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, more stable than SYBR Green & 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
• SYBR Safe - sensitivity similar to EtBr; 400µl 77€ S33102
• GelRed, GelGreen producer website

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
• SYBR stains may save money because their greater sensitivity enables cost reduction for expensive size standards [1]

Toxicity

• No direct evidence implicating ethidium bromide as a carcinogen in animals. It is actually used to treat sleeping sickness in cattle without increased incidence of cancer. [2]
• harmful but not at concentrations used in the lab [3]

"MSDS for SYBR safe reports a LD50 for rats of >5g/kg, which is higher than that of EthBr (1.5g/kg). As both these LD50s are many orders of magnitude higher than the concentrations used in molecular biology, toxicity of gel staining solutions is trivial compared to the risks of of burns from melted agarose or slipping on spilled gel buffer."

• SYBR Green I is more cytotoxic to bacteria than EtBr, PMID 10029672

"In the bacterial strains tested, SYBR Green I stain shows higher cytotoxicity per unit mass than does ethidium bromide. The maximal dose of SYBR Green I stain that showed no toxicity was 33.3 μg per plate (toxicity was observed at much lower doses for some strains), whereas toxicity was only observed at doses of 250–500 μg per plate for ethidium bromide."

• SYBR Green I increase the rate of UV induced mutagenesis in a bacterial test system more than EtBr, PMID 11377248
• both GelRed/Green [4] and EtBr [5] but not SYBR dyes are excluded from intact cells reducing their mutagenic potential

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

• ethidium bromide, SYBR Green I, SYBR Green II, SYBR Gold, DAPI
• comparison of EtBr alternatives at bitesizebio
• article on nucleic acid dyes at The Scientist

Wikipedia entries for:

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

• Life technology page on nucleic acid detection