Introduction

Nucleic acid extraction systems are used for automating DNA and RNA extractions from samples such as serum, body fluids, plasma, and other virus-infected cell cultures. It uses the magnetic bead method for high-quality nucleic acid extraction in the biological laboratory and clinical medicine department. The nucleic acid produced from this extraction can be used directly for qPCR and qRT-PCR detection. 

The extraction of nucleic acid is a crucial part of molecular biology. It is considered a starting point for thousands of downstream applications such as diagnosis, clinical research, product development, and other experiments. Nucleic acid can only be useful in scientific processes if it retains high quality. For years, scientists relied on manual nucleic acid extraction, but this process was time-consuming, required a lot of human work, and increased contamination risk. An automated extraction system was designed to simplify and increase the output of DNA/RNA extraction. It significantly reduces the working time and labor costs and increases the safety and quality of the overall extraction process. 

Principle

The nucleic acid extraction system involves the separation of nucleic acids from their complex structures by utilizing complementary hybridization. (Ali, Rampazzo, Costa, & Krieger, 2017)

This system uses a kit that contains magnetic beads and buffers that play a significant role in extraction. When the magnetic beads, along with the sample, are placed inside the extraction machine, these magnetic beads bind to the nucleic acid present in the sample and get attached to the rods found inside the machine. The beads and nucleic acid are then transferred for further processing, i.e., lysing, washing, and elution. After these steps are completed, the nucleic acid obtained is high quality and pure. 

Apparatus

The inside chamber of the nucleic acid extraction system consists of 6 plate positions. Each plate varies in its function, i.e., plate 1 and 6 has vibration and heat function, whereas plate 5 has a heat and refrigeration function. It also has a magnetic sleeve frame, magnetic rod, and anti-drip plate, which moves inside the chamber to perform the extraction process. Moreover, the extraction system is equipped with various safety functions such as door opening protection, UV protection, and a wide window for better observation and safer results.

Procedure

• Place the instrument on a stable desktop, open its door and remove the foam placed inside the chamber. 
• Connect it to the power supply. 
• Clean the area properly by spraying pipettes and desktop with RNase RNA and DNA remover 
• Take the sample in the test tube and place it on the rack for later use. 
• Now take a pre-packed 96-well deep well plate and shake it several times to well-mix magnetic beads and reagent. 
• Slowly and carefully remove the aluminum foil from the plate.
• Add 20µl protease K in the 1st and 7th column of the 96-well plate in sequence by using a pipette. 
• Now add 200µl sample in the 1st and 7th column of 96-well plate in sequence.
• Open the chamber, and put the 96-deep well plate in the corresponding position of the instrument. Make sure that the plate is foxed properly. 
• Take out the magnetic rod sleeves and place them in the corresponding position. 
• Close the door of the chamber 
• Select the extraction program and run the experiment 
• Once the nucleic acid extraction is completed, open the door and remove the magnetic rod sleeves. 
• Take out the 96-deep well plate and transfer the 6th and 12th rows to a centrifugation tube for preservation. 
• Store the nucleic acid at -20°C to -80°C
• After the experiment is completed, close the door of the chamber. Now click “UV disinfection” and select the disinfection time. 

Applications

A nucleic acid extraction system ensures greater consistency, reliability, high sample throughput, and better-quality data by automating the extraction process. The fewer manual handling reduces the risk of contamination, saves time, and improves workflow efficiency. 

Yoon, Kang, Hwang, Song, & Jeong, (2016) conducted a study to purify nucleic acids from clinical stool samples using two different methods, i.e., a semi-automatic magnetic bead-based kit and a manual membrane column-based kit. The results predicted that the magnetic bead-based kit was more user-friendly and produced high yields in both DNA and RNA compared to the manual membrane column-based kit.

An automated nucleic acid extraction system was used to improve the accuracy of the HybriBio Human Papillomavirus (HPV) test for cervical swab samples. It was observed that the automated system produced high-quality DNA compared to DNA extracted from a cell lysis kit. The analytical sensitivity of testing and the reproducibility was increased. It increased accuracy and amplified the efficiency of HPV detection. (Wang, Zhou, Ren, Xia, & Guo, 2017)

Strengths and Limitations

Strength

The nuclear acid extraction system streamlines the extraction process and helps achieve uniformity in extraction steps such as lysis, washing, and elution. It saves your time, speeds up your workflow, and leaves you with samples ready for downstream applications. The nucleic acid extracted from this process is of high quality and pure. As the extraction process is automated, it greatly reduces the risk of contamination and errors. Thus, providing more reliable and consistent data.

Moreover, it has the capability to process a large number of samples with greater speed. Depending upon the reagent, the extraction system takes about 15 to 60 minutes to complete the extraction process. This significantly increases the scope of research. The bright and spacious window makes it easier for the workers to monitor the working conditions. The UV light disinfection feature reduces cross infection and contamination of samples.

Limitations

The major drawback of the nucleic acid extraction system is that it is quite expensive and requires a high throughput of samples. It also poses a risk of contamination of samples with magnetic beads and can generate false-positive results due to contamination. (Knepp, Geahr, Forman, & Valsamakis, 2003) Moreover, laboratory professionals are required to handle extraction systems. 

Precautions

• Place the instrument in a dry and well-ventilated environment
• Make sure that the door of the instrument is shut properly while the program is running; otherwise, the program will be suspended. 
• If the obtained nucleic acid is not used immediately, then tore it at -20°C or -80°C
• Disinfect the instrument after the program is completed. 
• Use latex gloves during the process to avoid contamination 
• Spray the instrument with 75% alcohol after every experiment and clean it with dust-free papers. 
• Always switch off the instrument once the experiment is completed. 

Summary 

• The automated nucleic acid extraction system is a robust solution for getting high-quality, pure nucleic acid extracts from bacteria cells, plant tissues, blood, plasma, serum, viruses, and fungal tissues.
• It uses the magnetic beads isolation method to extract the nucleic acid from the sample.
• This system is efficient, minimizes contamination risk, and produces DNA/RNA extraction with greater speed.
• The nucleic acid extraction obtained is used for multiple downstream applications such as experimental and clinical research.

References

• Ali, N., Rampazzo, R. de C. P., Costa, A. D. T., & Krieger, M. A. (2017). Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. BioMed Research International, 2017, 1–13. https://doi.org/10.1155/2017/9306564
• Yoon, J. G., Kang, J. S., Hwang, S. Y., Song, J., & Jeong, S. H. (2016). Magnetic bead-based nucleic acid purification kit: Clinical application and performance evaluation in stool specimens. Journal of Microbiological Methods, 124, 62–68. https://doi.org/10.1016/j.mimet.2016.03.011
• Wang, Z., Zhou, Y., Ren, J., Xia, Z., & Guo, Q. (2017). Evaluation of a Magnetic Cellulose-Based DNA Extraction System to Improve the Performance of HybriBio Human Papillomavirus Genotyping and Screening Tests for Cervical Swab Samples. Clinical Laboratory, 63(10/2017). https://doi.org/10.7754/clin.lab.2017.170416
• ‌Knepp, J. H., Geahr, M. A., Forman, M. S., & Valsamakis, A. (2003). Comparison of Automated and Manual Nucleic Acid Extraction Methods for Detection of Enterovirus RNA. Journal of Clinical Microbiology, 41(8), 3532–3536. https://doi.org/10.1128/jcm.41.8.3532-3536.2003