Question

What is the function of unlabeled competitor DNA in various footprint assays?

A. Stops double-stranded DNA from melting, thus making protein binding to DNA more feasible.

B. Substitutes for the labeled probe originally bound to the protein of interest (outcompeting it) and allows for the analysis of kinetics (off-constants) and/or specificity/strength of binding.

C. Protects first nucleotides as they form the first phosphodiester bond in DNA footprinting assays.

D. Helps stabilize double-stranded DNA structure and makes protein:DNA binding stronger.

Answer 1

Unlabeled competitor DNA in footprint assays functions as a substitute for the labeled probe to analyze the kinetics and binding specificity or strength of the protein-DNA interaction.

Step-by-step explanation:

The function of unlabeled competitor DNA in various footprint assays is to substitute for the labeled probe originally bound to the protein of interest, outcompeting it.

This competition allows for the analysis of kinetics, such as off-rates of the protein-DNA interaction, and/or the specificity/strength of binding between the protein and different potential DNA regions.

The presence of the unlabeled competitor provides insight into how strongly or specifically a protein binds to its DNA target compared to other sequences.

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Answer 2

The function of unlabeled competitor DNA in various footprint assays is to substitute for the labeled probe originally bound to the protein of interest (outcompeting it) and allows for the analysis of kinetics (off-constants) and/or specificity/strength of binding.

So, the correct answer is B.

Step-by-step explanation:

Unlabeled competitor DNA in footprint assays functions as a substitute for the labeled probe, competing for binding with the protein of interest to analyze binding kinetics and specificity.

Essentially, unlabeled competitor DNA competes with the labeled DNA for binding to the protein. This competition allows researchers to analyze the kinetics and/or specificity of the binding by observing how well the competitor DNA can outcompete the labeled probe.

Specifically, the correct answer choice is option B: Substitutes for the labeled probe originally bound to the protein of interest (outcompeting it) and allows for the analysis of kinetics (off-constants) and/or specificity/strength of binding.