3.3. All-in-One Biomolecules Extraction
Generally, the extraction or purification techniques or kits available in the market can only allow the extraction of one type of nucleic acid, either DNA or RNA, or protein from a targeted organism. When the cellular material is limiting, it is desirable to extract DNA, RNA and protein from the same source.
A variation on the single-step isolation method of Chomczynski and Sacchi (1987), that the guanidinium thyicyanate homogenate is extracted with phenol:chloroform at reduced pH, allows the preparation of DNA, RNA and protein from tissue or cells. This method involves the lysis of cells with guanidine isothiocyanate and phenol in a single-phase solution. A second phase forms after the addition of chloroform where DNA and proteins are extracted, leaving RNA in the aqueous supernatant. The DNA and proteins can be isolated from the organic phase by precipitation with ethanol or isopropanol and the RNA precipitated from aqueous phase with isopropanol [15].
Several all-in-one extraction kits have been introduced in the market nowadays. For example, a column-based extraction kit that designed to purify genomic DNA, total RNA and total protein from a single biological sample simultaneously, without the usage of toxic substances such as phenol or chloroform and alcohol precipitation [46]. It is compatible with small amounts of a wide range of cultured cells and harvested tissue of animal and human origin. The targeted sample does not need to be separated into 3 parts before the purification of DNA, RNA and protein [46].
A solution-based 3-in-1 extraction kit that is available in the market is another example of non-organic solutions kit that can extract and purify DNA, RNA and protein, from different organisms in any types and sizes [47]. Its three simple steps protocol, which takes around 15 to 30 minutes, provides a fast and easy way to do the extraction of different biomolecules. Therefore, higher yield can be expected as fewer steps leads to fewer loss [47].
3.4. Automated Extraction System
Automated extraction system, a large, expensive and complex instrumentation designed for high-throughput sample processing, has helped to simplify the isolation of nucleic acids [48]. This system was designed for medium to large laboratories which has grown in presence over recent years [49]. Automating nucleic acid extraction process is potentially beneficial for a number of reasons including to reduce working time, decrease labor costs, increase worker safety and in the midst provides opportunity in increasing reproducibility and quality of results [50]. Besides, it is a key solution to increasing the laboratory efficiency [48].
In clinical laboratories, purification of high-quality biomolecules such as DNA, RNA and protein from a variety of starting material will be used in downstream testing applications. It is crucial to obtain purified samples in sufficient quality and purity [48]. Therefore, automated extractions should be more consistent and reproducible. The speed, accuracy and reliability of the whole extraction process should be maximal and at the same time minimize the risk of cross-contamination [49]. A solution has to be introduced to increase sample preparation efficiency without sacrificing the quality. The possibility of cross-contamination should be reduced and the systems are amenable to bar-coded sample tracking [51].
An extraction system that is available in the market has met the requirements stated above. It offers forensic laboratories fast and reliable sample processing along with high-quality automated DNA purification [52]. It is a paramagnetic-particle handling system to process sample and provide consistent yield and purity as there is no detectable cross-contamination between samples. The whole extraction process takes about 20 minutes from start to the end because only three simple steps are needed: add liquid samples to reagent cartridge; place reagent cartridges into the machine; press Start button. DNA is eluted into elution buffer at the end of the process [52].
Another example of automated system that is flexible and efficient for extraction of nucleic acids and proteins has been introduced [53]. Various starting materials can be processed by using this system, which is designed for small and medium sample throughput. It utilized surface-functionalized paramagnetic particles to adsorb the isolated nucleic acid [53]. The flexibility of this system allows the extraction of nucleic acid from up to twelve samples simultaneously. The extraction process requires around 20 to 40 minutes depending on the application. The kits that optimized for this system can extract genomic DNA, cellular RNA, viral or bacterial nucleic acids [53].
4. Possible Future Direction
Biomolecules extraction is the first step that needs to be performed for the following analysis or manipulation process. The liquid handling requirement is the most challenging aspect. Therefore, any automatic system must include not only automatic equipment for each extraction step but also equipment for automating the transfer of liquid between machines. Automation has aided in increasing the throughput and improving the reliability of the process, but these systems are still designed for use in a laboratory environment only. Some of the nucleic acid extraction system that are available in the market are large and require manual pre-processing stages by laboratory staff with technical expertise [54]. Therefore, robotic workstations for nucleic acid extraction should fulfill a true “walk-away” automation, which means a fully automated process [49]. A combination of all-in-one biomolecules extraction solution and method with fully automated extraction system can be a prospective invention in the future. The purification of DNA, RNA or protein from various organisms can be performed simultaneously using this type of extraction system with just a single extraction method.
It is often inconvenient that targeted biomolecules sample from an animal, plant or even a clinical sample must be sent to a laboratory for it to be extracted and analyzed [54]. The samples, especially clinical sample such as blood, need to be refrigerated and transferred to the nearest laboratory for extraction and analyzing. Hence, a portable biomolecules extraction system, which brings several advantages such as reduced labour, reduced waste and increased speed of extracting process, can be a potential development in the future [54]. The combination of portable extraction system with DNA, RNA, or protein analyzer can be build up in the future to help researchers in reducing working time and increasing the work efficiency.
Continued improvement in miniaturization will be the future trend of robotic automation in the laboratory [28]. Many clinical laboratories are performing workflow analysis and finding that smaller systems with lower throughput are more consistent with clinical laboratory workload. Besides, this automation system can be implemented at relatively low cost, improving the turnaround times and also reduce the labor costs [55].
5. Conclusion
Since the first DNA isolation was successfully done by Friedrich Miescher in 1869 and the initial DNA extraction developed from density gradient centrifugation strategies by Meselson and Stahl in 1958, many techniques for biomolecules purification has been developed. From guanidinium thiocyanate-phenol-chloroform extraction to the column-technology that is widely used in DNA and RNA extraction, and chromatography purification method to immunoblotting that used to extract proteins, biomolecules extraction has helped researchers and scientists in manipulating subsequent molecular biology analysis in order to have a better understanding in the biological materials of the earth.
The automated nucleic acid extraction system has been developed due to the influence of rapid growth of automation technology nowadays. Automating nucleic acid extraction process is potentially beneficial for a number of reasons including to reduce working time, decrease labor costs, increase worker safety and at the same time provides opportunity in increasing reproducibility and quality of results. However, improvement of the weaknesses for some of the instruments needs to be conducted all the time. In the mean time, an all-in-one biomolecules extraction system, or the invention of a miniature and portable extraction system can become a prospective development in the future.