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Clinical Chemistry 50: 1936-1939, 2004; 10.1373/clinchem.2004.037333
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(Clinical Chemistry. 2004;50:1936-1939.)
© 2004 American Association for Clinical Chemistry, Inc.

Abstracts of Oak Ridge Posters

Photo-Removable Protecting Groups for in Situ DNA Microarray Synthesis

Farhana Afroz, Anthony D. Barone, Paul A. Bury, Chuan Chen, Andrea Cuppolettia, Robert G. Kuimelis, Handong Li and Glenn H. McGall

1 Affymetrix Research Laboratories, Affymetrix, Inc., 3380 Central Expressway, Santa Clara, CA 95051

aauthor for correspondence: fax 408-731-5408, e-mail andrea_cuppoletti@affymetrix.com

The first 20% of the full text of this article appears below.

High-density DNA probe arrays are finding widespread use in biomedical research and diagnostics because of their ability to simultaneously address large numbers of genes. GeneChip® probe arrays are manufactured by use of photolithography techniques (1)(2)(3)(4). At the base of the current Affymetrix process of synthesis of oligo-DNA probes is the use of nucleoside monomers protected with photo-removable groups (Fig. 1A ). Irradiation of the partially built oligomer with near-ultraviolet wavelengths (mainly 365 nm) deprotects the terminal hydroxyl group, and the use of appropriate masks allows for control of the sequence of the probe and the size of the features. The sensitivity of DNA to ultraviolet radiation limits the range of wavelengths usable for the photolitographic step to mainly the Hg atomic emission at 365 nm. Therefore, the choice of photo-removable hydroxyl protecting groups depends on the absorbance at this wavelength (4).


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  		Figure 1. Photoremovable protecting group (PG) used as monomer for the photolithographic synthesis of DNA (A), and mechanism of photocleavage of indolines in nucleophilic solvents (B).

MeOH, methanol.

Our ongoing investigations concerning the fabrication of DNA microarrays have several goals, including increasing the rate and the efficiency of photo-deprotection. The rate . . . [Full Text of this Article]






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