Simple. Nontoxic. Inexpensive. Genomic DNA Extraction

AquaGenomic™ is a multifunctional aqueous reagent for genomic DNA extraction. It may be used to extract DNA from all types of specimens, from bacteria to plant and animal tissues. The extraction protocols are simple, fast, and scalable. AquaGenomic is nontoxic and its lysate may be used for PCR directly without DNA purification. AquaGenomic can efficiently extract DNA from dried specimen swabs. It may facilitate the use of dried specimen swabs for low-cost biobanking, biosurveillance and epidemiological studies.

AquaGenomic Brief Protocol

(Download AquaGenomic User Manual for protocols to extract DNA from animal tissues, saliva, swabs, blood, stool, soil, plants, bacteria, avian blood collected in Queen’s lysis buffer, and more)

1. Harvest the Cells

Pellet ~0.5-2 million cultured cells in a 1.5-ml microfuge tube by centrifugation at 12,000 xg for 60 sec. Aspirate or decant to discard the supernatant. (Note: For convenience, cell culture may be mixed with 1 vol of AquaGenomic for DNA extraction without needing to pellet the cells.)

2. Extract the DNA

Add 100 ul of AquaGenomic to the cell pellet. Suspend and lyse the cells by vortex vigorously for 30-60 sec. Incubate at room temperature or at 75 °C for 20 min (75 °C incubation produces better lysis and inactivates any residual DNases). (Note: To use the lysate for PCR, dilute an aliquot of the lysate with 10-20 vol of water and then use 0.25 ul of the diluted lysate in a 25-ul PCR reaction.)

3. Pellet the DNA

Add 0.8 vol of 100% isopropanol (e.g., to 100 ul crude lysate, add 80 ul isopropanol) and vortex for 30-60 sec to mix well. Centrifuge at 12,000 xg for 5 min to pellet the DNA. Decant to discard the supernatant.

4. Rinse the DNA

Gently fill up the tube and its lid with 70% ethanol from a squirt bottle and then flip the tube to discard the ethanol solution. Repeat the 70% ethanol rinse once. Flip the tube forcefully a few times and tap it on a paper towel to remove residual ethanol. Let the DNA pellet air-dry for 5-10 min.

5. Solubilize the DNA

Add 100 ul of TE buffer or deionized water to the DNA pellet, pipette or vortex vigorously to suspend the DNA. Incubate at 22 °C for 15 min (Optional: To fully solubilize and recover the DNA, incubate at 65-75 °C for 15 min or at room temperature overnight). Centrifuge at 12,000 xg for 5 min to pellet the insoluble and transfer the clear DNA solution to a new tube.

FAQ about AquaGenomic

1. Do I need to keep AquaGenomic in the freezer?

No, AquaGenomic Solution is stable at room temperature (~22 °C) for >1 year.

2. Does AquaGenomic Solution contain Proteinase K?

No. AquaGenomic can be used to extract DNA from most cells and tissues without needing protease digestion. However, adding Proteinase K (50 mg/ml) to AquaGenomic solution can increase DNA yield and is required for mitochondrial DNA extraction. You may homogenize the sample in AquaGenomic containing Proteinase K, incubate it at 55 °C for 1-2 hrs and then at 95 °C for 10-15 min to inactivate the Proteinase K.

3. I am worried about cross-contamination using homogenizers, any tips?

Between uses, you may wash the homogenizer with soap and running water, soak it in 10% bleach for ~5 min, and then rinse it with running deionized water. If you still feel uneasy, you may use Proteinase K digestion without using a homogenizer, or use a multichannel bead beater for homogenization in screw-capped tubes.

4. How may I maximize the DNA yield?

Incubating the DNA pellet in TE buffer or deionized water at 22 or 4 °C overnight before centrifuging to remove the insoluble may maximize DNA recovery.

5. Do I have to use the lysate immediately for PCR?

No, you may store the lysate at 4 °C until analysis. If the lysate has been incubated at 75-85 °C for 20 min, it may even be left at room temperature until analysis.

6. I got a weak PCR amplification using the lysate directly, how may I improve it?

You may try a few things to optimize the amplification: a) try to use different amount of lysate for the PCR, from 0.25 ml undiluted lysate to 20x diluted lysate, b) add 0.1 mg/ml BSA to the PCR reaction, c) add 1 mg/ml DTT to the PCR reaction, and d) increase the PCR cycle number to 45 cycles.

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