Compositions and methods involving direct write optical lithography

Abstract

An improved optical photolithography system and method provides predetermined light patterns generated by a direct write system without the use of photomasks. The Direct Write System provides predetermined light patterns projected on the surface of a substrate (e.g., a wafer) by using a computer controlled means for dynamically generating the predetermined light pattern, e.g., a spatial light modulator. Image patterns are stored in a computer and through electronic control of the spatial light modulator directly illuminate the wafer to define a portion of the polymer array, rather than being defined by a pattern on a photomask. Thus, in the Direct Write System each pixel is illuminated with an optical beam of suitable intensity and the imaging (printing) of an individual feature is determined by computer control of the spatial light modulator at each photolithographic step without the use of a photomask. The Direct Write System including a spatial light modulator is particularly useful in the synthesis of DNA arrays and provides an efficient means for polymer array synthesis by using spatial light modulators to generate a predetermined light pattern that defines the image patterns of a polymer array to be deprotected.

1 . A method for deprotecting reaction sites on a substrate comprising the steps of: 
 providing a substrate having protected reaction sites;    modulating light direction with a spatial light modulator so as to generate a predetermined light pattern used for deprotecting selected portions of said protected reaction sites.    
     
     
         2 - 36 . (canceled)  
     
     
         37 . An apparatus for constructing DNA probes comprising: 
 (a) a reactor providing a reaction site at which nucleotide addition reactions may be conducted;    (b) a light source providing a light capable of promoting nucleotide addition reactions;    (c) a set of electronically addressable micromirrors positioned along an optical path between the light source and the reactor to receive and reflect the light, the micromirrors separated by lanes having lane widths; and    (d) projection optics positioned along the optical path between the reaction site and the image generator to focus an image of the lanes on the reaction site;    wherein the resolution of the projection optics expressed as a separation distance between resolvable line pairs is greater than half the lane width.    
     
     
         38 . The apparatus of  claim 37  wherein the resolution expressed as a separation distance between resolvable line pairs is greater than the lane width.  
     
     
         39 . The apparatus of  claim 37  wherein the resolution expressed as a separation distance between resolvable line pairs is greater than twice the lane width.  
     
     
         40 . The apparatus of  claim 37  wherein the resolution is calculated according to the formula:  
       
         
        
         LW=kλ/NA  
        
         where:  
         k is within a range of 0.7 to 0.5,  
         λ is the wavelength of the light, and  
         NA is the numeric aperture of the projection optics.  
       
     
     
         41 . The apparatus of  claim 40  wherein NA is measured as the sine of the half angle of a cone of light received from the projection optics by a central point of the reactor.  
     
     
         42 . The apparatus of  claim 40  wherein the numeric aperture is approximated by the aperture of a final element of the projection optics divided by twice a focal length of that final element.  
     
     
         43 . The apparatus of  claim 37  wherein the reactor is a flow cell having one or more reaction chambers in which nucleotide addition reactions may be conducted.  
     
     
         44 . The apparatus of  claim 43  wherein the flow cell further comprises a housing composed of a lower base, an upper cover section and a gasket mounted on the base, wherein a transparent substrate is secured between the upper cover section and the base to define a sealed reaction chamber between the substrate and the base that is sealed by the gasket, and wherein at least one channel extends through the housing from an input port to the reaction chamber and from the reaction chamber to an output port, wherein the active surface of the substrate faces the sealed reaction chamber.  
     
     
         45 . The apparatus of  claim 43  wherein the flow cell contains a plurality of reaction chambers in which nucleotide addition reactions may be conducted in solution phase.  
     
     
         46 . The apparatus of  claim 43  wherein the flow cell comprises a cell member having an upper surface and a lower surface and defining a plurality of channels permitting fluid communication between said upper surface and lower surface, said channels defining a plurality of reaction chambers in which nucleotide addition reactions can be conducted in solution phase.  
     
     
         47 . The apparatus of  claim 37  wherein the projection optics include focusing lenses and an adjustable iris, wherein one of the lenses passes light through the adjustable iris and the other lens receives the light passed through the iris and focuses that light into the reactor.  
     
     
         48 . The apparatus of  claim 37  wherein the projection optics include a concave mirror and a convex mirror, the concave mirror reflecting light from the electronically addressable micromirrors to the convex mirror which reflects it back to the concave mirror which reflects the light into the flow cell where it is imaged.  
     
     
         49 . The apparatus of  claim 37  wherein the projection optics form an Offner optical system.  
     
     
         50 . The apparatus of  claim 37  wherein the projection optics are telecentric.  
     
     
         51 . The apparatus of  claim 37  further comprising a filter receiving the light from the light source and which selectively passes only desired wavelengths through to the set of electronically addressable micromirrors.  
     
     
         52 . The apparatus of  claim 37  further comprising a computer connected to the set of electronically addressable micromirrors to provide command signals to control the positioning of the micromirrors to provide a desired pattern for projection into the reactor.  
     
     
         53 . The apparatus of  claim 37  wherein the light is in the range of ultraviolet to near ultraviolet wavelengths.  
     
     
         54 . The apparatus of  claim 37  wherein the image of the lanes is substantially the same size as the lanes in the electronically addressable micromirrors array.  
     
     
         55 . The apparatus of  claim 37  further comprising a DNA synthesizer connected to supply reagents to the reactor.  
     
     
         56 . The apparatus of  claim 37  wherein the lanes are gaps between adjacent electronically addressable micromirrors.  
     
     
         57 . The apparatus of  claim 56  wherein the resolution expressed as a separation distance between resolvable line pairs is greater than one micrometer.  
     
     
         58 . The apparatus of  claim 56  wherein the resolution expressed as a separation distance between resolvable line pairs is greater than two micrometers.  
     
     
         59 . The apparatus of  claim 37  wherein the lanes are electronically addressable micromirrors receiving a fixed signal to direct light away from the projection optics.  
     
     
         60 . The apparatus of  claim 37  wherein the projection optics provides a magnification substantially of one.