A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay (see Research Technique 8.1), and the following gel bands are observed. Match these conditions to a specific lane of the gel. 3.5-kb fragment plus TFIIB, TFIID, TFIIF, and RNA polymerase II

Key Concepts

Transcription Factors

Transcription factors are proteins that bind to specific DNA sequences to regulate gene expression. They play crucial roles in initiating and controlling the transcription of genes by facilitating the assembly of the transcription machinery, including RNA polymerase II. In the context of the gel electrophoresis, the presence of transcription factors like TFIIB, TFIID, and TFIIF indicates their involvement in the formation of a transcription complex with the DNA segment.

Gel Electrophoresis

Gel electrophoresis is a laboratory technique used to separate DNA, RNA, or proteins based on their size and charge. In this method, samples are loaded into a gel matrix and subjected to an electric field, causing the molecules to migrate. Smaller fragments move faster and farther than larger ones, allowing visualization of different bands on the gel, which can indicate the presence of specific DNA-protein complexes or the size of DNA fragments.

Promoter and Polyadenylation Site

The promoter is a DNA sequence located upstream of a gene that serves as the binding site for RNA polymerase and transcription factors, initiating transcription. The polyadenylation site, found downstream of the gene, signals the end of transcription and is crucial for mRNA processing. Understanding these elements is essential for interpreting the results of the band shift assay, as they define the regions of DNA that interact with transcription factors and RNA polymerase II.