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

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)

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 
ProtocolMicroscopy protocolMicroscopy protocolMicroscopy 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 33342Hoechst 34580SYTO 9 Green Fluorescent Nucleic Acid StainSYTO 82 Orange Fluorescent Nucleic Acid StainSYTO Deep Red Nucleic Acid Stain, for live cells
ReadoutFluorescent staining of nucleic acids
TargetMembrane-permeable dyes targeting RNA and DNA
Common filter setUV / DAPIViolet / DAPIFITCTRITCCy5
LabelsHoechst 33342Hoechst 34580SYTO 9SYTO 82SYTO Deep Red
Ex/Em (nm)350/461392/440483/503541/560652/669
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYes
Live cellsYesYesYesYesYes
Fixed cellsNoNoNoNoNo
Detectable after fixationYesYesYesYesYes
PlatformImagingImagingImagingImagingImaging
Protocol   Imaging protocol 
Format10 mL5 mg100 μL250 μL5 vials
Cat. No.H3570H21486S34854S11363S34901
 DAPISYTOX Blue Nucleic Acid StainSYTOX Green Nucleic Acid StainSYTOX Orange Nucleic Acid StainTO-PRO-3 IodideSYTOX Deep Red Nucleic Acid Stain
ReadoutFluorescent staining of nucleic acids 
TargetMembrane-permeable dyes targeting RNA and DNA 
Common filter setDAPIViolet/DAPIFITCRFP/TRITCCy5Cy5
LabelsDAPISYTOX BlueSYTOX GreenSYTOX OrangeTO-PRO-3SYTOX Deep Red
Ex/Em (nm)360/460444/480483/503547/570642/661660/682
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYesYes
Live cellsNoNoNoNoNoNo
Detectable after fixationYesYesYesYesYesYes
FixableYesYesYesYesNoYes
PlatformImagingImagingImagingImagingImagingImaging
Protocol  Imaging protocol Imaging protocol 
Format250 μL250 μL250 μL250 μL1 mL5 x 50 μL
Cat. No.62247S11348S7020S11368T3605S11381
 
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 protocolHCS 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 
ProtocolMicroscopy protocolMicroscopy protocolMicroscopy 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 33342Hoechst 34580SYTO 9 Green Fluorescent Nucleic Acid StainSYTO 82 Orange Fluorescent Nucleic Acid StainSYTO Deep Red Nucleic Acid Stain, for live cells
ReadoutFluorescent staining of nucleic acids
TargetMembrane-permeable dyes targeting RNA and DNA
Common filter setUV / DAPIViolet / DAPIFITCTRITCCy5
LabelsHoechst 33342Hoechst 34580SYTO 9SYTO 82SYTO Deep Red
Ex/Em (nm)350/461392/440483/503541/560652/669
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYes
Live cellsYesYesYesYesYes
Fixed cellsNoNoNoNoNo
Detectable after fixationYesYesYesYesYes
PlatformImagingImagingImagingImagingImaging
Protocol   Imaging protocol 
Format10 mL5 mg100 μL250 μL5 vials
Cat. No.H3570H21486S34854S11363S34901
 DAPISYTOX Blue Nucleic Acid StainSYTOX Green Nucleic Acid StainSYTOX Orange Nucleic Acid StainTO-PRO-3 IodideSYTOX Deep Red Nucleic Acid Stain
ReadoutFluorescent staining of nucleic acids 
TargetMembrane-permeable dyes targeting RNA and DNA 
Common filter setDAPIViolet/DAPIFITCRFP/TRITCCy5Cy5
LabelsDAPISYTOX BlueSYTOX GreenSYTOX OrangeTO-PRO-3SYTOX Deep Red
Ex/Em (nm)360/460444/480483/503547/570642/661660/682
Signal-to-noise ratio
Photostability
MultiplexingYesYesYesYesYesYes
Live cellsNoNoNoNoNoNo
Detectable after fixationYesYesYesYesYesYes
FixableYesYesYesYesNoYes
PlatformImagingImagingImagingImagingImagingImaging
Protocol  Imaging protocol Imaging protocol 
Format250 μL250 μL250 μL250 μL1 mL5 x 50 μL
Cat. No.62247S11348S7020S11368T3605S11381
 
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 protocolHCS protocol
HCS protocol
Format
65 µL
125 µL
400 µL
Cat. No.