Mar 05, 2026
DNA extraction protocol for the thraustochytrid Aurantiochytrium limacinum
- Ben Leyland1
- 1State University of New York at Stony Brook
- Collier Lab
- Dr. Ben Leyland
Protocol Citation: Ben Leyland 2026. DNA extraction protocol for the thraustochytrid Aurantiochytrium limacinum. protocols.io https://dx.doi.org/10.17504/protocols.io.14egno79pl5d/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 04, 2026
Last Modified: March 05, 2026
Protocol Integer ID: 251351
Keywords: Thraustochytrid, DNA extraction, Genomic DNA, Genomic DNA extraction, DNA extraction buffer, gDNA, PCR, Aurantiochytrium, Aurantiochytrium limacinum, Lysis buffer, dna extraction protocol for the thraustochytrid aurantiochytrium limacinum, dna extraction protocol, method for rapid genomic dna extraction, rapid genomic dna extraction, thraustochytrid aurantiochytrium limacinum, aurantiochytrium limacinum, usable for polymerase chain reaction, pcr, polymerase chain reaction, thraustochytrid, use with the thraustochytrid, including yeast, suitable for other similar organism
Abstract
This is a "quick & dirty" method for rapid genomic DNA extraction usable for polymerase chain reactions (PCR). Reliable for use with the thraustochytrid, Aurantiochytrium limacinum, but is suitable for other similar organisms as well, including yeast or microalgae.
Materials
**10% Triton solution:**
- Triton-100: 10 mL
- DDW: 90 mL
**1 M Tris-HCl (pH 8):**
- Tris-HCl: 12.61 g
- DDW: 80 mL
**0.5 M EDTA:**
- EDTA: 11.69 g
- DDW: 80 mL
**DNA extraction buffer:**
- 10% Triton: 5 mL
- 1 M Tris-HCl (pH 8): 1 mL
- 0.5 M EDTA: 200 µL
Troubleshooting
DNA Extraction
Colonies should be grown on an agar-media plate for 4 days, and no older than 2 months.
Add 20 µL of DNA Extraction Buffer to a PCR tube.
Scrape some colony using a plastic pipette tip.
Resuspend the colony in the 20 µL DNA Extraction Buffer.
Heat at 95°C for 10 minutes.
Immediately remove PCR tube from thermocycler, and allow to cool to room temperature on the benchtop. [Room temperature cooling is important for several reasons. It allows for re-annealing of DNA to the more stable dsDNA form, as well as the precipitation of cellular debris.]
Allow 15-30 minutes for cooling.
Once cooled to room temperature, add 80 µL of sterile nuclease-free deionized water, and mix by gently pipetting up and down.
Centrifuge cellular debris.
Sample is now ready for use. 1-2 µL should be sufficient for a 50 µL PCR reaction. If not using, freeze at -20°C. For temporary storage, keep on ice, or in ice water, or at 4°C.
DNA Extraction Buffer
| A | B | |
| Compound | Amount | |
| 10% Triton | 5 mL | |
| 1 M Tris-HCl (pH 8) | 1 mL | |
| 0.5 M EDTA | 200 µL |
DNA Extraction Buffer.
Note: Filter sterilize.