Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX

In vitro experiments that characterize DNA-protein interactions by artifici al selection, such as SELEX, are often performed with the assumption that t he experimental conditions are equivalent to natural ones. To test whether SELEX gives natural results, we compared sequence logos composed from natur ally occurring leucine-responsive regulatory protein (Lrp) binding sites wi th those composed from SELEX-generated binding sites. The sequence logos we re significantly different, indicating that the binding conditions are disp arate. A likely explanation is that the SELEX experiment selected for a dim eric or trimeric Lrp complex bound to DNA. In contrast, natural sites appea r to be bound by a monomer. This discrepancy suggests that in vitro selecti ons do not necessarily give binding site sets comparable with the natural b inding sites.