The identification of DNA sequences is useful in the mapping of plant and animal genes as well as in other research and commercial applications.
One method of identifying DNA sequences uses an array of oligonucleotide probes constructed using photolithographic techniques. Each probe of the array is designed to hybridize with a particular DNA target, the latter of which may be coupled to a fluorescent target. By observing where the DNA hybridizes, the identity of the DNA may be deduced. This technique is described generally in Pease, et al., “Light-Generated Oligonucleotide Arrays for Rapid DNA Sequence Analysis,” Proc. Natl. Acad. Sci. USA, 91:5022–5026 (May 1994).
The probes are constructed on a substrate coated with photolabile protecting groups. Exposure by light passing through a photolithographic mask causes certain locations on the substrate to become reactive. DNA monomers are washed over the substrate and attached at the reactive sites. The exposed ends of the monomers are also protected by a photolabile material which in turn may be made reactive by selective illumination.
This process may be repeated with different monomers or short oligomers until arbitrary DNA polymers are built up at the various reaction sites. By changing the photolithographic mask, different DNA sequences may be synthesized at different locations in the array.
Photolithographic masks are cumbersome and expensive. For this reason, in an alternative approach, an array of switchable optical elements such as a two-dimensional array of electronically addressable micro mirrors may be used instead of the masks. Projection optics focus an image of the micro mirrors on the substrate where the nucleotide addition reactions are conducted. Under the control of a computer, each of the micro mirrors is selectively switched between a first position at which it projects light on the substrate through the optical system and a second position at which it deflects light away from the substrate. The cost of the masks and the time consuming process of exchanging mask is eliminated
Careful alignment of the masks or micro mirrors (henceforth collectively termed “pattern generator”), the projection optics, and the substrate is required for reliable high-density synthesis of DNA probes. This complex and time-consuming process may need to be repeated over time as the system is used. Complicating the alignment process is the extremely small size of the details in the projected image and the fact that the light energy is typically in the ultraviolet range.