Misplaced Pages

SYBR Green I: Difference between revisions

Article snapshot taken from Wikipedia with creative commons attribution-sharealike license. Give it a read and then ask your questions in the chat. We can research this topic together.
Browse history interactively← Previous editContent deleted Content addedVisualWikitext
Revision as of 21:27, 29 August 2011 editSfnagle (talk | contribs)22 editsNo edit summary← Previous edit Latest revision as of 15:55, 1 January 2025 edit undoInnerstream (talk | contribs)Autopatrolled, Extended confirmed users4,057 editsmNo edit summary 
(72 intermediate revisions by 50 users not shown)
Line 1: Line 1:
{{short description|Dye used for molecular genetics}}
<!-- Below the chembox. Notes:
* Parameters work only in their own section.
* When a parameter is not needed, please leave it empty, when a parameter is wrong, just clear its contents.
* When a section is really not needed, delete the whole section.
For more information, see ]. -->
{{Chembox {{Chembox
| Verifiedfields = changed
⚫ | verifiedrevid = 385623798
| Watchedfields = changed
⚫ | ImageFile = SYBR Green I.png
⚫ | verifiedrevid = 447380975
⚫ | ImageFile = SYBR green I.svg
| ImageSize = | ImageSize =
| IUPACName = N',N'-dimethyl-N--1-phenylquinolin-1-ium-2-yl]-N-propylpropane-1,3-diamine | IUPACName = ''N',N'''-dimethyl-''N''--1-phenylquinolin-1-ium-2-yl]-''N''-propylpropane-1,3-diamine
| OtherNames = | OtherNames =
| Section1 = {{Chembox Identifiers |Section1={{Chembox Identifiers
| PubChem = 10436340 | PubChem = 10436340
| ChEMBL_Ref = {{ebicite|changed|EBI}}
| ChEMBL = 1198924
| CASNo_Ref = {{cascite|correct|??}}
| CASNo = 163795-75-3 | CASNo = 163795-75-3
| SMILES = CCCN(CCCN(C)C)C1=CC(=Cc2sc3ccccc32C)c2ccccc2N1c1ccccc1
| SMILES = }}
| 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
⚫ | Section2 = {{Chembox Properties
| InChIKey = CGNLCCVKSWNSDG-UHFFFAOYSA-N }}
⚫ | Formula = C<sub>32</sub>H<sub>37</sub>N<sub>4</sub>S<sup>+<sup>
⚫ |Section2={{Chembox Properties
⚫ | MolarMass = 509.73 ]·]<sup>−1</sup>
⚫ | Formula = C<sub>32</sub>H<sub>37</sub>N<sub>4</sub>S<sup>+</sup>
⚫ | MolarMass = 509.73{{nbsp}}]/]
| Appearance = | Appearance =
| Density = | Density =
| MeltingPt = | MeltingPt =
| BoilingPt = | BoilingPt =
| SolubleOther = Soluble in ] }} | SolubleOther = Normally supplied solvated in ] }}
| Section3 = {{Chembox Hazards |Section3={{Chembox Hazards
| MainHazards = | MainHazards =
| FlashPt = | FlashPt =
| Autoignition = }} | AutoignitionPt = }}
}}
}}<!-- Text starts below-->

'''SYBR Green I''' ('''SG''') is an asymmetrical ]<ref>{{cite journal |author=Zipper H, Brunner H, Bernhagen J, Vitzthum F |title=Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications |journal=Nucleic acids research |volume=32 |issue=12 |pages=e103 |year=2004 |pmid=15249599 |pmc=484200 |doi=10.1093/nar/gnh101 |url=}}</ref> used as a ] ] in ]. SYBR Green I binds to ]. The resulting DNA-dye-complex absorbs blue light (λ<sub>max</sub> = 497&nbsp;nm) and emits green light (λ<sub>max</sub> = 520&nbsp;nm). The stain preferentially binds to double-stranded DNA, but will stain single-stranded DNA with lower performance. SYBR green can also stain ] with a lower performance than DNA. '''SYBR Green I''' ('''SG''') is an asymmetrical ]<ref>{{cite journal |author=Zipper H|author2=Brunner H|author3=Bernhagen J|author4=Vitzthum F |title=Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications |journal=Nucleic Acids Research |volume=32 |issue=12 |pages=e103 |date=2004 |pmid=15249599 |pmc=484200 |doi=10.1093/nar/gnh101 }}</ref> used as a ] ] in ]. The SYBR family of dyes is produced by ], now owned by ]. SYBR Green I binds to ]. The resulting DNA-dye-complex best absorbs 497 nanometer blue light (λ<sub>max</sub> = 497&nbsp;nm) and emits green light (λ<sub>max</sub> = 520&nbsp;nm). The stain preferentially binds to double-stranded DNA, but will stain single-stranded (ss) DNA with lower performance. SYBR Green can also stain ] with a lower performance than ssDNA.

⚫ ] illuminated by blue light in an ]. The SYBR green in the sample binds to the sperm DNA and, once bound, fluoresces giving off green light when illuminated by blue light]]
⚫ ]


==Uses== ==Uses==
⚫ SYBR Green finds usage in several areas of ] and ]. It is used as a dye for the quantification of double stranded DNA in some methods of ].<ref>{{cite journal |author=Mackay IM|author2= Arden KE|author3=Nitsche A |title=Real-time PCR in virology |journal=Nucleic Acids Res. |volume=30 |issue=6 |pages=1292–305 |date=March 2002 |pmid=11884626 |pmc=101343 |doi= 10.1093/nar/30.6.1292|url=}}</ref> It is also used to visualise DNA in ]. Higher concentrations of SYBR Green can be used to stain ]s 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 ] and ]. In these cases ] treatment may be required to reduce background from RNA in the cells.
⚫ ] ] stained with ] in a ] illuminated by blue light in an epifluorescence microscope. The SYBR green in the sample binds to the herring sperm ] and, once bound, fluoresces giving off green light when illuminated by blue light.]]

⚫ ]
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. <ref name=" Comprehensive Study of Thiazole-Orange-Based DNA Dyes ">{{cite journal |last1=Domahidy |first1=Farkas |last2=Kovács |first2=Beatrix |last3=Cseri |first3=Levente |last4=Katona |first4=Gergely |last5=Rózsa |first5=Balázs |last6=Mucsi |first6=Zoltán |last7=Kovács |first7=Ervin |display-authors=5 |title=Comprehensive Study of Thiazole-Orange-Based DNA Dyes |journal=ChemPhotoChem |date=19 June 2024 |doi=10.1002/cptc.202400080 |language=en |issn=2367-0932|doi-access=free }}{{Creative Commons text attribution notice|cc=by4|from this source=yes}}</ref>
⚫ SYBR green finds usage in several areas of ] and ]. It is used as a dye for the quantification of double stranded DNA in some methods of ].<ref>{{cite journal |author=Mackay IM, Arden KE, Nitsche A |title=Real-time PCR in virology |journal=Nucleic Acids Res. |volume=30 |issue=6 |pages=1292–305 |year=2002 |month=March |pmid=11884626 |pmc=101343 |doi= 10.1093/nar/30.6.1292|url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=11884626}}</ref> It is also used to visualise DNA in ]. Higher concentrations of SYBR green can be used to stain ]s 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 ] and ]. In these cases ] treatment may be required to reduce background from RNA in the cells.
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== ==Safety==
SYBR Green I is marketed as a replacement for the ] ], as both safer to work with and free from the complex waste disposal issues of ethidium. However anything capable of binding DNA with high affinity is a possible ], including SYBR. SYBR Green I is marketed as a replacement for ], a potential human ], as both safer to work with and free from the complex waste disposal issues of ethidium bromide. However any ] capable of binding DNA with high affinity is a possible ], including SYBR Green.


In a study using the ], which measures the ability of chemicals to cause mutations, when assayed at the same concentration there was no clear pattern in the relative mutagenicities of ethidium bromide and SYBR green I.<ref name=Singer>{{cite journal |author=Singer VL, Lawlor TE, Yue S |title=Comparison of SYBR Green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the Salmonella/mammalian microsome reverse mutation assay (Ames test) |journal=Mutation research |volume=439 |issue=1 |pages=37–47 |year=1999 |month=February |pmid=10029672 |doi= |url=}}</ref> Ethidium bromide was more mutagenic at higher concentrations, however SYBR green I could not be tested at these concentrations as it was ] at a much lower concentration than ethidium bromide.<ref name=Singer/> SYBR green I readily penetrates living cells, whereas ethidium bromide is efficiently excluded from live cells.<ref name=Singer/> In a study using the ], 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.<ref name=Singer>{{cite journal |author=Singer VL|author2=Lawlor TE|author3= Yue S |title=Comparison of SYBR Green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the Salmonella/mammalian microsome reverse mutation assay (Ames test) |journal=Mutation Research |volume=439 |issue=1 |pages=37–47 |date=February 1999 |pmid=10029672 |doi= 10.1016/s1383-5718(98)00172-7|bibcode=1999MRGTE.439...37S }}</ref>


==Related dyes== == Similar cyanine dyes ==
* ] (PG)
Similar cyanine dyes:
* SYBR Green II * ]
* SYBR Gold * ]
* ] (TO)
* YO (Oxazole Yellow)
* ] (YO)
* TO (Thiazole Orange)
* Safe-Green
* PG (PicoGreen)
* Chai Green

== See also ==
* ]


== References == == References ==
{{reflist}} {{Reflist}}


{{DEFAULTSORT:Sybr Green I}} {{DEFAULTSORT:Sybr Green I}}
] ]
] ]
]
] ]
] ]
]

]
]
]
]
]
]
]
]
]

Latest revision as of 15:55, 1 January 2025

Dye used for molecular genetics
SYBR Green I
Names
IUPAC name N',N'-dimethyl-N--1-phenylquinolin-1-ium-2-yl]-N-propylpropane-1,3-diamine
Identifiers
CAS Number
3D model (JSmol)
ChEMBL
PubChem CID
CompTox Dashboard (EPA)
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+1Key: CGNLCCVKSWNSDG-UHFFFAOYSA-N
SMILES
  • CCCN(CCCN(C)C)C1=CC(=Cc2sc3ccccc32C)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 , 100 kPa). ☒N verify (what is  ?) Infobox references
Chemical compound

SYBR Green I (SG) is an asymmetrical cyanine dye 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 (λmax = 497 nm) and emits green light (λmax = 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

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. 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. 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.

Similar cyanine dyes

See also

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.
Categories: