Correction for illumination non-uniformity during the synthesis of arrays of oligomers

Abstract

The present invention provides an apparatus and a method for the synthesis of arrays of oligomers that have tight illumination intensity requirement. The apparatus and the method contain a mechanism to correct for illumination non-uniformity during the oligomer array synthesis process. To correct for illumination non-uniformity, the illumination intensity of different oligomer synthesis positions across an area in which oligomers are synthesized are determined first. Then, the differences in illumination intensity among the positions are evaluated mathematically. Next, any non-uniformity in illumination intensity is corrected by either reducing the intensity of the light for the brighter positions before the light reaches the illumination area or reducing the illumination time of the brighter positions during one protection group deprotection period.

1 . An apparatus for synthesizing arrays of oligomers such as DNA probes and polypeptides, the apparatus comprising:
 a) a flow cell having one or more reaction chambers in which monomer addition reactions can be conducted,   b) a light source providing a light beam,   c) an array of optical elements placed to receive the light bean from the light source and arranged such that each element of the array can be positioned to direct light along an optical axis or to not direct light along the optical axis,   d) projection optics capable of receiving the light reflected from the array of optical elements along the optical axis and imaging the pattern of the optical elements onto the flow cell, and   e) an optical element switch mechanism capable of adjusting the durations of on and off positions of each optical element during one protection group deprotection period to correct for non-uniformity in illumination intensity of the light that the projection optics project onto the flow cell.   
     
     
         2 . An apparatus for synthesizing arrays of oligomers such as DNA probes and polypeptides, the apparatus comprising:
 a) a flow cell having one or more reaction chambers in which monomer addition reactions can be conducted,   b) a light source providing alight beam,   c) an array of optical elements placed to receive the light beam from the light source and arranged such that each element of the array can be positioned to direct light along an optical axis or to not direct light along the optical axis,   d) projection optics capable of receiving the light reflected from the array of optical elements along the optical axis and imaging the pattern of the optical elements onto the flow cell, and   e) a lithographic mask placed between the projection optics and the flow cell with different areas of the mask darkened to different gray scales to correct for non-uniformity in illumination intensity of the light that the projection optics project onto the flow cell.