Automated DNA Extraction: Three Key Considerations for Choosing a Method

CyBio Felix deck with labware for performing nucleic acid extraction

Both automated DNA extraction and automated RNA extraction are procedures for purifying nucleic acids (NA) via a liquid handling robot or electronic full-plate pipettor. Automating these processes can save hands-on time, improve sample quality, and increase your lab’s capacity.

There are many choices to be made when automating nucleic acid extraction. If you are considering adopting automation, this article will help you decide your goals as well as your technical requirements and preferred method.

Why automate DNA extraction and isolation?

Identifying the main benefit that you hope to achieve from automating DNA extraction will help you hone your system requirements.

Automation of DNA extraction has several benefits, including:

More reproducible results - automated DNA extraction methods tend to perform more consistently from sample to sample and batch to batch. Automation can also significantly reduce the risk of operator-to-operator variability.
Laboratory efficiency - implementing an automated process for repetitive steps over dozens or hundreds of samples for DNA isolation enables scientists and technicians to do more value-added work to move a project forward.
Supporting compliance - For regulated labs, adopting an automated DNA extraction process can help with record keeping, sample and reagent traceability.

For automated RNA extraction and isolation these advantages also apply. Use of a standardized, automated method for RNA extraction results in consistent yield and purity of preps, reducing the risk of failed runs and re-work. In addition, by automating RNA extraction you can reduce the risk of contamination by RNAses due to human contact.

Considerations for automating DNA extraction

When thinking about automating nucleic acid extraction and isolation in your laboratory, here are some technical aspects to consider:

Format for nucleic acid purification (filter plate or paramagnetic beads)
Degree of automation (modular/semi-automated or fully automated)
Laboratory setting – research lab or clinical testing environment

Defining these characteristics can help you and your automation vendor find the ideal solution for your NA extraction application. Read more about each aspect below.

Which automated DNA isolation format better meets your needs?

There are two major DNA/RNA isolation formats that are amenable to automation: paramagnetic beads and filter plates. Both operate on the principle of binding NA to a silica-based solid phase in the presence of high concentrations of chaotropic salts, washing, then releasing under low salt conditions. However, there are key differences between these two approaches that impact the automation strategy.

Paramagnetic Bead-Based DNA Isolation: This method uses paramagnetic beads coated with silica. After release from cells, NA binds to the beads. A magnet is then used to separate the beads from the lysate, followed by washing steps and elution of purified NA. This method is widely used in commercial kits.
Silica Membrane Filter Plate-Based DNA Isolation: In this method, lysed and homogenized cells are passed through a silica-based membrane in a filter plate format. NA binds to the membrane while contaminants are washed away. The NA is then eluted using an appropriate buffer. Many automated NA isolation systems utilize pre-packaged kits for this approach.

Comparing formats for automated DNA isolation

DNA Isolation Format	Paramagnetic bead	Silica membrane filter plate
Pros	High throughput Easier to fully automate	Excellent for high volumes of sample (e.g. plasma, cell-free DNA) Lower cost per sample High binding capacity
Cons	Can be expensive for large preps	Requires centrifuge or vacuum manifold integration for full automation

Many excellent kits with optimized reagents and materials that yield high-quality nucleic acid are available for either separation technology. Ask your reagent vendor whether they offer automation-specific versions of your preferred manual kits.

How fully do you need to automate DNA extraction?

Nucleic acid extraction workflows can be classified as either semi-automated or fully automated. These terms reflect the amount of intervention required during a run and are not necessarily related to throughput.

Semi-automated DNA extraction

Semi-automated NA extraction platforms, comprising a 96-channel pipettor and (for example) a non-automated microplate centrifuge, require manual intervention to move the plate between the liquid handler and the accessory equipment. The benefits of a semi-automated DNA extraction workflow include high daily capacity, cost-effectiveness, and ease of operation.

Decrease time and increase consistency

For example, scientists at Ankur Seeds (India) Pvt. Ltd. use a 96-channel semi-automated pipettor in their process to extract DNA from plant material. Simultaneously pipetting 96 wells saves considerable time compared to a manual 8-channel pipettor and delivers consistent DNA yields in support of their cross-breeding and DNA fingerprinting programs.

Maintain clean samples

An additional benefit of a ‘simple’ semi-automated pipettor for automated nucleic acid extraction is that such a compact device can easily fit into a laminar flow cabinet, supporting a clean environment. Regardless of location, when using a semi-automated pipetting solution, it is advisable to keep the accessory equipment nearby to avoid mishaps during plate transfer.

Fully automated DNA isolation

Generally, a workflow that requires no manual intervention to go from sample to purified DNA is considered fully automated; the starting sample may be lysed ahead of the automated process. Fully automated DNA isolation systems have a robotic arm that can move plate to and from a magnet station during the run, manage tip boxes, and reach off-deck equipment such as a centrifuge.

Walk away and let the robot do the work

A key benefit of a fully automated DNA/RNA extraction system is the ability to set up a run and walk away, leaving the system unattended throughout the process. Although they do not always have the fastest turnaround time, they can enable you or your operator to focus on other important tasks, thereby increasing overall productivity.

Increase your daily DNA extraction capacity

As an example of a fully automated application, Crone et al. (2020) developed a high-throughput diagnostic workflow for SARS-CoV-2. The automation of RNA extraction supported the processing of 1000 samples in 12 hours with minimal user intervention, thereby increasing sample throughput, minimizing run times, standardizing sample processing, maximizing accuracy and reproducibility, and reducing human error.

In what type of laboratory will you implement automated DNA extraction?

Are you in a routine testing environment with hundreds of samples to process per day, or is your work more research oriented with a different batch size from run to run? High throughput NA extraction operations on full plates can greatly benefit from the use of a 96- or 384-channel pipetting heads. For DNA extraction on less than a full plate of samples, choose a solution that enables pipetting by column and/or single well.

Is lab space a constraint? Consider how much bench or other lab space your automation system will require. Look for the most compact system that delivers the flexibility and/or throughput you need.

Working in a regulated lab? Do you require sample tracking? Better liquid handling systems offer software to allow connection to instruments, databases, and/or LIMS systems.

Is contamination a concern? Look for a system that can either be outfitted with its own enclosure or is small enough to fit in a laminar flow hood. This is especially important when automating RNA extraction, in order to reduce the risk of contamination by RNases due to human contact.

Additional requirements for an automated NA extraction system

While rounding out your requirements for a nucleic acid extraction platform, consider the importance of these features to your workflow:

Pre-defined protocols for your sample and nucleic acid types (genomic, plasmid, mRNA)
Integrated plate shaking function to support lysis and elution
Availability of certified RNAse/DNAse-free consumables (tips and plates)

A high-quality vendor such as Analytik Jena US will be able to integrate any or all of these elements in an automated DNA extraction system to meet your particular workflow needs.

References

Crone, M.A., Priestman, M., Ciechonska, M. et al. A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics.Nat Commun 11, 4464 (2020) https://doi.org/10.1038/s41467-020-18130-3

Analytik Jena India. Ankur Seeds – Quality DNA with Less Turnaround Time.Blog, Dec 2024.

See examples of automated DNA extraction solutions:

Application Note: Automated plasmid DNA isolation from bacteria via paramagnetic beads

Blog: Automated plasmid DNA isolation from bacteria via silica filter plate

Web Seminar: Nucleic Acid Extraction

Application Note: Automated DNA size selection with magnetic beads

Category	Description	Status
Necessary	These cookies are responsible for the provision of the most important website functionalities, e.g. for saving data protection and content settings. They also enable us to measure and aggregate anonymous user behavior data to improve our website.
Statistics	These cookies measure - anonymously and aggregated - the success of our advertising. They measure visits and traffic sources in order to better tailor the website to your needs.
Marketing	These cookies provide you with interest-based advertising. They measure the success of our advertising, anonymized and aggregated. These cookies are also used to deliver you personalized and interest based content.