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. What length of DNA is bound by the transcriptional proteins? Explain how the gel results support this interpretation.

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 being cleaved by DNase I, an enzyme that cuts DNA. By comparing the patterns of DNA fragments on a gel before and after protein binding, researchers can determine which segments of DNA are protected, indicating the presence of bound proteins.

Transcription Factors and RNA Polymerase II

Transcription factors, such as TFIIB and TFIID, are proteins that bind to specific DNA sequences to regulate gene expression. RNA polymerase II is the enzyme responsible for synthesizing mRNA from DNA during transcription. The interaction of these transcription factors with DNA is crucial for the initiation of transcription, and their binding can be visualized through footprinting techniques, revealing the length of DNA they occupy.

Electrophoresis and Gel Analysis

Electrophoresis is a laboratory technique used to separate DNA fragments based on their size by applying an electric field to a gel matrix. Smaller fragments move faster and farther than larger ones. By analyzing the resulting gel, researchers can determine the sizes of the DNA fragments and identify which fragments are protected by bound proteins, thus inferring the length of DNA that is associated with transcriptional proteins.