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.

EvaGreen® dye is a green fluorescent nucleic acid dye with features that make the dye useful for several applications including qPCR and DNA melt curve analysis, real-time monitoring of thermophilic helicase-dependent amplification (tHDA), and capillary gel electrophoresis.

PMA (propidium monoazide) dye is a DNA modifier invented by scientists at Biotium. It is a photo-reactive DNA-binding dye that is useful for determination of microbial viability by qPCR.

DAPI is a popular blue fluorescent DNA dye. The dye binds to the minor groove of dsDNA with approximately 20-fold fluorescence enhancement.

Propidium iodide (PI) is a membrane-impermeant nucleic acid intercalator. The dye is commonly used to selectively stain dead cells in a cell population and also used as a counterstain in multicolor fluorescent imaging.