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.

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.

CellLight® Nucleus-CFPEnlarge image

Live-cell nuclear dyes

Nucleic acid stains that permeate live cells are frequently used as counterstains for cellular identification, localization, and counting. Ideal live-cell nuclear dyes should be permeant to eukaryotic and prokaryotic membranes, exhibit affinity for both DNA and RNA, display enhanced fluorescence upon binding, and result in minimal toxicity to the cell. We offer a selection of Molecular Probes® nucleic acid stains with a choice of wavelengths for multiplexing and colocalization. ReadyProbes® reagents for live-cell staining are provided in a dropper bottle and are stored at room temperature for ease of use.

NucBlue™ Live Cell Stain Enlarge image

Fixed-cell nuclear dyes

Nuclear dyes for use with fixed cells should exhibit enhanced fluorescence upon binding nucleic acids, and affinity for both RNA and DNA with minimal sequence selectivity. Some of the highest-affinity DNA stains used with fixed cells are also used as dead-cell stains in cell health studies because they are impermeant to eukaryotic or prokaryotic cell membranes. We offer a selection of Molecular Probes® fixed-cell nuclear stains with a range of wavelengths for multiplexing and colocalization. ReadyProbes® reagents for fixed-cell staining are provided in a dropper bottle and are stored at room temperature for ease of use.

TO-PRO®-3 reagent Enlarge image

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.

SYTO® RNASelect™ green-fluorescent cell stainEnlarge image
Selection guides
 
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.
 
Readout
Fluorescent staining of nucleic acids
Target
 Membrane-permeable dyes targeting RNA and DNA
Common filter set
DAPI
FITC
TRITC
Cy®5
Labels
Hoechst 33342
SYTO® 9
SYTO® 82
NucRed® Live
Ex/Em (nm)
490/516
483/503
541/560
638/686
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Yes
Live cells
Yes
Yes
Yes
Yes
Fixed cells
No
No
No
No
Fixable
Yes
Yes
Yes
No
Platform
Imaging 
 Imaging
Imaging 
Imaging 
Format
6 x dropper bottles
100 μL
250 μL
6 x dropper bottles
Cat. No.
 
Readout
Fluorescent staining of nucleic acids
Target
Membrane impermeable dyes target RNA and DNA
Common filter set
DAPI
FITC
Texas Red®
Cy®5
Labels
DAPI
SYTOX® Green
Propidium iodide
TO-PRO®-3
Ex/Em (nm)
360/460
483/503
535/617
642/661
Signal-to-noise ratio
Photostability
Multiplexing
Yes
Yes
Yes
Yes
Live cells
No
No
No
No
Fixed cells
Yes
Yes
Yes
Yes
Fixable
No
No
No
No
Platform
Imaging 
Imaging 
Imaging 
Imaging 
Format
6 x dropper bottles
250 μL
6 x dropper bottles
1 mL
Cat. No.
 
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.
For Research Use Only. Not for use in diagnostic procedures.