Isolating DNA or RNA from various sample types is a fundamental step in research applications. As your lab grows and your projects and scope change, it’s important to stay well-equipped. This article covers the basics your lab needs to perform high-quality DNA and RNA extractions from the most common sample types.
If you’re looking to add DNA/RNA extraction capabilities to your lab, there are many items you’ll need. The good news is you’ll find that many of the items used for DNA or RNA extraction are things you already have in your lab.
That being said, nucleic acid extraction does require specialized instrumentation, protocols and management solutions to help your lab ensure the quality of your extractions at scale. Depending on your throughput goals and downstream applications for isolated DNA or RNA, you should consider exactly what is most prudent for your lab to start investing in.
This list of the basic items needed for optimized DNA and RNA extraction is designed to help you begin that process. We’ll start with some of the considerations around specialized automated instruments and end with some of the more general all-purpose items you may already have but would still be remiss to overlook in this list.
#1: DNA & RNA Extraction Instrumentation
Specialized Extraction Automation Instruments
Of course, nucleic acid can be isolated through manual processes. The issues are these processes take time, produce inconsistent results and result in yield qualities that are not suitable for many downstream applications.
There are a wide range of DNA/RNA extraction automation instruments on the market, and like many things in the article, the instrument or instruments you choose will vary on your funding, sample type, throughput and quality needs.
Sample Vortexers
A vortexer is an essential piece of extraction lab equipment. It’s designed to ensure a consistent and repeatable mix of the sample and reagent needed to begin the isolation of nucleic acid.
If your lab is running biological samples in any capacity, you may already have one of these in your lab, and it can be put to work mixing samples for nucleic acid extraction.
Centrifuge
Another essential piece of equipment is a centrifuge. This instrument is designed to separate substances with different densities within a liquid by spinning samples at high speeds.
They can be used before isolation to separate specific types of cells you may want to extract DNA or RNA from, and they can be used to isolate the finished DNA or RNA pellet.
Water Bath
A water bath is exactly what it sounds like. It’s a container filled with water heated to a specific temperature to ensure samples maintain a constant and uniform temperature. There are many different steps in a DNA or RNA extraction workflow that require temperature control, making a water bath essential.
Pipettors
Pipettors are a great investment if you don’t already have them in your lab. They ensure that small volumes of liquid are measured accurately and applied consistently during key steps in the nucleic acid extraction process.
They are available in many designs, including single-channel, multi-channel, and automated systems.
Quantification & QC Tools
Another form of instrumentation to consider is quantification.
After isolating your sample, how will you know if you had a good extraction without measuring results? It’s important to determine the quality of the sample to ensure it’s suitable for your downstream applications.
There are tools like a NanoDrop, Qubit, or others like a TapeStation that assist you in determining whether you’ve achieved good quality in your extractions is key. Without it, your downstream methods will suffer, and you may be wasting the expense of costly downstream procedures.
#2: Chemical Reagents and Consumables
Nucleic acid extractions require specific chemical reagents and consumable collection kits. The exact reagents and kits you will need will depend on your sample type, protocol and instrumentation.
Here is a general list of the most commonly used chemical reagents.
- Lysis buffers: Break down cell membranes and release nucleic acids.
- Proteinase K: An enzyme that digests proteins.
- RNase for DNA isolation: Removes RNA contaminants in DNA preparations.
- DNase for RNA isolation: Removes DNA contaminants in RNA preparations.
- Ethanol and isopropanol: For nucleic acid precipitation.
- Buffer solutions: For washing and elution steps to collect purified nucleic acids.
#3: Sample Management, Tracking and Storage Items
As with everything in rigorous scientific study, strict sample management and tracking protocols are needed to make sure your samples are properly processed at every step of the way. DNA and RNA extraction processes are no exception. Here are some sample management and storage considerations.
Barcoded tubes & SBS Format Racks
Sample mix-ups and mislabeling can set your entire project back. That’s why every lab needs barcoded samples and LIMS software to keep track of samples every step of the way. Every sample should be scanned in and recorded through every protocol step and every human interaction with the sample.
If something goes wrong, it can be quickly spotted and determined exactly what happened and when. This minimizes the damage of mistakes and keeps your samples flowing through the isolation process.
Freezer Storage
Cold storage is essential, especially if your lab intends to keep samples in storage before isolation. For example, blood samples require cold storage at -80 C. Without it, those samples will become unusable within a matter of days. Cold storage means your lab needs the space, freezers and the energy budget to run it all.
#4: General-Purpose Items
If your lab is already well-established and running other types of procedures, you will likely have many of these items on hand. Still, these general items play vital roles in ensuring nucleic acid isolations are of the highest quality possible. Plus, this section can serve as a good reminder for general best practices lab management and safety.
Personal Protective Equipment (PPE) & Safety Protocols
Every lab, from pharmaceutical to CRO to academic and basic testing, needs a full supply of personal protective equipment and safety protocols for the handling of hazardous chemicals. Depending on the samples you’re isolating from and the protocols you’re following, there are many different chemical reagents that require the use of PPE.
Make sure you have a full supply of safety goggles, gloves and lab coats. Your lab tech also needs to wear closed-toed shoes. Also, hand-washing and emergency eye-washing stations should be present anywhere hazardous chemicals are handled.
All-Purpose Lab Supplies
Lastly, you’ll want to make sure you have enough single-use plastics and containers on hand. Have full sets of standard beakers and tubes on hand as well.
Outsource Extraction: An Alternative to In-House DNA/RNA Extraction
As you take stock of your lab assets and future needs, you may find that investing in the needed equipment for DNA and RNA is beyond your budget or scope.
That’s where an outsourced provider can help. The right partner will already have a fully equipped extraction lab that can help you process your samples quickly. This allows your lab to avoid the upfront investment of instrumentation and storage. Plus, you may also get better extraction results that will improve the quality of your study.
When choosing between providers, one critical area many labs neglect is clear and consistent communication. Make sure that they keep in consistent contact at every step of the process. And when you call, a person should answer. That person should have full knowledge of your project and be equipped to answer any questions clearly and with transparency.
Conclusion
If your lab is looking to bring nucleic acid isolation in-house, this checklist is a good place to start. With it, you can begin to make the determinations on what your lab needs to invest in and what you already have on hand.
At the end of the day, the quality of your extraction should guide your decisions. If you’re able to invest in the equipment needed to extract high-quality nucleic acid in your own lab, then those funds are certainly not going to waste.
Still have questions? The DNA and RNA extraction experts at AutoGen can help. Get in touch, and we can help you determine the best way your lab can get high-quality nucleic acid extraction.