Analytics of Protein–DNA Interactions by Verena Beier, Cora Mund, Jörg D. Hoheisel (auth.), Harald

By Verena Beier, Cora Mund, Jörg D. Hoheisel (auth.), Harald Seitz (eds.)

Analytics of Protein-DNA Interactions covers traits in smooth biotechnology. All points of this interdisciplinary know-how, the place wisdom, equipment and services are required from chemistry, biochemistry, microbiology, genetics, chemical engineering and desktop technology, are handled. additional info in addition to the digital model is obtainable at springer.com.

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Samples spanning concentrations tenfold above and below the Kd , estimated from gel shifts or footprints, are diluted on ice in running buffer and kept at 4 ◦ C. Buffer-only injections evenly spaced throughout the experiment are recommended. One after another the samples are injected using the “kinject” [11] command using a high flow rate (50–100 µl min–1 ). At the end of each cycle, bound protein is removed with a 5-s pulse of regeneration fluid (Sect. 6). To equilibrate the system after regeneration back to the running buffer, 150 µl of buffer is passed through the system before the next sample injection.

The Rmax for DnaA-ATP was used for both DnaA-ATP and DnaA-ADP Figure 7 shows the ATP-induced cooperative binding of DnaA protein from Streptomyces coelicolor to DNA containing two DnaA binding sites (Majka and Messer, unpublished data). 97. Since for ADPDnaA saturation was not reached, the Rmax value for ATP-DnaA was used for analysis of both DnaA forms. A similar analysis was carried out to determine the Hill coefficient for the interaction between ethR repressor and ethA operator [19] (Sect. 6).

The plot kobs vs C is linear (Eq. 2) and the slope of this function represents the kon rate constant (Fig. 4b). The intercept of kobs = kon · C + koff corresponds to the koff rate constant. However, this method for evaluation of koff is not reliable since a small change in kon results in a large alteration of koff . ln 24 J. Majka · C. Speck Fig. 4 Plots used during quantitative data analysis. 3 Dissociation During the dissociation phase of an experiment, the protein solution is replaced by buffer and the response change represents solely the decay of the DNA · PROTEIN complex.

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