Properties of classic nucleic acid stains—Table 8.4

Cat #	Dye	Ex/Em *	Fluorescence Emission Color	Applications †
A666	Acridine homodimer	431/498	Green	Impermeant AT-selective High-affinity DNA binding
A1301 A3568 ‡	Acridine orange	500/526 (DNA) 460/650 (RNA)	Green/Red	Permeant RNA/DNA discrimination measurements Lysosome labeling Flow cytometry Cell-cycle studies
A1310	7-AAD (7-amino-actinomycin D)	546/647	Red	Weakly permeant GC-selective Flow cytometry Chromosome banding
A7592	Actinomycin D	442	None	Chromosome banding
A1324	ACMA	419/483	Blue	AT-selective Alternative to quinacrine for chromosome Q banding Membrane phenomena
D1306 D3571 D21490	DAPI	358/461	Blue	Semi-permeant AT-selective Cell-cycle studies Mycoplasma detection Chromosome and nuclei counterstain Chromosome banding
D1168 D11347 D23107	Dihydroethidium	518/605	Red §	Permeant Blue fluorescent until oxidized to ethidium
15585-011	Ethidium bromide	518/605	Red	Impermeant dsDNA intercalator Dead-cell stain Chromosome counterstain Electrophoresis Flow cytometry Argon-ion laser excitable
E1169	Ethidium homodimer-1 (EthD-1)	528/617	Red	Impermeant High-affinity DNA labeling Dead-cell stain Electrophoresis prestain Argon-ion and green He-Ne laser excitable
E3599	Ethidium homodimer-2 (EthD-2)	535/624	Red	Impermeant Very high-affinity DNA labeling Electrophoresis prestain
E1374	Ethidium monoazide	464/625 (unbound)**	Red	Impermeant Photocrosslinkable Compatible with fixation procedures
H7593	Hexidium iodide	518/600	Red	Permeant, except gram-negative bacteria Stains nuclei and cytoplasm of eukaryotes and some bacteria
H1398 H3569 ‡ H21491	Hoechst 33258 (bis-benzimide)	352/461	Blue	Permeant AT-selective Minor groove–binding dsDNA-selective binding Cell-cycle studies Chromosome and nuclear counterstain
H1399 H3570 ‡ H21492	Hoechst 33342	350/461	Blue	Permeant AT-selective Minor groove–binding dsDNA-selective binding Cell-cycle studies Chromosome and nuclear counterstain
H21486	Hoechst 34580	392/498	Blue	Permeant AT-selective Minor groove–binding dsDNA-selective binding Cell-cycle studies Chromosome and nuclear counterstain
H22845	Hydroxystilbamidine	385/emission varies with nucleic acid	Varies	AT-selective Spectra dependent on secondary structure and sequence RNA/DNA discrimination Nuclear stain in tissue
L7595	LDS 751	543/712 (DNA) 590/607 (RNA)	Red/infrared	Permeant High Stokes shift Long-wavelength spectra Flow cytometry
N21485	Nuclear yellow	355/495	Yellow	Impermeant Nuclear counterstain
P1304MP P3566 ‡ P21493	Propidium iodide (PI)	530/625	Red	Impermeant Dead-cell stain Chromosome and nuclear counterstain
* Excitation (Ex) and emission (Em) maxima in nm. All excitation and emission maxima were determined for dyes bound to double-stranded calf thymus DNA in aqueous solution, unless otherwise indicated. † Indication of dyes as "permeant" or "impermeant" are for the most common applications; permeability to cell membranes may vary considerably with the cell type, dye concentrations and other staining conditions. ‡ Available in aqueous solution for those wishing to avoid potentially hazardous and mutagenic powders. § After oxidation to ethidium. ** Prior to photolysis; after photolysis the spectra of the dye/DNA complexes are similar to those of ethidium bromide–DNA complexes.