Adapting in Vitro Selected oligoDNAs for Recognition of Natural Sites and for Analysis of SNPs and Mutagenesis

In vitro selection of DNA binding proteins is an up-to-date technology being developed during the last decade, for sieving a pool of synthetic oligomers through repeated cycles of PCR-amplification and protein-binding selection [8]. Following this approach, we have earlier reported about SELEX DB database accumulating in vitro selected DNAs and supplemented by the tools for site recognition [5]. Since disease may be caused not only by mutation altering the true-site, but also by appearance of the noise-site (e.g., -376G>A in hTNF gene promoter generates the OCT site associated with severe malaria [4]), in vitro selected DNAs seem to be informative for SNP-analysis. At the same time, in prokaryotes, the discrepancies between in vitro and in vivo selected sites by nucleotide-position frequency matrices have been comprehensively demonstrated [9, 10]. In prokaryotes, the in vivo selection is directed to alteration of biological activity, but not of the protein-affinity. In eukaryotes, in vitro selected TBP-fitting DNAs provide the TATA-activity [1]. On the contrary, in vitro selected YY1-fitting DNAs repress the gene-reporter [2]. Moreover, its activity measured in vivo is different depending on the type of the plasmid/cell pair [2]. Hence, from [2, 9, 10], it is not clear whether in vitro selected DNAs fit to recognition of natural sites or not.