Project: New Photochemical Phosphate Bond-Forming Reactions for Oligonucleotide Chips

The production of microarrays has grown from a few experiments hybridizing genetic material to oligonucleotides on glass slides in the early 1980s to a ~ $500 million/year industry (1). Applications include gene sequencing, detection of mRNAs in order to monitor protein expression, discovery of bioactive proteins. Rapid identification of microorganisms is of particular interest in both clinical and environmental applications. For environmental analysis, “gene chips”will permit rapid on-site detection of pathogens in both indoor and outdoor settings, such as in building ventilation ducts, sewage-spill sites and areas where other biological hazards are suspected. While clinical use of the technology is still in the future, the potential is obvious, so there is a lot of interest in cheaper and simpler microarray fabrication methods. A number of systems have been developed to make oligonucleotides (“oligos”) on gene chips. All use microfluidics and/or laser imaging to control which chemicals are applied, in order to produce unique sequences in small areas (2). While all these methods have successfully produced chips which are useful for biomedical and pharmaceutical research, the chip fabrication technologies remain expensive and time-consuming because of the many steps required for manufacture.

Our new concept for chip surface oligo synthesis uses cyclic silicon-substituted esters of P(III) and P(V) with aromatic groups to absorb long-wave UV radiation. When exposed to light, these are expected to break apart to give reactive “low-valent” species which react immediately with alcohols to give phosphorus esters of the same types which are useful in oligo synthesis. By using a variety of UV chromophores, different monomers would be selectively activated in the presence of others. The ultimate goal is to have a set of compounds which can be used to add any of a group of monomers, for example the four DNA nucleotides (deoxyadenine, deoxycytidine, deoxyguanidine and thymidine) from a common precursor "cocktail". A synthesizer using this chemistry is expected to be simpler and faster because multiple liquid transfer and washing operations are eliminated.

REU project work will focus on the photochemical reaction itself, including GC/MS analysis to identify and quantitate photoproducts, as well as possibly synthesizing additional photoreaction precursors and measuring quantum yields.

1) Flanagan, N. Genetic Engineering News, 2007, 27(11), 1

2) Gao, X. Biopolymers, 2004, 73, 579

3) Quin, L.D. “A Guide ot Organophosphorus Chemistry” Wiley, NY, 2000, Ch. 10 (p 307-350)