Transforming Nucleic Acid Extraction with Automation

By storing and transmitting genetic information, nucleic acids underpin cellular processes involved in health and disease. Consequently, the isolation of DNA and RNA molecules from biological samples, such as cells, tissues, blood, or microbial cultures, is a crucial step in many experimental procedures, diagnostic evaluations, pathogen surveillance programs, and therapeutic development processes.¹ Researchers often use the extracted genetic material as an input for downstream applications including DNA and RNA sequencing, polymerase chain reaction assays, and microarray analysis.

Comparing Nucleic Acid Isolation Techniques

To obtain high-quality, purified nucleic acids, scientists can use several different methods, including phenol-chloroform extraction, cesium chloride/ethidium bromide (CsCl/EtBr) gradient centrifugation, alkaline extraction, silica column-based isolation, and magnetic bead-based extraction. However, each technique has its advantages and disadvantages depending on factors such as sample and nucleic acid type, the quality and yield required, time constraints, and downstream applications.

Phenol-chloroform extraction was once one of the most popular DNA isolation methods, and scientists have also modified this protocol to extract RNA molecules.² The technique leverages the varying solubilities of nucleic acids, proteins, and lipids in phenol and chloroform to partition the molecules into different phases. While this method allows researchers to acquire a high yield of nucleic acids at a low cost, phenol-chloroform extraction is time-consuming, labor-intensive, and requires hazardous chemicals.

The CsCl/EtBr gradient centrifugation method fractionates DNA and RNA molecules based on their density, where EtBr labels the nucleic acid bands.³ Scientists have used this technique to extract large quantities of highly pure chromosomal, plasmid, mitochondrial, and ribosomal DNA.² However, this isolation method is costly, complicated, and laborious.

Alkaline extraction is a common technique that researchers employ to isolate plasmid DNA from bacterial cells.² This simple and quick method uses an alkaline solution to lyse the cells and denature proteins and nucleic acids. Upon sample neutralization and genomic DNA precipitation, scientists obtain plasmid DNA, albeit at a lower purity than other techniques. Additionally, researchers cannot use this method for genomic DNA and RNA isolation.

By exploiting the attraction of nucleic acids to silica matrices under high-salt conditions, silica column-based isolation is a fast and easy protocol that yields high-purity DNA and RNA extracts.⁴ However, this technique often cannot efficiently extract small nucleic acid molecules.²

Magnetic bead-based extraction uses magnetic beads coated with nucleic acid binding agents, such as silica, oligo (dT), or carboxyl groups, to capture genomic DNA, RNA, plasmid DNA, and mitochondrial DNA from a sample.⁵ Scientists then employ a magnet to isolate the beads and a buffer to elute the pure nucleic acids.² As this efficient method does not require a centrifuge and can extract the DNA and RNA from various sample types, magnetic bead-based isolation is gaining popularity. However, when performed manually, the time-consuming multistep protocol is highly susceptible to human error and cross-contamination, which can compromise results obtained from experiments using these nucleic acid extracts.

Choosing a Superior Extraction Method

To overcome the limitations of manual nucleic acid purification, scientists need an advanced automated method that enhances efficiency and accuracy. The IndiMag 2 is an automated magnetic bead-based extraction system from INDICAL BIOSCIENCE, designed with an optimized magnet that enhances nucleic acid isolation efficiency compared to traditional extraction methods. This improves the isolation of nucleic acids from a range of sample types. The versatile and compact benchtop instrument can run up to 48 samples at a time with four possible washing steps. The automated process minimizes human errors during sample preparation and delivers consistent DNA and RNA extracts that are superior to those obtained through standard magnetic bead-based extraction protocols.

The IndiMag 2 offers precise temperature control, heating up to 100°C or cooling to 4°C, with separate strips for lysis and elution steps. This ensures that conditions are optimal throughout sample processing and storage and enhances the method’s efficiency. Additionally, the automated extractor uses a built-in UV light to decontaminate its entire processing chamber, which reduces the risk of cross-contamination between samples and improves the reliability of results from downstream experiments. The system also comes equipped with a user-friendly and intuitive touchscreen interface that enables researchers to start a pre-loaded protocol or create a custom protocol without needing a computer. Overall, the IndiMag 2 provides scientists with an efficient, scalable DNA and RNA extraction solution that seamlessly integrates into existing laboratory workflows.