Dyes and stains

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Dyes and stains

This information was collected from various online sources. It is for informational purposes only.

DAPI

  • 358/461
  • double stranded nucleic acid dye, associates with the minor groove of dsDNA, preferentially binds AT clusters
  • stains both live and dead cells
  • can be excited with a mercury-arc lamp or with the UV lines of the argon-ion laser
  • better photostability than Hoesht dyes
  • blue-fluorescent

Fluorescein diacetate

  • fluorescein (494/518) is formed by intracellular hydrolysis of FDA
  • bacteria can hydrolyze this
  • leaks from cells
  • fluorescein has a relatively high rate of photobleaching
  • pH-sensitive fluorescence ref (pKa ~6.4) that is significantly reduced below pH 7
  • relatively broad fluorescence emission spectrum (not good for multicolor use)

Carboxyfluorescein Diacetate

  • fluorescein is formed by intracellular hydrolysis of CFDA
  • carboxyfluorescein contains extra negative charges (structure) and is therefore better retained in cells
  • been used in bacteria
  • CFDA is moderately permeant to most cell membranes with uptake greater at pH 6.2 than at pH 7.4
  • Oregon Green 488 (496/524) carboxylic acid diacetate is a more photostable version and less pH sensitive
  • timing issues with how long you have to wait for the compound to be hydrolyzed ?

Propidium iodide

  • 535/617
  • nucleic acid dye
  • preferentially stains dead cells
  • excited by 488 laser
  • red-fluorescent

SYTO

  • from Molecular Probes now owned by Invitrogen
  • nucleic acid dye
  • membrane permeant
  • series of blue-, green-, orange and red-fluorescent dyes
  • says that better results are obtained in buffers without phosphate so no PBS?
  • would require some optimization

Acridine Orange

  • 500/526 for DNA, 460/650 for RNA
  • nucleic acid binding dye
  • cell-permeant
  • emits green fluorescence when bound to dsDNA (525 nm) and red fluorescence when bound to ssDNA or RNA (650 nm).
  • more common for eukaryotes?

Hoechst 33342

  • 350/461
  • double stranded DNA, minor groove–binding DNA stains
  • cell-permeant nuclear counterstain
  • excited with the UV spectral lines of the argon-ion laser and by most conventional fluorescence excitation sources
  • emits blue fluorescence when bound to dsDNA.

SYBR Green I

  • nucleic acid dye, better for DNA
  • membrane permeant
  • excited by 488 laser
  • fluoresces green (maximum at 521 nm)
  • tends to be used as a gel stain more often

SYBR Green II

  • nucleic acid dye, better for RNA
  • membrane permeant
  • excited by 488 laser
  • fluoresces green (maximum at 521 nm)
  • tends to be used as a gel stain more often but also cited in flow cytometry
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