**2. DNA-protein interactions**

The cis-regulatory DNA elements' interactions with the transcription factors seem to be critical components of transcriptional regulatory networks [14]. The genome with the complete cDNA sequences contains large numbers of transcription factors with their binding DNA sequences. It is expected that a comprehensive analysis of DNA-transcription factor interactions will provide a deep understanding of the mechanisms of drug metabolism in critical processes such as cell proliferation, developmental processes in tissue morphogenesis, and disease manifestation [14]. The combined use of chromatin immunoprecipitation (ChIP) assay with DNA microarrays (ChIP-chip) [14, 15] are the most widely used high-throughput method for discovering non-coding region but important (cis-regulatory) DNA elements for a transcription factor [16]. Albeit, the development of high-throughput methods for discovering transcription factors for DNA regulatory elements remains in its infancy, even though the yeast one-hybrid method [17] and phage display [16] are attractive candidates, in this regard. However, these methods have some shortcomings including, they are not easily scalable because of the use of living cells. Further, the overexpression of transcription factors are thoughts to affects cellular metabolism, and as such, making transcription factors difficult to screen. Thus, to avoid these difficulties, focus totally on in-vitro mRNA display technology such as in-vitro virus (IVV) method [11, 16] for the discovery of DNA-protein interactions serve as a good alternative.

To map out the transcriptional regulatory networks at a wider genome level, a comprehensive analysis of DNA-protein interactions is important Thus, the IVV method had been employed for in vitro selection of DNA-binding protein heterodimeric complexes [18]. Using improved selection conditions, enhanced with a TPA-responsive element (TRE) as a bait DNA, known interactors such as; c-fos and c-jun were simultaneously enriched about 100-fold from a model library (a 1:1:20000 mixture of c-fos, c-jun, and gst genes) after one round of selection [18]. Moreover, the AP-1 family genes, including c-jun, c-fos, junD, junB, atf2, and b-atf, were successfully selected from an IVV library constructed from a mouse

brain poly A+ RNA after six rounds of selection [19]. These results indicated that this method (IVV selection system) have the potential to identify a variety of DNA binding protein complexes in a single experiment. Since almost all transcription factors form hetero-oligomeric complexes towards binding with their target DNA, this method should be most useful to search for DNA-binding transcription factor complexes [11, 16], which will further illuminate the understanding of drug repurposing in disease state conditions.
