A 1.0-kb DNA fragment from the end of the mouse gene described in the previous problem is examined by DNA footprint protection analysis (see Research Technique 8.1). Two samples are end-labeled with ³²P and one of the two is mixed with TFIIB, TFIID, and RNA polymerase II. The DNA exposed to these proteins is run in the right-hand lane of the gel shown below and the control DNA is run in the left-hand. Both DNA samples are treated with DNase I before running the samples on the electrophoresis gel. Draw a diagram of this DNA fragment bound by the transcriptional proteins, showing the approximate position of proteins along the fragment. Use the illustration style seen in Research Technique 8.1 as a model.

Key Concepts

DNA Footprint Protection Analysis

DNA footprint protection analysis is a technique used to identify the specific binding sites of proteins on DNA. When proteins bind to DNA, they protect certain regions from cleavage by DNase I, allowing researchers to determine where these proteins interact with the DNA. By comparing the patterns of protected and unprotected regions on a gel, scientists can infer the locations of protein binding sites.

Transcription Factors

Transcription factors are proteins that bind to specific DNA sequences to regulate gene expression. In this context, TFIIB and TFIID are essential transcription factors that assist in the formation of the transcription initiation complex with RNA polymerase II. Understanding their roles is crucial for interpreting how they influence the transcription of the mouse gene in the experiment.

Electrophoresis

Electrophoresis is a laboratory technique used to separate DNA fragments based on their size and charge. In this experiment, DNA samples are subjected to an electric field, causing them to migrate through a gel matrix. The resulting pattern allows researchers to visualize the presence of protected regions, indicating where transcription factors have bound, and to compare the experimental sample with the control.