SYBR Safe

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).

SYBR Safe
Names
IUPAC name
(Z)-4-((3-Methylbenzo[d]thiazol-2(3H)-ylidene)methyl)-1-propylquinolin-1-ium 4-methylbenzenesulfonate
Identifiers
3D model (JSmol)
  • InChI=1S/C21H21N2S.C7H8O3S/c1-3-13-23-14-12-16(17-8-4-5-9-18(17)23)15-21-22(2)19-10-6-7-11-20(19)24-21;1-6-2-4-7(5-3-6)11(8,9)10/h4-12,14-15H,3,13H2,1-2H3;2-5H,1H3,(H,8,9,10)/q+1;/p-1
    Key: YTHKVAWQFBVEJQ-UHFFFAOYSA-M
  • CCC[n+]1ccc(C=C2Sc3ccccc3N2C)c2ccccc21.Cc1ccc(S(=O)(=O)[O-])cc1
Properties
C28H28N2O3S2
Molar mass 504.66 g·mol−1
Solubility Soluble in dimethylsulfoxide
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
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Infobox references

Safety

SYBR Safe is marketed as a safer alternative to ethidium bromide.[3] 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,[4][5][6] 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.[7] 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
  • GelGreen - competing product with a different molecular structure and size

Notes and references
  1. Evenson WE; Boden LM; Muzikar KA; O'Leary DJ (2012). "1H and 13C NMR Assignments for the Cyanine Dyes SYBR Safe and Thiazole Orange". Journal of Organic Chemistry. 77 (23): 10967–10971. doi:10.1021/jo3021659. PMID 23137048.
  2. it is most commonly used as a DNA stain in agarose gel electrophoresis
  3. Haines, Alicia M.; Tobe, Shanan S.; Kobus, Hilton J.; Linacre, Adrian (March 2015). "Properties of nucleic acid staining dyes used in gel electrophoresis". Electrophoresis. 36 (6): 941–944. doi:10.1002/elps.201400496. PMID 25546455. S2CID 27324826.
  4. O'Neil, Casey S.; Beach, Jacie L.; Gruber, Todd D. (June 2018). "Thiazole orange as an everyday replacement for ethidium bromide and costly DNA dyes for electrophoresis". Electrophoresis. 39 (12): 1474–1477. doi:10.1002/elps.201700489. PMID 29645293. S2CID 4790798.
  5. Evenson, William E.; Boden, Lauren M.; Muzikar, Katy A.; O’Leary, Daniel J. (27 November 2012). "1H and 13C NMR Assignments for the Cyanine Dyes SYBR Safe and Thiazole Orange". The Journal of Organic Chemistry. 77 (23): 10967–10971. doi:10.1021/jo3021659. PMID 23137048.
  6. Biancardi, Alessandro; Tarita, Biver; Alberto, Marini; Benedetta, Mennucci; Fernando, Secco (2011). "Thiazole orange (TO) as a light-switch probe: a combined quantum-mechanical and spectroscopic study". Physical Chemistry Chemical Physics. 13 (27): 12595–12602. Bibcode:2011PCCP...1312595B. doi:10.1039/C1CP20812H. PMID 21660321.
  7. Evenson WE; Boden LM; Muzikar KA; O'Leary DJ (2012). "1H and 13C NMR Assignments for the Cyanine Dyes SYBR Safe and Thiazole Orange". Journal of Organic Chemistry. 77 (23): 10967–10971. doi:10.1021/jo3021659. PMID 23137048.
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