Properties of classic nucleic acid stains

Cat. No. 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.
For Research Use Only. Not for use in diagnostic procedures.