We have recently succeeded in synthesizing long oligonucleotides (90-mers) with high yield. This synthesis requires 360 virtual masks, and thus puts challenges on image placement and local contrast. We have updated our DNA synthesis modeling to Monte Carlo simulation from numerical approach. We also devised a method, called “Inverted Capping,” to remove sequence errors from edge scattering of light, which provides a large error reduction and the possibility of fabrication of higher resolutions. Finally, we have also implemented an image locking method to eliminate image drifts.

Articles you may be interested inFluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold 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. 1͒, 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.