Purpose of Genomic DNA Extraction & Tips For Success

When learning about genomic DNA, a frequent question that comes up is ‘what is the purpose of genomic DNA extraction?’

The Purpose of Genomic DNA Extraction

Genomic DNA extraction is one of the most ubiquitous procedures performed in the life sciences. Genomic DNA contains all the genetic, chromosomal material of an organism and it encodes all the components necessary for life. The purpose of genomic DNA extraction is to separate this genetic material from the rest of the cell (proteins, RNA, cell membrane, etc.). Once purified, scientists can study individual genes, sequence the entire genome, modify sections of DNA, and more.

However, all of these downstream applications begin with the genomic DNA purification. Therefore, it’s important to make sure that you are getting the highest quality DNA. That’s why we compiled a list of the best tips for genomic DNA purification.

How to Get More From Genomic DNA Extractions

More or Less Sample

Each sample 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) is bursting with excess DNA. It becomes good practice to follow the guidelines for sample loading as too much sample can reduce lysis efficiency and potentially clog the column, which will affect kit performance.

Sample Types for Genomic DNA Extraction

The first step of any genomic DNA extraction is to lyse the cells in order to break the cell membrane and release the contents. It is crucial that the lysis step is performed to completion. Improper lysis can greatly reduce yields (since the DNA is trapped within the cells) or reduce purity (as excess cellular debris can leech salts). 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!

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.

Bacteria & Fungi

• Bacteria and Fungi have cell walls, which makes them more difficult to break open.  There are some enzymatic and chemical methods that can get around this, but efficiency will vary depending on species, age, and stage of life cycle. Therefore, to ensure complete lysis, it is best to use a physical method such as beating the cells with ceramic beads.

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.

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 sample.

Slow and Steady

When it comes to genomic DNA extraction, one of the best tips is to operate at a pace you feel most comfortable with. Whether it’s removing spin columns and placing into new collection tubes or washing with the correct buffer, handling plays a huge role in DNA extraction performance.

Best Tips for Pure Eluates

Most binding buffers contain salts. If they get into the eluate, it dramatically reduces the 260/230 ratios and results in impure preps. 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 the ethanol wash buffers. We recommend running the pipette tip along the wall of the column to flush all the salts 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 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.

Finish Strong- Get more DNA back in the Eluate

The elution step is the one of the most critical in the entire 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.

Secret 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 most sample types. Plus, 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. Also, the Zymo Research technical support team is always available to help ensure successful DNA extractions in any workflow.

Genomic DNA Extraction - Tips

High-quality DNA can be recovered from a variety of sample types by remembering these genomic DNA extraction tips:

• Proper sample amount
• Complete lysis
• Elution conditions
• Mitigating procedural errors

Extracting DNA can be tough, but hopefully these tips and tricks help you make the most of your genomic DNA preps. Also, all-inclusive products, like those listed above, can simplify the extraction procedure, and are supported by free technical support teams that can provide any additional recommendations and help anyone become a DNA extraction master!