SYBR Safe explained

SYBR Safe is a cyanine dye[1] used as a nucleic acid stain in molecular biology.[2] SYBR Safe is one of a number of SYBR dyes made by the Life Technologies Corporation. SYBR Safe binds to DNA. The resulting DNA-dye-complex absorbs blue light (λmax = 509 nm) and emits green light (λmax = 524 nm).

A comprehensive study of Thiazole-Orange-Based DNA Dyes was published, involving SYBR Safe, SYBR Green, PicoGreen, SYTO-16, SYTO-9 and a new derivative TOPhBu. Here, the synthesis of these compounds are published and characterised spectroscopically to quantify their fluorescence enhancement upon binding to double-stranded DNA. The ability of the dyes to detect DNA at low concentrations was evaluated using two new metrics, absolute fluorescence enhancement (AFE) and relativefluorescence enhancement (RFE). They were tested in qPCR experiments showing some important differences in the sensitivity and qPCR efficiency, which facilitates the DNA marker selection for analytical purposes. [3]

Safety

SYBR Safe is marketed as a safer alternative to ethidium bromide.[4] However, as the molecule itself is quite a bit larger than ethidium bromide, it does not bind to the column of a gel extraction as easily, making it less efficient when trying to clone a DNA fragment into a plasmid.SYBR Safe has a very similar structure to thiazole orange,[5] [6] [7] which has a methyl group attached to the charged nitrogen, whereas SYBR Safe has an N-propyl group. Thiazole Orange has been shown to be three to four times less mutagenic than ethidium bromide whereas SYBR Safe is four to five times less mutagenic.[8] Additionally, according to the Life Technologies website, SYBR Safe is not lethal in rats at doses as high as 5 g/kg, and rats don't show symptoms of acute toxicity. Thiazole orange does show toxicity at this dose.

Similar cyanine dyes

See also

Notes and References

  1. Evenson WE. Boden LM. Muzikar KA. O'Leary DJ . 1H and 13C NMR Assignments for the Cyanine Dyes SYBR Safe and Thiazole Orange. Journal of Organic Chemistry . 77 . 23 . 10967–10971 . 2012 . 23137048 . 10.1021/jo3021659 .
  2. it is most commonly used as a DNA stain in agarose gel electrophoresis
  3. Domahidy . Farkas . Kovács . Beatrix . Cseri . Levente . Katona . Gergely . Rózsa . Balázs . Mucsi . Zoltán . Kovács . Ervin . 5 . Comprehensive Study of Thiazole‐Orange‐Based DNA Dyes . ChemPhotoChem . 19 June 2024 . 10.1002/cptc.202400080 . en . 2367-0932. free .
  4. Haines . Alicia M. . Tobe . Shanan S. . Kobus . Hilton J. . Linacre . Adrian . Properties of nucleic acid staining dyes used in gel electrophoresis . Electrophoresis . March 2015 . 36 . 6 . 941–944 . 10.1002/elps.201400496. 25546455 . 27324826 .
  5. O'Neil . Casey S. . Beach . Jacie L. . Gruber . Todd D. . Thiazole orange as an everyday replacement for ethidium bromide and costly DNA dyes for electrophoresis . Electrophoresis . June 2018 . 39 . 12 . 1474–1477 . 10.1002/elps.201700489. 29645293 . 4790798 .
  6. Evenson . William E. . Boden . Lauren M. . Muzikar . Katy A. . O’Leary . Daniel J. . 1H and 13C NMR Assignments for the Cyanine Dyes SYBR Safe and Thiazole Orange . The Journal of Organic Chemistry . 27 November 2012 . 77 . 23 . 10967–10971 . 10.1021/jo3021659 . 23137048.
  7. Biancardi. Alessandro . Tarita. Biver . Alberto . Marini . Benedetta . Mennucci . Fernando . Secco . Thiazole orange (TO) as a light-switch probe: a combined quantum-mechanical and spectroscopic study . Physical Chemistry Chemical Physics . 2011 . 13 . 27 . 12595–12602 . 10.1039/C1CP20812H . 21660321 . 2011PCCP...1312595B .
  8. Evenson WE. Boden LM. Muzikar KA. O'Leary DJ . 1H and 13C NMR Assignments for the Cyanine Dyes SYBR Safe and Thiazole Orange. Journal of Organic Chemistry . 77 . 23 . 10967–10971 . 2012 . 23137048 . 10.1021/jo3021659 .

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