A Low-cost£¬Automated Nucleic Acid Extraction System Converted from the Open-Source RepRap 3D Printer

KeyWord:molecular diagnosis  ?magnetic separation  ?nucleic acid detection  ?open-source hardware

Abstract:

      Automatic nucleic acid extraction is essential for nucleic acid detection such as DNA amplification and high-throughput sequencing. Currently£¬most commercial nucleic acid extractors are mainly based on magnetic separation technology£¬adopting a highly integrated structural design or a closed solution£¬which is too costly and not conducive to use in resource-limited areas. In addition£¬it is difficult to update the functionality of the instruments once the functional module is determined. To address these challenges£¬a desktop automated nucleic acid extraction system was built in this work£¬which was converted from a low-cost 3D printer based on the Self-Replicating Rapid Prototyping £¨RepRap£© open-source project. With the RepRap open-source design£¬the module function of the system could be flexibly designed and programmable£¬thus allowing updates as needed£¬which significantly shortened the manufacturing and testing cycle of the system. In the developed system£¬the modular function of the heating£¬mechanical motion and multi-channel magnetic separation could be fully integrated with the open-source 3D printing hardware. an 8-channel magnetic separation based nucleic acid extraction module was designed£¬which could be assembled onto the original 3-axis motion platform by replacing the 3D printer extruder. The motion path planning required for automatic extraction was realized by G-code programming. The experimental protocols and control software were developed for the automated nucleic acid extraction in this work. The 3-axis motion platform and nucleic acid extraction module could be effectively controlled by the host computer and the module drive circuit£¬respectively. The heating module consisted of 4 custom-made aluminum heating bases and the heating plate on the 3D printer. The heating bases were adapted to a 96 deep-well plate£¬so that the deep-well plate is well attached to the heating block for high heating efficiency. By using the ¦ËDNA as the standard nucleic acid samples£¬the extraction performance of the system had been verified by evaluating extraction purity£¬and efficiency including consistency and stability. From the results£¬the system showed a better extraction purity and efficiency for the samples with high concentration than that with low concentration. Additionally£¬the 8-channel extraction experiment for the plasmid DNA from the cultured E. coli cells had been successfully carried out on the automated system in this study. This validation further demonstrated that the automated system can be utilized for extracting nucleic acids from real cell samples. Overall£¬the nucleic acid extraction system developed in this study is expected to provide a cost-effective means for rapid point-of-care molecular testing in resource-limited environments outside the laboratory.