SYBR Green I

SYBR Green I (SG) is an asymmetrical cyanine dye^[1] used as a nucleic acid stain in molecular biology. The SYBR family of dyes is produced by Molecular Probes Inc., now owned by Thermo Fisher Scientific. SYBR Green I binds to DNA. The resulting DNA-dye-complex best absorbs 497 nanometer blue light (λ_max = 497 nm) and emits green light (λ_max = 520 nm). The stain preferentially binds to double-stranded DNA, but will stain single-stranded (ss) DNA with lower performance. SYBR Green can also stain RNA with a lower performance than ssDNA.

A sample of herring sperm stained with SYBR Green in a cuvette illuminated by blue light in an epifluorescence microscope. The SYBR green in the sample binds to the sperm DNA and, once bound, fluoresces giving off green light when illuminated by blue light

Spectrogram of SYBR Green I

SYBR Green I

Names
IUPAC name N',N'-dimethyl-N-[4-[(E)-(3-methyl-1,3-benzothiazol-2-ylidene)methyl]-1-phenylquinolin-1-ium-2-yl]-N-propylpropane-1,3-diamine
Identifiers
CAS Number	163795-75-3 Y
3D model (JSmol)	Interactive image
ChEMBL	ChEMBL1198924 N
PubChem CID	10436340
CompTox Dashboard (EPA)	DTXSID60936871
InChI InChI=1S/C32H37N4S/c1-5-20-35(22-13-21-33(2)3)31-23-25(24-32-34(4)29-18-11-12-19-30(29)37-32)27-16-9-10-17-28(27)36(31)26-14-7-6-8-15-26/h6-12,14-19,23-24H,5,13,20-22H2,1-4H3/q+1 Key: CGNLCCVKSWNSDG-UHFFFAOYSA-N
SMILES CCCN(CCCN(C)C)C1=CC(=Cc2sc3ccccc3[n+]2C)c2ccccc2N1c1ccccc1
Properties
Chemical formula	C32H37N4S+
Molar mass	509.73 g/mol
Solubility	Normally supplied solvated in dimethylsulfoxide
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). N verify (what is YN ?) Infobox references

Uses

SYBR Green finds usage in several areas of biochemistry and molecular biology. It is used as a dye for the quantification of double stranded DNA in some methods of quantitative PCR.^[2] It is also used to visualise DNA in gel electrophoresis. Higher concentrations of SYBR Green can be used to stain agarose gels in order to visualise the DNA present. In addition to labelling pure nucleic acids, SYBR Green can also be used for labelling of DNA within cells for flow cytometry and fluorescence microscopy. In these cases RNase treatment may be required to reduce background from RNA in the cells.

A comprehensive Study of Thiazole-Orange-Based DNA Dyes were 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 spectro-scopically 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 facilitate the DNA marker selection for analytical purposes. ^[3] This study showed that Sybr Green exhibits the highest fluorescence enhancement (AFE) and provided the best characteristic for PCR methods. The second best was TOPhBu, which is close in values to Sybr Green.

Safety

SYBR Green I is marketed as a replacement for ethidium bromide, a potential human mutagen, as both safer to work with and free from the complex waste disposal issues of ethidium bromide. However any small molecule capable of binding DNA with high affinity is a possible carcinogen, including SYBR Green.

In a study using the Ames test, which measures the ability of chemicals to cause mutations, when assayed at the same concentration SYBR Green I was on the order of 30 times less mutagenic than ethidium bromide.^[4]

Similar cyanine dyes

• PicoGreen (PG)
• SYBR Safe
• SYBR Gold
• Thiazole orange (TO)
• Oxazole yellow (YO)
• Safe-Green
• Chai Green

See also

• GelGreen

References

1. Zipper H; Brunner H; Bernhagen J; Vitzthum F (2004). "Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications". Nucleic Acids Research. 32 (12): e103. doi:10.1093/nar/gnh101. PMC 484200. PMID 15249599.
2. Mackay IM; Arden KE; Nitsche A (March 2002). "Real-time PCR in virology". Nucleic Acids Res. 30 (6): 1292–305. doi:10.1093/nar/30.6.1292. PMC 101343. PMID 11884626.
3. Domahidy, Farkas; Kovács, Beatrix; Cseri, Levente; Katona, Gergely; Rózsa, Balázs; et al. (19 June 2024). "Comprehensive Study of Thiazole-Orange-Based DNA Dyes". ChemPhotoChem. doi:10.1002/cptc.202400080. ISSN 2367-0932. This article incorporates text from this source, which is available under the CC BY 4.0 license.
4. Singer VL; Lawlor TE; Yue S (February 1999). "Comparison of SYBR Green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the Salmonella/mammalian microsome reverse mutation assay (Ames test)". Mutation Research. 439 (1): 37–47. Bibcode:1999MRGTE.439...37S. doi:10.1016/s1383-5718(98)00172-7. PMID 10029672.