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

  1. Author:
    Shultzaberger, R. K.
    Schneider, T. D.

  2. Author Address

    Schneider TD NCI, Math Biol Lab, Frederick Canc Res & Dev Ctr POB B,Bldg 469,Room 144 Frederick, MD 21702 USA NCI, Math Biol Lab, Frederick Canc Res & Dev Ctr Frederick, MD 21702 USA Catoctin High Sch Thurmont, MD 21788 USA
    1. Year: 1999
  2. Journal: Nucleic Acids Research
    1. 27
    2. 3
    3. Pages: 882-887
  4. Type of Article: Article
  1. Abstract:

    In vitro experiments that characterize DNA-protein interactions by artificial selection, such as SELEX, are often performed with the assumption that the experimental conditions are equivalent to natural ones. To test whether SELEX gives natural results, we compared sequence logos composed from naturally occurring leucine-responsive regulatory protein (Lrp) binding sites with those composed from SELEX-generated binding sites. The sequence logos were significantly different, indicating that the binding conditions are disparate. A likely explanation is that the SELEX experiment selected for a dimeric or trimeric Lrp complex bound to DNA. In contrast, natural sites appear to be bound by a monomer. This discrepancy suggests that in vitro selections do not necessarily give binding site sets comparable with the natural binding sites. [References: 44]

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