Easy Yeast RNA isolation without the Trizol

Recently BsB author Yevgeniy Grigoryev shared a total RNA isolation protocol. The one I use is even simpler—no expensive Trizol, which is a mix of phenol and some salts, all that is required is some Tris, SDS and phenol/chloroform mix. I have never used this protocol on non-yeast cells but I am almost sure that it can be applied to any cell type after the homogenization step in the RNA buffer. Changing the buffer pH from neutral to acidic – pH 4.5 – will allow you to isolate aminoacylated tRNAs as well.

1. Grow 25–100 ml of cells to OD 600 0.25–0.5 (You don’t even need a spectrophotometer for this).

2.    Spin cells, wash them in 1 ml dH₂O and transfer to a screw-cap tube. You can snap-freeze pellet at this stage.

3.    To 1 volume of cold RNA buffer add SDS to final concentration 0.5% (1/40 volume 20% SDS).

4.  Resuspend frozen pellet in 200µl cold SDS/RNA buffer.

5.    Add 1 volume phenol/chloroform; fill with beads to reach above solution.

6.    Break open (usually 30 sec/ 1 min on ice/30 sec on maximum Ribolyser setting) but your routine breakage procedure can be just as effective.

7.    Fill tube with RNA buffer (no SDS added), vortex, and spin 5 min keeping cold.

8. You will see phenol/chloroform fraction at the bottom of the tube, white layer of debris, and top buffer level. Take the top level and transfer to a fresh RNAse free Eppendorf.

9.    Extract aqueous fraction with phenol/chloroform twice, shaking for 5 min.  Add 0.9–1 volume of isopropanol, mix, and spin at RT 15–20 min. Because the buffer contains a lot of salt, no additional sodium acetate is necessary

(If 1/10 3M sodium acetate is accidentally added, get rid of the salts by dissolving the dried pellet in 600 µl RNA buffer, incubating 5 min with shaking, adding 600 µl of isopropanol and spinning 10–5 min. After this go to step 9).

10.  Wash pellet with 70%, air dry, resuspend in 30-50 µl dH₂O or TE and measure OD260/280 ratio.

RNA buffer (50 ml)

·         100 mM EDTA pH8.0 (10 ml 0.5M stock)

·         100mM NaCl (1 ml 5M stock)

·         50 mM Tris-HCl pH8.0 (2.5 ml 1M stock)

·         36.5 ml  dH₂O

For Easy Yeast  DNA—both genomic and plasmid—isolation see this article.

Have you any tips for inexpensive nucleic acid isolation in the lab?