Question

Describe how the results of the DNA footprinting assay in the lecture would look like as an EMSA assay.

Answer 1

1. DNA footprinting assay reveals the approximate location of binding site on the probe. EMSA reveals the location of binding site which can be determined but only by mutagenesis of probe.

2. DNA footprinting assay reveals location of binding site for multiple protein on the same probe. EMSA can reveal a unique complex for each protein that binds the probe.

3. DNA footprinting assay with large foot printing can suggest that two or more protein binds adjacent element to the probe.

4. EMSA can be difficult to determine if a complex contain two protein that cooperatively bind adjacent sites. Proteolysed protein will yield unique complexes which can be misleading.

5. DNA footprinting assay is particularly useful for scanning a large DNA fragments(50-200bp) for protein DNA interaction.

6. EMSA assay is useful for analysing protein DNA interaction on a small fragment(20-30bp).