Nucleus/Nucleolus Structure

The nucleus of the cell is a membrane-bound organelle that includes the nuclear envelope, nucleoli, and nuclear lamina and is the site of gene expression. Nuclear structure can be selectively visualized by staining nuclear proteins or directly staining nucleic acids. Cell-permeant nucleic acid stains make it possible to stain live cells or tissues with minimal processing to reveal the natural location of cells in tissues and provide a means to follow nuclear changes throughout cellular processes, from mitosis to apoptosis.

ReadyProbes nuclear dyes

ReadyProbes reagents provide the easiest fluorescent staining method for nucleic acids. Formulated for room-temperature storage, they are provided in convenient dropper bottles for ease of use. Just add two drops per milliliter of solution to stain your cells. We offer a selection of ReadyProbes nucleic acid stains with a choice of wavelengths for multiplexing and colocalization in either live or fixed cells

CellLight reagents for nuclear proteins

A choice of CellLight reagents for labeling the nucleus allows you to label histone proteins using a histone 2B sequence (13.7 kDa) to follow the dynamics of chromosomal behavior, or localize fluorescent protein to the nucleus using an SV40 nuclear localization sequence (1.0 kDa). CellLight proteins can be multiplexed with other fluorescent probes for analysis in live cells, or after fixation for colocalization studies. These ready-to-use constructs express fluorescent fusion proteins after a simple transfection step, and they work like cell stains with minimal toxicity or chemical disruption.

High-performance nuclear dyes

Ideal nuclear dyes should exhibit affinity for both DNA and RNA and display enhanced fluorescence upon binding. For live-cell staining they should be permeant to eukaryotic and prokaryotic membranes and result in minimal toxicity to the cell. For fixed-cell staining, they should be stable and selective. Some of the highest-affinity DNA stains used with fixed cells are also used as dead-cell stains because they are impermeant to eukaryotic or prokaryotic cell membranes

We offer a selection of Molecular Probes nucleic acid stains with a choice of wavelengths for multiplexing and colocalization in either live or fixed cells.

Staining the nucleolus

Nucleoli are non–membrane-bound bodies found within the nucleus and are 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. 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. The SYTO RNASelect stain can be used to detect the nucleoli, and cells may be counterstained with a nuclear stain such as DAPI.

High-content screening (HCS)

Versatile HCS NuclearMask stains can be used to measure DNA content and perform cell demarcation with live or formaldehyde-fixed cells on high-content imaging and analysis (HCS) platforms. HCS NuclearMask stains are available in a choice of colors for multiplexing flexibility with other functional and structural probes to ask complex biological questions.

Selection guides

 
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 
Protocol Microscopy protocol Microscopy protocol Microscopy protocol
Format
6 x dropper bottles
6 x dropper bottles
6 x dropper bottles
Cat. No.
 
Readout
 Expression of fluorescent fusion protein
Expression of fluorescent fusion protein
Target
 Labels histone proteins within the chromosome
 Localizes flruorescent 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.
  Hoechst 33342 Hoechst 34580 SYTO 9 Green Fluorescent Nucleic Acid Stain SYTO 82 Orange Fluorescent Nucleic Acid Stain SYTO Deep Red Nucleic Acid Stain, for live cells
Readout Fluorescent staining of nucleic acids
Target Membrane-permeable dyes targeting RNA and DNA
Common filter set UV / DAPI Violet / DAPI FITC TRITC Cy5
Labels Hoechst 33342 Hoechst 34580 SYTO 9 SYTO 82 SYTO Deep Red
Ex/Em (nm) 350/461 392/440 483/503 541/560 652/669
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
Detectable after fixation Yes Yes Yes Yes Yes
Platform Imaging Imaging Imaging Imaging Imaging
Protocol       Imaging protocol  
Format 10 mL 5 mg 100 μL 250 μL 5 vials
Cat. No. H3570 H21486 S34854 S11363 S34901
  DAPI SYTOX Blue Nucleic Acid Stain SYTOX Green Nucleic Acid Stain SYTOX Orange Nucleic Acid Stain TO-PRO-3 Iodide SYTOX Deep Red Nucleic Acid Stain
Readout Fluorescent staining of nucleic acids  
Target Membrane-permeable dyes targeting RNA and DNA  
Common filter set DAPI Violet/DAPI FITC RFP/TRITC Cy5 Cy5
Labels DAPI SYTOX Blue SYTOX Green SYTOX Orange TO-PRO-3 SYTOX Deep Red
Ex/Em (nm) 360/460 444/480 483/503 547/570 642/661 660/682
Signal-to-noise ratio
Photostability
Multiplexing Yes Yes Yes Yes Yes Yes
Live cells No No No No No No
Detectable after fixation Yes Yes Yes Yes Yes Yes
Fixable Yes Yes Yes Yes No Yes
Platform Imaging Imaging Imaging Imaging Imaging Imaging
Protocol     Imaging protocol   Imaging protocol  
Format 250 μL 250 μL 250 μL 250 μL 1 mL 5 x 50 μL
Cat. No. S11368 S11348 S7020 S11368 T3605 S11381
 
Readout
 Fluorescent staining
Target
 Selective for RNA
Common filter set
FITC
Labels
SYTO RNASelect
Ex/Em (nm)
490/530
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Live cells
No
Fixed cells
Yes
Fixable
Yes
Platform
Imaging 
Format
100 μL
Cat. No.
 
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 protocol HCS protocol
HCS protocol
Format
65 µL
125 µL
400 µL
Cat. No.
 
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 
Protocol Microscopy protocol Microscopy protocol Microscopy protocol
Format
6 x dropper bottles
6 x dropper bottles
6 x dropper bottles
Cat. No.
 
Readout
 Expression of fluorescent fusion protein
Expression of fluorescent fusion protein
Target
 Labels histone proteins within the chromosome
 Localizes flruorescent 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.
  Hoechst 33342 Hoechst 34580 SYTO 9 Green Fluorescent Nucleic Acid Stain SYTO 82 Orange Fluorescent Nucleic Acid Stain SYTO Deep Red Nucleic Acid Stain, for live cells
Readout Fluorescent staining of nucleic acids
Target Membrane-permeable dyes targeting RNA and DNA
Common filter set UV / DAPI Violet / DAPI FITC TRITC Cy5
Labels Hoechst 33342 Hoechst 34580 SYTO 9 SYTO 82 SYTO Deep Red
Ex/Em (nm) 350/461 392/440 483/503 541/560 652/669
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
Detectable after fixation Yes Yes Yes Yes Yes
Platform Imaging Imaging Imaging Imaging Imaging
Protocol       Imaging protocol  
Format 10 mL 5 mg 100 μL 250 μL 5 vials
Cat. No. H3570 H21486 S34854 S11363 S34901
  DAPI SYTOX Blue Nucleic Acid Stain SYTOX Green Nucleic Acid Stain SYTOX Orange Nucleic Acid Stain TO-PRO-3 Iodide SYTOX Deep Red Nucleic Acid Stain
Readout Fluorescent staining of nucleic acids  
Target Membrane-permeable dyes targeting RNA and DNA  
Common filter set DAPI Violet/DAPI FITC RFP/TRITC Cy5 Cy5
Labels DAPI SYTOX Blue SYTOX Green SYTOX Orange TO-PRO-3 SYTOX Deep Red
Ex/Em (nm) 360/460 444/480 483/503 547/570 642/661 660/682
Signal-to-noise ratio
Photostability
Multiplexing Yes Yes Yes Yes Yes Yes
Live cells No No No No No No
Detectable after fixation Yes Yes Yes Yes Yes Yes
Fixable Yes Yes Yes Yes No Yes
Platform Imaging Imaging Imaging Imaging Imaging Imaging
Protocol     Imaging protocol   Imaging protocol  
Format 250 μL 250 μL 250 μL 250 μL 1 mL 5 x 50 μL
Cat. No. S11368 S11348 S7020 S11368 T3605 S11381
 
Readout
 Fluorescent staining
Target
 Selective for RNA
Common filter set
FITC
Labels
SYTO RNASelect
Ex/Em (nm)
490/530
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Live cells
No
Fixed cells
Yes
Fixable
Yes
Platform
Imaging 
Format
100 μL
Cat. No.
 
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 protocol HCS protocol
HCS protocol
Format
65 µL
125 µL
400 µL
Cat. No.

Resources

Research tools

Molecular Probes Handbook

BioProbes 70 Journal article

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