Nucleic Acids Research, Vol 27, Issue 3 882-887, Copyright © 1999 by Oxford University Press
RK Shultzaberger and TD Schneider
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.
ARTICLES
Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepanciesbetween natural selection and SELEX
Catoctin High School, 14745 Sabillasville Road, Thurmont, MD 21788, USA.
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