DNA dyes

DNA dyes stain deoxyribonucleic acid for laboratory purposes such as detection and quantification. Many DNA dyes also bind to RNA and could be more broadly described as nucleic acid stains. Common dyes included ethidium bromide (EtBr), esp. for agarose gel electrophoresis of DNA, and DAPI for staining the cell nucleus in fluorescent microscopy.

Dyes for DNA in agarose gel electrophoresis

• ethidium bromide - traditional DNA stain, quantum yield 0.2; 5g >98% pure €73 7870.2, 4x cheaper than SYBR Gold
• SYBR Gold - DNA & RNA, 10x more sensitive than EtBr, quantum yield 0.6, 500µl 10'000x €165 S-11494
• SYBR Green I - better for DNA, 20x more sensitive than EtBr (60 pg per band with 300 nm transillumination), quantum yield 0.8; l000µl 690€ S-7585
• SYBR Green II - better for RNA, detection limit is 500 pg of RNA per band in non-denaturing gels with 300 nm transillumination, quantum yield 0.5

Costs per gel compared

• 50ml gel
• EtBr 0.5µg/ml = 25mg / gel; €0.4/gel
• SYBR Gold 10'000x solution => 5µl / gel; €1.6/gel

Dyes for DNA in fluorescent microscopy

• DAPI - traditional nuclear stain, emission max. 461 nm (blue)
• Hoechst 33258 and 33342 - emission max. 461 nm (blue)
• Propidium iodide - emission max. 617 nm (red)

Binding mode

• intercalating: EtBr, propidium iodide
• minor groove: DAPI (esp. AT rich), Hoechst

See also

• agarose gel electrophoresis
• ethidium bromide, SYBR Green I, SYBR Green II, SYBR Gold
• DAPI

Wikipedia entries for:

• ethidium bromide, SYBR Green 1, SYBR safe
• DAPI, Hoechst, propidium iodide, YOYO 1

• Life technology page on nucleic acid detection