DNA dyes

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Line 2: Line 2:
== Dyes for DNA in agarose gel electrophoresis ==
== Dyes for DNA in agarose gel electrophoresis ==
-
* [[ethidium bromide]] - traditional DNA stain, quantum yield 0.2; 5g >98% pure '''€73''' [http://www.carlroth.com/catalogue/catalogue.do;jsessionid=9F02901CF5F4C7782E84893A7B319246?id=20202&favOid=0000000100000e1700020023&act=showBookmark&lang=de-de&market=DE 7870.2], '''4x cheaper''' than SYBR Gold
+
* [[ethidium bromide]] - traditional DNA stain, quantum yield 0.2; 5g >98% pure '''€73''' [http://www.carlroth.com/catalogue/catalogue.do;jsessionid=9F02901CF5F4C7782E84893A7B319246?id=20202&favOid=0000000100000e1700020023&act=showBookmark&lang=de-de&market=DE 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''' [http://www.lifetechnologies.com/order/catalog/product/S11494 S-11494]
* [[SYBR Gold]] - DNA & RNA, '''10x more sensitive''' than EtBr, quantum yield 0.6, 500µl 10'000x '''€165''' [http://www.lifetechnologies.com/order/catalog/product/S11494 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€''' [https://www.lifetechnologies.com/order/catalog/product/S7585?CID=search-product S-7585]
+
* [[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€''' [https://www.lifetechnologies.com/order/catalog/product/S7585?CID=search-product 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 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€''' [http://www.lifetechnologies.com/de/de/home/life-science/dna-rna-purification-analysis/nucleic-acid-gel-electrophoresis/dna-stains/sybr-safe.html S33102]
 +
* GelRed, GelGreen [http://biotium.com/technology/gelred-gelgreen-nucleic-acid-gel-stains/ producer website]
=== Costs per gel compared ===
=== Costs per gel compared ===
Line 11: Line 13:
* EtBr 0.5µg/ml = 25mg / gel;  €0.4/gel
* EtBr 0.5µg/ml = 25mg / gel;  €0.4/gel
* SYBR Gold 10'000x solution => 5µl / gel;  €1.6/gel
* SYBR Gold 10'000x solution => 5µl / gel;  €1.6/gel
 +
 +
=== 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. [http://bitesizebio.com/95/ethidium-bromide-a-reality-check/]
 +
* SYBR Green I is more cytotoxic to bacteria than EtBr, PMID 10029672
 +
:<small>"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."</small>
 +
* SYBR Green I increase the rate of UV induced mutagenesis in a bacterial test system more than EtBr, PMID 11377248
 +
* both GelRed/Green [http://biotium.com/technology/gelred-gelgreen-nucleic-acid-gel-stains/] and EtBr [http://www.ncbi.nlm.nih.gov/pubmed/3267449] but not SYBR dyes are excluded from intact cells reducing their mutagenic potential
 +
See also
 +
- [http://www.researchgate.net/post/Can_anyone_suggest_alternatives_for_ethidium_bromide_in_terms_of_a_non-toxic_DNA_staining_dye user discussion]
 +
== Dyes for DNA in fluorescent microscopy ==
== Dyes for DNA in fluorescent microscopy ==

Revision as of 10:38, 13 June 2014

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.

Contents

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

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. [1]
  • 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 [2] and EtBr [3] but not SYBR dyes are excluded from intact cells reducing their mutagenic potential

See also - user discussion


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

Wikipedia entries for:

Personal tools