Jul 08, 2024
Yeast gDNA isolation
- 1UIUC
Protocol Citation: is Sparrow 2024. Yeast gDNA isolation. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2lyjm7elx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 07, 2024
Last Modified: July 08, 2024
Protocol Integer ID: 96323
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Abstract
This protocol is based on https://cshprotocols.cshlp.org/content/2020/10/pdb.prot098152.full doi:10.1101/pdb.prot098152
The protocol details how to perform a small scale yeast gDNA isolation including a proteinase K incubation step to visualize linear cytoplasmic protein primed plasmids.
This is used in combination with the system OrthoRep which relies on error prone replication of linear cytoplasmic plasmids.
Rix, G., Watkins-Dulaney, E.J., Almhjell, P.J. et al. Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities. Nat Commun 11, 5644 (2020). https://doi.org/10.1038/s41467-020-19539-6
Materials
Sorbitol buffer:
1M Sorbitol
0.1M Na2EDTA
Zymolyase solution:
Zymolyase 20T (12.5 mg/mL) or Zymolyase 100T (2.5 mg/mL) in Sorbitol buffer
Yeast resuspension buffer:
50 mM Tris-HCl pH 7.5
20 mM Na2EDTA
TE solution:
10mM Tris pH 7.4
1mM Na2EDTA
DNA extraction
DNA extraction
2h 12m
Start a 10 mL yeast culture and grow to saturation overnight or over 2 days
Note: for p1_wt (but not p1_rec) containing strains, p1 can be lost if grown in YPD for prolonged periods of time (based on my estimations, 2 or 3 1:1000 passages). Be mindful of this.
Aliquot 5 mL of culture to a 15 mL falcon tube and centrifuge 3000 x g, 00:05:00
5m
Pour off supernatant and pipette out the rest.
Resuspend the cells in 1 mL 0.9 % w/v NaCl solution
Centrifuge e 3000 x g, 00:02:00 , discard supernatant
2m
Resuspend in 500 µL sorbitol buffer
Sorbitol buffer:
1M Sorbitol
0.1M Na2EDTA
Add 20 µL of zymolyase solution
Zymolyase solution:
Zymolyase 20T (12.5 mg/mL) or Zymolyase 100T (2.5 mg/mL) in Sorbitol buffer
Incubate 37 °C 01:00:00 with gentle shaking
1h
Centrifuge e 3000 x g, 00:05:00 , discard supernatant
5m
Resuspend the cells in 500 µL yeast resuspension buffer
Yeast resuspension buffer:
50 mM Tris-HCl pH 7.5
20 mM Na2EDTA
Add 50 µL 10 % w/v SDS and shake vigorously
Add 5 µL of 20 mg/mL Proteinase K
Note: NEB proteinase K solution comes at this concentration
Incubate at 65 °C for 00:30:00
30m
Add 200 µL of 5M potassium acetate
Incubate On ice 00:30:00
30m
DNA isolation
DNA isolation
1h 15m
Pellet by centrifugation at max speed for 00:05:00
5m
Note:
At this step, a "short" protocol can be done - it will not produce sufficient DNA for visualization of p1, but is sufficient for PCR amplification from p1.
Recover supernatant and place into a miniprep kit silica column. Wash as per manufacturer instructions or with homemade Wash 1 / Wash 2 buffers, and elute in water or EB.
Note: this short protocol is not suitable for electrophoresis visualization of gDNA and should only be used for PCR amplification from the eluted DNA.
Recover supernatant in a fresh microcentrifuge tube. Aim to get 500<x<700 uL of sample, and avoid getting debris.
Add pure isopropanol equal to the volume of the sample (~765 µL ) and mix gently
Incubate for 00:05:00 Room temperature
Note: do not allow more than 5 minutes to pass
5m
Centrifuge at max speed for 00:10:00
10m
Discard supernatant
Air dry the pellet 00:10:00
10m
Add 300 µL of TE solution and add 0.75 µL of RNAse A at 20 mg/mL
Note: NEB RNAse A comes in this concentration
TE solution:
10mM Tris pH 7.4
1mM Na2EDTA
Incubate 37 °C 00:30:00
30m
Add 30 µL 3M sodium acetate and mix by inversion
Add 200 µL isopropanol and mix, then centrifuge at max speed for 00:00:20
20s
Discard supernatant
Allow pellet to air dry 00:10:00
10m
Resuspend in 50-150 µL TE solution
TE solution:
10mM Tris pH 7.4
1mM Na2EDTA
Pellet might be hard to resuspend especially if there is a lot of DNA. Be gentle, but persistent.
Quantify using NanoDrop. Remember to blank using TE instead of water.
DNA is clean enough for PCR or sequencing.
Gel analysis
Gel analysis
Optional step for p1 analysis
Cast a 0.75% agarose 1X TAE gel
Load ~ 1 µg gDNA
Run at 85 V for 100+ minutes
Look for the following bands and no others
p2_wt: 13.5 kb
p1_wt (size will be variable depending on landing pad used - for GA-Y319 = 8.9 kb; for GR-Y718 = 5.6 kb)
p1_rec (size will be variable = your construct size + 4.6 kb)