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

Verified step by step guidance

1. Step 1: Understand the experimental setup. A band shift assay is used to study protein-DNA interactions. In this case, the 3.5-kb DNA fragment is mixed with TFIIB, a transcription factor, and the gel electrophoresis is used to observe the resulting bands.
2. Step 2: Analyze the gel image. Each lane represents a different condition. Lane 1 likely contains the DNA fragment alone, as it shows a single band corresponding to the unbound DNA. Lanes 2-5 show additional bands, indicating interactions between the DNA and TFIIB.
3. Step 3: Match the conditions to the lanes. The presence of shifted bands in lanes 2-5 suggests that TFIIB is binding to the DNA fragment. The degree of shift and the number of bands can indicate the strength and specificity of the interaction.
4. Step 4: Interpret the results. The shifted bands in lanes 2-5 represent DNA-TFIIB complexes. The position of the bands can be used to infer the binding affinity and the number of binding sites for TFIIB on the DNA fragment.
5. Step 5: Conclude the analysis. Based on the gel image, the interaction between the 3.5-kb DNA fragment and TFIIB is confirmed. The specific lane assignments depend on the experimental conditions, such as varying concentrations of TFIIB or additional factors influencing the binding.

Key Concepts

Promoter Sequence

The promoter sequence is a region of DNA located upstream of a gene that initiates transcription. It contains specific binding sites for transcription factors and RNA polymerase, which are essential for the regulation of gene expression. Understanding the promoter's role is crucial for interpreting how genes are activated or repressed in response to various signals.

Band Shift Assay

A band shift assay, also known as an electrophoretic mobility shift assay (EMSA), is a technique used to study protein-DNA interactions. In this assay, DNA fragments bound to proteins migrate more slowly through a gel than unbound DNA, resulting in distinct bands. This method helps identify specific proteins that interact with DNA sequences, such as transcription factors.

TFIIB

TFIIB is a general transcription factor that plays a critical role in the initiation of transcription by RNA polymerase II. It helps recruit RNA polymerase to the promoter and is involved in the formation of the transcription pre-initiation complex. Understanding TFIIB's function is essential for analyzing how transcription is regulated and how specific genes are expressed.