Automatic system for DNA fragmentation

Abstract

Genomics have become a fundamental instrument in diverse areas such as medicine, epidemiology, microbiome studies, biotechnology, and industry. There are multiple technologies that allow genomic sequencing; one of the main steps in this experimental process of DNA sequencing being DNA fragmentation.Nowadays there is only one standardized commercial method for DNA fragmentation in compatible sizes with third generation sequencing technologies. However, it´s main disadvantage is tflucenhe high cost of the fragmentation in comparison with its sequencing cost [1]. Consequently, a protocol was developed, in which DNA fragmentation is mechanically produced by using a syringe [2]. This method, though effective, is not as easily reproducible because hand force used by different operatives in the manipulation of the syringe, could alter the results.The purpose of this project was to develop a prototype that could automate and make reproducible the designed DNA fragmentation protocol using a syringe. An electromechanical, as well as an electronic structure of a device that allows the rise and fall of a syringe plunger with controlled velocity was developed. The rise and fall velocities, which are independent, are in a range between 0 to 3,5 cm/ , more than double of the standard velocity. The device has a user interface which allows configuration through a computer, therefore being able to modify the different parameters for the realization of the protocol: number of cycles, velocity, aspirated volume. Moreover, an electronic display and a set of buttons are included in the device to check on the experiment whilst it is done. In conclusion the developed device allows for the customization and automation of the protocol.