An estimated 20 percent of cellular proteins are transcription factors. Thus, it is not a surprise that they are of great interest to the research community and pharmaceutical industry. Transcription factors play a major role in all imaginable cell events. However, functional analysis of these factors is challenging, especially when researchers decide to do high throughput analysis that is not biased to a certain factor or family of factors. For the Phase I research, we propose to develop a new approach for functional high throughput analysis of transcription factors. This approach is based on chimerical DNA oligonucleotides with two different portions in the molecule. The first portion consists of a specific recognition site for certain transcription factors. The second portion is called Tag sequence. It is critical that the proposed Phase 1research be based on the use of hybridization assays between tagged targets and complement tags immobilized on a solid support. Arrays, which are related to the current research, are based on immobilization of arbitrary sequence oligonucleotide probes (tag complements or bar codes), and are not complementary to the genomic DNA or cDNA of target sequences. For target preparation, which will allow the analysis of the target composition in a high throughput manner, the tag sequence will be combined with a specific recognition sequence to the related transcription factor. Phase I will address the questions of optimizing Tag sequences, which will satisfy the conditions described above, the conditions of the interaction of tagged specific recognition sequences to related transcription factors in in vitro assays, and to develop assays.
