In situ DNA synthesis on glass substrate for microarray fabrication using self-focusing acoustic transducer

Abstract

This paper presents a droplet-ejection-based technique for synthesizing deoxyribonucleic acid (DNA) sequences on different substrates, such as glass, plastic, or silicon. Any DNA sequence can be synthesized by ejecting droplets of DNA bases by a self-focusing acoustic transducer (SFAT) that does not require any nozzles. An SFAT can eject liquid droplets around 3-5 /spl mu/m in diameter, which is significantly smaller than those ejected by commercial ink jet printers and reduces the amount of reagents needed for the synthesis. An array of SFATs is integrated with microchannels and reservoirs for delivery of DNA bases to the SFATs. Poly-l-lysine-coated glass slide is patterned, and is used as a target substrate for in situ synthesis of multiple T bases. The significant advantage of this scheme over some of the existing commercial solutions is that it can allow geneticists to synthesize any DNA sequence within hours using a computer program at an affordable cost in their own labs. This paper describes the concept and scheme of the on-demand DNA synthesis (with an acoustic ejector integrated with microfluidic components) along with the results of an actual DNA synthesis by an SFAT. Note to Practitioners-Deoxyribonucleic acid (DNA) microarrays allow geneticists to monitor the interactions among thousands of genes simultaneously in a chip. There are commercial systems for producing DNA microarrays, but none of them give flexibility to synthesize DNA microarrays on-demand in the geneticist's own lab. Affymetrix's GeneChip technology produces DNA probe sequences premade at Affymetrix with a set of 4n photomasks for n-mers. Other techniques transfer premade DNA sequences to a substrate (glass, plastic, or silicon) through ink-jet printing or contact dispensing. Agilent and Rosetta use their ink-jet printing technology to produce DNA probe sequences at their factories. The ink-jet print heads used for printing microarrays use either piezoelectric or thermal actuation, and eject liquid droplets through nozzles. Thus, the smallest droplet size ejected from these devices depends on the size of the nozzle. The small nozzles are difficult to construct with good uniformity and tend to get clogged. The idea presented in this paper is to develop a microelectromechanical-system (MEMS)-based portable system for synthesizing DNA on different substrates, using nozzleless, heatless, lensless, acoustic droplet ejectors. The future research is to synthesize longer DNA sequences with a combination of different bases, using directional droplet ejectors.