Purpose of Genomic DNA Extraction and Tips For Success

Each sample type is unique and varies in levels of DNA. Some sample types (e.g. muscle tissue) contain low amounts of DNA while others (e.g. nucleated blood) contain an extremely abundant amount of DNA. It is good practice to follow the protocol’s guidelines regarding sample amount, as too much sample can reduce lysis efficiency and potentially clog the column, while too little sample can result in insufficient DNA recovery.

The first step of any genomic DNA extraction is to break open the cells to release their contents, which is commonly referred to as the lysis step. It is crucial that the lysis step is performed to completion. Improper lysis can leave DNA trapped in the cells, leading to greatly reduced yields and purity as excess cellular debris can prevent complete removal of salts and macromolecules. To ensure the best lysis conditions, consider the sample type that you are starting with:

• Cells and biological fluids: Cells and biological fluids (blood, semen, saliva, milk, etc.) are generally straightforward, requiring a quick proteinase K digestion at 55°C. If the sample is completely homogeneous after digestion, you should be good to go! The Quick-DNA Plus Kits include an advanced proteinase K formulation and lysis buffer, making them ideal for the rapid extraction of genomic DNA from cells and biological fluids.
• Tissue: Since tissue is a 3D solid matrix, it requires a more intense lysis procedure. The fastest way to digest tissue is to cut up the sample as small as possible to increase the surface area. This allows more space for the proteinase K to break apart the small sections of tissue. Doing this will greatly speed up digestion time so you don’t have to incubate overnight. The Quick-DNA Plus Kits are equipped with an optimized proteinase K and lysis buffer formulation for improved genomic DNA extraction from solid tissues.
• Bacteria and fungi: Bacterial and fungal cells have robust cell walls, which makes them more difficult to lyse. There are some enzymatic and chemical methods that are specially designed to effectively disrupt hardy cell walls. However, a more effective technique to break open microbial cell walls are physical methods such as beating the cells with ceramic beads. Efficiency will vary depending on species, age, and stage of life cycle but employing physical and chemical means to break down bacterial and fungal cell walls will help drastically improve your gDNA yield and purity. The Quick-DNA Fungal-Bacterial Kits utilize a lysis buffer and bashing bead technology that has been optimized to lyse even the most robust bacterial and fungal cell walls.
• Plants and seeds: Plant tissue contains cells that have a thick cell wall, making them highly resistant to chemical modes of lysis. Thus, the plant tissue must be ground or cut into smaller pieces followed by a physical method of lysis, such as disrupting the tissue with ceramic beads, to ensure complete cell lysis. The Quick-DNA Plant/Seed Kit comes with a lysis buffer and bashing beads to enable complete lysis of thick plant cell walls.
• Environmental samples: Environmental DNA (eDNA) extracted from samples such as soil, water or feces can be particularly difficult to analyze due to a high presence of polyphenolics (humic/fulvic acid, tannins, etc.). Polyphenolics inhibit PCR and NGS reactions and must be removed for effective downstream analysis. Our Quick-DNA Fecal/Soil Kits are equipped with specialized PCR inhibitor removal technology, making these kits ideal for extracting genomic DNA from environmental samples.
• Everything else: No matter the sample, Zymo Research has chemistries that can purify DNA from even the most difficult sample types like honey or coral. Contact us for guidance.

When it comes to genomic DNA extraction, one of the best tips is to operate at a mindful pace, taking the time to conduct each step with care. Whether it’s washing with the correct buffer or removing spin columns and placing them into new collection tubes, handling plays a huge role in DNA extraction performance.

Most binding buffers contain salts that are crucial to the genomic DNA extraction process. However, if these salts get into the eluate, it dramatically reduces the A260/230 ratios and results in impure preps that will potentially affect the results of downstream experiments. There are several methods that you can try to help reduce the amount of salt contamination in your final DNA eluate.

• Ensure that you are using the proper centrifugation speeds to remove these salts completely from the column and matrix.
• Prevent splash back and salt contamination by thoroughly washing the columns with ethanol wash buffers. We recommend running the pipette tip along the wall of the column to flush all the salt out.
• If you are using capped columns, try inverting the closed columns during the wash steps to remove any trace salts that may have splashed onto the cap.
• Be sure to mind the tip of the column. Do not let it touch any of the binding or wash buffers. For those wanting to be especially cautious, we recommend using a new collection tube with each wash.
• Do not let the elution buffer touch any part of the column except the matrix. If it does, you run the risk of picking up any trace amounts of salts that may not have washed off.
• If you are working with samples that are high in PCR inhibitors, such as environmental samples, consider adding the OneStep PCR Inhibitor Removal Kit to your extraction method to ensure your eluate is pure enough for downstream applications.

Knowing that genomic DNA extraction is not a one-size fits all process, Zymo Research has developed a wide array of the best genomic DNA extraction kits that are tailored to fit different sample types. In addition, most of these DNA extraction kits are available in various formats (i.e. Microprep, Miniprep, 96-well, Magnetic Bead, etc.) to suit different input amounts and throughput.

As a reference, the following table shows specific sample types with the recommended DNA extraction method/kit from Zymo Research. Our dedicated technical support team is also always available to help ensure successful DNA extractions with any workflow.