Gate-controlled Microfluidic Chamber with Magnetic Bead for Dna Sequencing-by-synthesis Technology

In this paper we present a novel microfluidic platform for DNA sequencing-by-synthesis methods (e.g. pyrosequencing). The proposed platform is based on the valve-controllable PDMS channel technology with DNA-coated magnetic beads. The encapsulation of the reaction of DNA polymerization in picoliter-sized wells provides for excellent isolation and control for detection. This separation prevents cross-talk amongst neighbor reactors which is one of the most limitations for higher integration of the current technologies. Through application of an external magnetic field the beads can be allocated with better accuracy. In addition this property can help mixing for the reaction. The proposed system is useful for a number of other bio-species detection and sorting templates. This paper illustrates the design and experimental results of a primary template as well as different advantages and potential applications of the Gate-Controlled Magnetic Bead (GCMB) platform in the world of DNA sequencing and genetics. INTRODUCTION The revolution that the Sanger method of DNA sequencing (1) and its subsequent array automation (2) has made in biology and genetics was followed with the sequencing of the human genome and the completion of the Human Genome Project (3, 4). The Sanger dideoxy DNA sequencing method has been the most commonly used method for DNA sequencing thus far, particularly in large-scale genomic sequencing, but inherent limitations of this state-of-the-art technology such as cost, throughput and read length, and enzymatic complexity make it impractical to deliver the current needs of DNA sequencing for clinical applications, disease detection and discovery, genomics studies, diagnostics and drug delivery, and personalized medicine. The Human Genome Project was accomplished after a reduction in the cost of DNA sequencing by three orders of magnitude. It is desired to reduce the cost by another three orders of magnitude to enable profiling of the individual genome. To achieve this goal, a highly integrated platform with high throughput and reliability will be needed. The increase of large-scale DNA sequencing projects in recent years has driven a search for alternative methods to reduce cost and time. (6, 7, 8, 9, 12) Many efforts have been investigated toward achieving a high-throughput and low cost assay for DNA sequencing such as high-density parallel sequencing with step-wise enzymatic cleavage and ligation (5, 14), base addition with deprotection steps (21), mass spectroscopy (22, 23, 24, 25), sequencing by hybridization (26), microfluidic device sequencing-by-synthesis (14), nanopore sequencing, polymerase colonies (27, 28, 29, 30) and pyrosequencing (8, 11, 12, 15, 32, 33, 35). Amongst all the different assays, pyrosequencing more likely seems to be the