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I don't know if here is the correct place to make this question, but I've been noticing that protocols for the extraction of photosynthetic organisms DNA don't use phenol. Only CTAB / Chloroform.

Why?

Because bacterial or animal extraction are phenol:chloroform based.

Thank you

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CTAB is for removing polyphenols and polysaccharides which are found in plant tissues. Animal cells/bacteria don't have these. You can do an additional phenol-chloroform extraction if you want.

See this protocol by Monsanto.

  1. Weigh out 6g of processed tissue into a 50ml conical tube appropriate for centrifugation. Note: For unprocessed tissue, weighing m ay occur prior to processing as long as entire processed sample is transferred to the conical tube.

  2. For each 6g sample add 25ml of a solution consisting of 24.25ml, pre-warmed (55°C) CTAB extraction buffer, 0.5ml 2-mercaptoethanol (2-ME), and 0.25 ml of 10mg/ml proteinase K for a final concentration of 2% (2-ME) and 100µg/ml (proteinase K).

  3. Incubate the tube for 60 minutes at 55°C. Cool the tube briefly on bench (10 minutes)

  4. Add 20ml of phenol:chloroform:isoamyl alcohol (PCI, 25:24:1). Cap the tube and mix vigorously by vortex or inversion.

  5. Centrifuge for 10 minutes at 13,000×g and 20-25°C to separate the aqueous and organic phases. Transfer the upper aqueous phase to a clean 50ml conical tube.

  6. Repeat extraction two times for a total of three extractions (steps 4-5).

  7. Transfer upper aqueous phase to a new tube and add approximately 2/3 volume of -20°C isopropanol and gently invert the tube several times to mix.

  8. To precipitate the DNA place the tubes at -20°C for at least 30 minutes and up to three days.

  9. To pellet the DNA centrifuge the tubes at approximately 13,000×g for 20 minutes at 4°C.

  10. Redissolve the pellet in 4 ml of TE pH 8.0. Transfer to a 13ml Sarstedt tube and add approximately 40µl of 10mg/ml RNase, then incubate at 37°C for 30 minutes.

  11. To extract the DNA add 4ml of chloroform:isoamyl alcohol (CIA, 24:1). Centrifuge for 10 minutes at approximately 13,000×g at room temperature. Transfer the upper aqueous phase to a clean Sarstedt tube.

  12. Repeat step 11 then add half volume of 7.5M ammonium acetate, gently mix by inversion/pipette and add 2 volumes of 100% ethanol. Mix by inversion/pipette and place at -20°C for 30 minutes to overnight.

  13. Centrifuge at 13,000×g for 20 minutes at 4°C to pellet the DNA.

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I have used phenol:chloroform many times for algal DNA and RNA extractions. These protocols needed only minor tweaks to adapt it to a particular species (some cell walls can be extremely though). The general principle behind phenol chloroform works on almost any sample once you have lysed/pulverised the cells. The only major issues occur when tissues are extremely fatty or full of carbohydrates.

I have also used CTAB but it seems to be less universally applicable to algal samples.

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