Genetics: Analysis and Principles 5th Edition by Robert Brooker

Exercise 54

A gel retardation assay can be used to study the binding of proteins to a segment of DNA. In the experiment shown here, a gel retardation assay was used to examine the requirements for the binding of RNA polymerase II (from eukaryotic cells) to the promoter of a protein-encoding gene. The assembly of general transcription factors and RNA polymerase II at the core promoter is described in Chapter 12 (Figure 12.14). In this experiment, the segment of DNA containing a promoter sequence was 1100 bp in length. The fragment was mixed with various combinations of proteins and then subjected to a gel retardation assay.
a.
Explain which proteins (TFIID, TFIIB, or RNA polymerase II) are able to bind to this DNA fragment by themselves. Which transcription factors (i.e., TFIID or TFIIB) are needed for the binding of RNA polymerase II
FIGURE 12.14 Steps leading to the formation of the open complex. The DNA is first denatured at the TATA box to form an open complex. In this diagram, the open complex has moved to the transcriptional start site, which is usually about 25 bp away from the TATA box.