DNA microarrays: An imaging study

DNA chips are used to study the composition of genetic material. We report the results of an experimental study of the synthesis of DNA microarrays using a maskless photodeprotection process. In these "chips," the quality of the final product is dependent on the type and frequency of errors in the synthesis of the oligonucleotides. Contrary to photoresist, the photochemistry is linear and thus more prone to the introduction of defects. To understand and characterize the exposure process, we have developed a theoretical image formation model based on standard lithographic modeling tools. Experimentally, we have used a microarray synthesizer similar to that described in (Ref. 1), but using an argon ion laser as radiation source. To characterize the process, we have acquired aerial images using a CCD camera, a photosensitive film, and fluorescence image of a T-base monomer. We will discuss the imaging properties of the optical system, the models used to analyze the data and the relation between measured images and DNA stepwise synthesis yield. (C) 2003 American Vacuum Society.