Ryan K. Shultzaberger

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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)(More)
Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy,(More)
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base −7, rather than −11, of the −10 may be flipping to initiate transcription. We found that the sequence conservation of σ 70 binding sites is 6.5 ± 0.1 bits. Some(More)
Information theory was used to build a promoter model that accounts for the -10, the -35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base -7, rather than -11, of the -10 may be flipping to initiate transcription. We found that the sequence conservation of σ 70 binding sites is 6.5 ± 0.1 bits. Some(More)
Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur binding, which was then refined by adding 13 experimentally confirmed sites. When the refined model was scanned across all available footprinted sequences, sequence(More)
Sequence logos: A new way to display consensus sequences. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. Visual display of sequence conservation as an aid to taxonomic classification using PCR amplification. information conservation implies that at least three proteins bind independently to(More)
Computation of K D values See reference [1] for definitions of symbols, methods and the equations used. The competitor EMSA experiments were repeated three times with different competitor concentrations (C 0). K Dw and R 0 were simultaneouly adjusted to fit two criteria. First, the K D of the Hin-180 oligo was made to match the published value of HinD , 2 ×(More)
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