DNA Binding Dyes

Acridine orange (AO) stains dsDNA green (525 nm) and RNA or single stranded DNA red (650 nm). The dye is membrane-permeant and its nucleic acid binding property has been used for cell-cycle studies.

Actinomycin D is a nonfluorescent GC-selective intercalator. Similar to 7-AAD (cat. no. 40038), actinomycin D has also been used for chromosome banding studies.

DiSC₂(5) (3,3′-Diethylthiadicarbocyanine, iodide) binds to DNA-DNA or PNA-DNA duplexes with a large blue-shift of the absorption spectrum. Binding of the dye to PNA-DNA hybrid, in particular, blue-shifts the dye absorption spectrum by as much as 115 nm, offering a visual method to detect nucleic acid hybridization (1,2).

DODC (DiOC₂(5)) has been reported to bind to triplex DNA as well as dimeric hairpin quadruplex DNA (1). Binding of the dye to triplex DNA quenches the fluorescence of the dye and red-shifts the dye absorption peak.

Ethidium bromide (EtBr) is a widely used nucleic acid gel stain although it is also a known potent mutagen. EtBr is an intercalating DNA-binding dye with little sequence preference.

Hoechst dyes are cell membrane-permeant, minor groove-binding blue fluorescent DNA stains. Hoechst dyes are widely used in cell cycle and apoptosis studies as nuclear counterstains.

Viability PCR dye, a new and improved version of the popular viability dye propidium monoazide (PMA).

A membrane-impermeant nucleic acid intercalator. The dye is commonly used to selectively stain dead cells in a mixed live-dead population and also used as a counterstain in multicolor fluorescent assays.

A photo-reactive DNA-binding dye typically used in viability PCR (v-PCR) of microorganisms like bacteria, viruses, and fungi.

A photo-activated fluorescent nucleic acid binding dye used to selectively and covalently label dead cells in the presence of live cells for viability PCR, fluorescent microscopy, and flow cytometry.