DNA microarrays: An imaging study

Abstract

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.

Biological lithography: Improvements in DNA synthesis methods

“…1(a) and 1(d), progressively leading to a complicated pattern of sequence errors. 4 We note that first order exponential deprotection reactions do not allow the beneficial threshold formed in photoresist. 4 This DNA synthesis process has been modeled into a Monte Carlo simulation.…”

“…4 We note that first order exponential deprotection reactions do not allow the beneficial threshold formed in photoresist. 4 This DNA synthesis process has been modeled into a Monte Carlo simulation. To track all the sequences of the strands in a simulated region, the distribution of delivered photons is obtained from a calculated aerial image by 2D Monte Carlo simulation.…”

“…The pixels of hand-drawn slanted lines represent the locations where 90-mers of random sequences (thus not visible from single target hybridization) are synthesized to study the effect of spacing of adjacent pixels. 4 Notice that 3 ϫ 3 array surrounded by 5 ϫ 5 outer square ring of random sequences at the left-bottom corner of Fig. 4 shows evidence of diffraction effects (lower 3.…”

“…Notice the internal 8 pixels are set to be inactive to reduce the diffraction effect from immediately adjacent pixels. 4 The white and black hand-drawn lines in Fig. 2 represent the edges of a micromirror.…”

“…We have developed a simulation model to quantitatively calculate the locations and amounts of specific species: ideal sequence, mutants and single deletions/additions. 4 To have a better knowledge about the sequence errors, we have updated the light-directed DNA synthesis modeling to predict the sequences of all the traced errors in addition to their amounts and locations, based on Monte Carlo simulation for photodeprotection events. From this, we have proposed a new method to improve the quality of the synthesis: "inverted capping.…”