Beyond the dna: a prototype for functional genomics
A prototype oligonucleotide ''functional chip'' has been developed to screen novel DNA repair proteins for their ability to bind or alter different forms of DNA. This chip has been developed as a functional genomics screen for analysis of protein-DNA interactions for novel proteins identified from the Human Genome Project The process of novel gene identification that has ensued as a consequence of available sequence information is remarkable. The challenge how lies in determining the function of newly identified gene products in a time-and cost-effective high-throughput manner. The functional chip is generated by the robotic application of DNA spotted in a microarray format onto a glass slide. Individual proteins are then analyzed against the different form of DNA bound to the slide. Several prototype functional chips were designed to contain various DNA fragments tethered to a glass slide for analysis of protein-DNA binding or enzymatic activity of known proteins. The technology has been developed to screen novel, putative DNA repair proteins for their ability to bind various types of DNA alone and in concert with protein partners. An additional scheme has been devised to screen putative repair enzymes for their ability to process different types of DNA molecules. Current methods to analyze gene expression primarily utilize either of two technologies. The oligonucleotide chip, pioneered by Fodor and co-workers and Affymetrix, Inc., consists of greater than 64,000 oligonucleotides attached in situ to a glass support. The oligonucleotide chip has been used primarily to identify specific mutations in a given gene by hybridization against a fluorescently-labeled substrate. The second method is the microarray, whereby DNA targets are systematically arranged on a glass slide and then hybridized with fluorescently-labeled complex targets for gene expression analysis (Jordan, 1998). By this technique, a large amount of information can be obtained examining global differences in gene expression among different cell populations; disease states and following drug treatments or toxic insult to whole cells. However, these technologies have yet to be extended beyond the examination of DNA/RNA molecules to dissect gene function. One of the most critical component of cellular biochemistry is the integrity of interaction between proteins and DNA. Protein-nucleic acid interactions are essential for the structural organization, replication, repair and expression of genetic information. Understanding the complexities of protein-DNA interactions is a fundamental step towards comprehending key aspects of disease biochemistry. The complexity of these cellular processes generally makes it necessary to analyze these interactions in vitro. Many techniques have been designed to offer insight into these processes including filter binding studies, electrophoretic mobility shift assays and footprinting technologies. But these techniques are laborious and time-consuming, and the development of high-throughput strategies for analysis of protein-DNA interactions would greatly propel these areas of research. Using an oligonucleotide chip approach, novel proteins can be analyzed for DNA binding or enzymatic characteristics. Proteins can be screened against the ''functional chip'' both individually and in combination.
- Research Organization:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Organization:
- US Department of Energy (US)
- DOE Contract Number:
- W-7405-ENG-48
- OSTI ID:
- 15005703
- Report Number(s):
- UCRL-ID-137852; TRN: US200324%%73
- Resource Relation:
- Other Information: PBD: 2 Mar 2000
- Country of Publication:
- United States
- Language:
- English
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