Acid StainSYTOX Green Nucleic Acid StainSYTOX Orange Nucleic Acid StainSYTOX Deep Red Nucleic Acid StainTO-PRO
ReadoutFluorescent staining of nucleic acids
TargetBinds double-stranded DNA
Common filter setDAPIViolet/DAPIFITCRFP/TRITCCy5Cy5
LabelsDAPISYTOX BlueSYTOX GreenSYTOX OrangeSYTOX Deep RedTO-PRO-3
Ex/Em (nm)360/460444/480483/503547/570660/682642/661
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYesYes
Live cellsSemi-permeantNoNoNoNoNo
Fixed cellsYesYesYesYesYesYes
FixableYesYesYesYesYesNo
PlatformImagingImagingImagingImagingImagingImaging
ProtocolImaging protocolImaging protocol
Format1 mL250 μL250 µL250 µL5 x 50 µL1 mL
Cat. No.62248S11348S7020S11368S11381T3605

SelectFX Nuclear Labeling Kit includes four spectrally distinct fluorescent dyes for staining nuclei in fixed cells: blue fluorescent DAPI, green-fluorescent SYTOX Green stain, red-fluorescent 7-aminoactinomycin D (7-AAD), and far red-fluorescent TO-PRO-3 dye.

CellLight fluorescent fusion proteins label histone proteins and can multiplexed with other fluorescent probes in live cells or after fixation.
Learn more about nuclear CellLight reagents

 
Readout
 Expression of fluorescent fusion protein
Expression of fluorescent fusion protein
Target
 Labels histone proteins within the chromosome
 Localizes fluorescent protein in the nucleus
Common filter set
FITC
TRITC
DAPI
FITC
TRITC
Labels
GFP
RFP
CFP
GFP
RFP
Ex/Em (nm)
488/520
555/584
435/485
488/520
555/584
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Yes
Yes
Live cells
Yes
Yes
Yes
Yes
Yes
Fixed cells
No
No
No
No
No
Fixable
Yes
Yes
Yes
Yes
Yes
Platform
 Imaging
 Imaging
Imaging 
Imaging 
 Imaging
Format
1 mL
1 mL
1 mL
1 mL
1 mL
Cat. No.

HCS NuclearMask stains can be used to measure DNA content and perform cell demarcation on high-content imaging and analysis (HCS) platforms. These stains can be applied to live or fixed cells—able to survive standard formaldehyde-based fixation and detergent-based permeabilized methods. HCS NuclearMask stains are available in a choice of colors for multiplexing flexibility with other functional and structural probes.
Learn more about HCS reagents

 
Readout
Stains nucleus for demarcation
Common filter set
DAPI
Texas Red
Cy5
Ex/Em (nm)
350⁄451
622⁄645
638⁄686
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Live cells
Yes
Yes
Yes
Fixed cells
Yes
Yes
No
Fixable
Yes
Yes
Yes
Platform
HCS
HCS
HCS
Protocol
HCS protocolHCS protocol
HCS protocol
Format
65 µL
125 µL
400 µL
Cat. No.

Live cell nuclear stains

SYTO nucleic acid stains

SYTO stains are cell-permeant stains that exhibit bright fluorescence upon binding to nucleic acids in live and dead cells (Figure 1). These dyes can also stain Gram-positive and Gram-negative bacteria. There are a range of wavelengths available, and each stain has a different fluorescence intensity, binding affinity, and nucleic acid selectivity. It is important to note that SYTO dyes do not exclusively stain the nucleus like DNA-selective dyes, such as DAPI or Hoechst 33342. Cells stained with SYTO dyes generally show cytoplasmic or mitochondrial staining.

Microscopic image of cell stained with red nucleus, blue lysosomes, and green tubulin
Figure 1. Multiplex image of live HeLa cells. HeLa cells were grown on a Greiner 96-well plate at a density of 5,000 cells/well, then stained with 1 μM SYTO Deep Red Nucleic Acid Stain (red), 1 µM LysoTracker Blue (blue), and 1 μM Tubulin Tracker Green (green) for 30 minutes. The cells were then washed and imaged on a confocal microscope.

SYTO RNASelect for nucleolus staining

The nucleolus is a non-membrane-bound structure found within the nucleus and is the site where ribosomal RNA is transcribed. The SYTO RNASelect Green Fluorescent Cell Stain is a cell-permeant nucleic acid stain that is selective for RNA. When bound to RNA, the RNASelect stain will fluoresce bright green but when bound to DNA, it will weakly fluoresce. The SYTO RNASelect stain can be used to detect nucleoli, and cells may be counterstained with a nuclear stain such as DAPI (Figure 2).

SYTO RNASelect Green Fluorescent Cell Stain can be used in live cells or fixed cells. After live cells have been stained, they may be methanol fixed with a minimal loss of staining pattern. Formaldehyde fixation is not recommended since the staining pattern will be altered.

Microscopic image of cells stained with green nucleoli and blue nuclei

Figure 2. Methanol-fixed MRC-5 cells stained with SYTO RNASelect green-fluorescent cell stain. Methanol-fixed MRC-5 cells stained with SYTO RNASelect green-fluorescent cell stain Nuclei were stained with DAPI; the densely stained areas are nucleoli.

Fixed cell nuclear stains

SYTOX nucleic acid stains

SYTOX nucleic acid stains are cell-impermeant, high-affinity nucleic acid stains that will cross a compromised membrane but will not cross the membrane of live cells. This makes them useful dead-cell stains. Upon binding nucleic acids, there is a >500-fold increase in fluorescence. SYTOX dead cell stains are available in a variety of colors for multiplexing and colocalization studies in fixed cells. They are also incorporated into several assays for apoptosis and cell viability.

SYTOX stains can be used in various applications. For example, SYTOX Blue and SYTOX Green nucleic acid stains have been used for DNA counterstains for chromosome labeling. They can also be used for Gram-negative and Gram-positive bacterial staining. SYTOX Deep Red nucleic acid stain has been used for single-cell analysis (Figure 3), tissue sections, 3D cell models, and bacteria.

Microscopic image of cells multiplexed with red nucleic acid stain
Figure 3. Staining of fixed cells. HeLa cells were grown on 96-well plates at a density of 5,000 cells/well. The cells were formaldehyde fixed and detergent permeabilized. The cells were then stained with rabbit polyclonal antibody against tubulin and mouse monoclonal antibody against complex V inhibitor protein followed by Donkey AntiRabbit Alexa Fluor Plus 488 and Donkey AntiMouse Alexa Fluor Plus 555, respectively. The cells were then stained with SYTOX Deep Red Nucleic Acid Stain and Alexa Fluor Plus 405 Phalloidin. Images were taken on an EVOS FL Auto Imaging System.

Nuclear fluorescent fusion proteins

CellLight fluorescent fusion proteins are available for nuclear and nuclear protein labeling. CellLight Nucleus (Figure 4) uses a SV40 nuclear localization sequence (1.0 kDa) for identification and demarcation of the nucleus in live-cell imaging experiments. CellLight Histone (Figure 5) uses a histone 2B sequence (13.7 kDa) to follow the dynamics of chromosomal behavior and is particularly useful for real-time imaging of mitotic cell division.

Introducing CellLight fluorescent proteins involves a simple transfection step using the BacMam technology, and they work like cell stains with minimal toxicity or chemical disruption. These nucleus fusion proteins are compatible with other fluorescent probes for multiplex analysis in live cells, or after formaldehyde fixation for colocalization studies.

Learn more about these and other CellLight fluorescent reagents

Microscopic image of cells stained with green and blue nuclei and red actin
Figure 4. HeLa cell Golgi and cytoskeleton imaged using the EVOS FL Auto imaging system. HeLa cells were transduced with CellLight Nucleus-GFP (nucleus, green), grown over night. Following fixation, permeabilization and block using the Image-iT Fixation/Permeabilization Kit, the cystoskeleton was stained using ActinRed555 ReadyProbes reagent (actin, red). Nuclei were counter-stained with NucBlue Fixed cell stain and images were acquired on the EVOS FL Auto imaging system using a 20x objective.
Microscopic image of cells with red histones and green tubulin undergoing mitosis
Figure 5. Live-cell imaging of cytoskeletal and histone dynamics during mitosis using CellLight reagents. U-2OS cells were transduced with CellLight Histone 2B-RFP and CellLight MAP4-GFP. The next day, cells were imaged in McCoy’s media and a 40X objective, with images collected every 5 minutes for 7 hours and 35 minutes. Imaging was performed on live cells using a DeltaVision Core microscope and standard DAPI/FITC/TRITC filter sets.