Comparison of the structures of in vitro selected and natural binding sites of transcription factors

The information compiled in TRRD_ARTSITE database was used to compare the structures natural and in vitro selected binding sites for transcription factors USF1, SP1, YY1, RAR/RXR, and E2F/DP1. The structures of the natural and in vitro selected binding sites for each transcription factor analyzed were found similar, suggesting that at least for the factors in question the structures of binding sites correlated with the affinities of the corresponding factors. Insignificant differences in frequencies of certain nucleotides detected reflect the general trend, namely, a higher occurrence of moderate affinity sites in the natural population of sequences compared with the sequences obtained in vitro.