What is Genomic DNA?
Genomic DNA, or gDNA, is the complete set of genetic information for a given organism. Genomic DNA encodes critical information for cell function and is passed from one cell to subsequent daughter cells. Genomic DNA is comprised of regions that encode a specific RNA or protein, known as genes or exons, and non-coding portions known as introns. Generally, gDNA is considerably large and must be organized into DNA-protein complexes known as chromosomes. Chromosomes can be several sizes and shapes depending on the organism. For instance, bacteria have a singular circular chromosome whereas human genomic DNA is organized into multiple, linear chromosomes. Genomic DNA extraction is regularly done for studies analyzing biological processes at the genetic level.
Genomic DNA Extraction
Genomic DNA contains a lot of valuable information for researchers, making genomic DNA extraction one of the most ubiquitous procedures performed in the life sciences. The purpose of genomic DNA extraction is to separate this genetic material from the rest of the cellular components (proteins, RNA, cell membrane, etc.) for further downstream analysis. Once purified, scientists can use the recovered DNA for a wide range of applications, from analyzing human genomic DNA for diseases to performing genetic engineering in plants and microorganisms. However, nearly all these downstream applications that use genomic DNA begin with recovering high-quality DNA. Included here are some of the top tips for successful genomic DNA extraction.
How to Get More From Your Genomic DNA Extraction Protocol
1. MORE OR LESS SAMPLE
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.
2. SAMPLE TYPES FOR GENOMIC DNA EXTRACTION
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 & Biological Fluids
- Cells and biological fluids (blood, semen, saliva, milk, etc.) are generally straight forward, 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 & 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 & 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. Read our How to Extract DNA from Plant Materials blog for a complete guide on how to successfully recover DNA from this notoriously difficult sample type.
Environmental Samples
- Environmental DNA or (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 & 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 tech@zymoresearch.com for guidance on how to process any genomic DNA sample.
3. SLOW AND STEADY
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.
4. BEST TIPS FOR PURE ELUATES
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.
5. FINISH STRONG- GET MORE DNA BACK IN THE ELUATE
The elution step is one of the most critical in the entire gDNA workflow. At this step, you will need to decide between yield or concentration. More DNA yield can be recovered with a larger elution volume. However, if you want a very concentrated sample, your overall DNA yield will be less. Keep this in mind before adding your elution buffer onto the column.
Heating the elution buffer to 55°C can help to increase the elution efficiency.
PRO TIP – Reload the eluate back onto the column to get any leftover DNA that might be on the column. Then incubate for 5 minutes and spin through for a second elution. This can increase the yield by up to 5% depending on the sample.
Choosing the Best DNA Extraction Kits for the Job
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, Table 1 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.
| Sample Type | Recommended Kit |
| Cells, Tissue, Blood, & other Biological Fluids | |
| Feces & Soil | |
| Microbial Cultures | |
| Plant & Seed Samples | |
| Urine | |
| Tissue Sections | |
| FFPE Samples | |
| cfDNA from Serum, Plasma, CSF, & Amniotic Fluid | |
| Insects (mosquitos, bees, drosophila, ticks, etc.) | |
| Feces, Soil, Biofilm, Water & Biological fluids for Microbiome and Metagenome Analysis | |
| Guthrie, FTA, & other Storage Papers | |
| Hair & Feather Samples |
Genomic DNA Extraction – Tips to Remember
High-quality DNA can be recovered from a variety of sample types by remembering these genomic DNA extraction tips:
- Use the Proper Sample Amount
- Ensure Complete Lysis
- Take it Slow
- Optimize Your Elution
Extracting DNA can be tough, but hopefully these tips and tricks help you make the most of your genomic DNA extractions. At Zymo Research, it is our mission to create high-quality extraction kits, simplify procedures, and provide exceptional technical support to help anyone become a DNA extraction master!