Genomic interaction mapping: DNA footprinting is best suited to identify which specific feature within a DNA fragment?

Introduction / Context:
DNA footprinting is a classic method to locate where DNA-binding proteins (e.g., transcription factors, repressors) contact DNA. By revealing protected regions against nuclease cleavage, it maps protein–DNA interaction sites at base-pair resolution.

Given Data / Assumptions:

• A labeled DNA fragment is incubated with and without a DNA-binding protein.
• Partial digestion with DNase I (or hydroxyl radicals) is performed.
• Fragments are resolved to compare cleavage patterns.

Concept / Approach:
Where a protein binds, the enzyme cannot cut, creating a “footprint” (a gap) in the ladder of fragments. The location of this gap indicates the protected binding site. This directly answers “where does the protein contact DNA?” rather than measuring RNA species or intron positions.

Step-by-Step Solution:

Verification / Alternative check:
Electrophoretic mobility shift assays (EMSA) confirm binding, while footprinting pinpoints the exact contact region, providing convergent evidence.

Why Other Options Are Wrong:

• mRNA/tRNA detection: Northern blot or RNA-seq are appropriate, not footprinting.
• Intron mapping: achieved by cDNA/genomic comparisons or RNA-seq.
• Methylation profiling: uses bisulfite sequencing or methylation-sensitive assays.

Common Pitfalls:
Over-digestion obscures footprints; titrate nuclease carefully and include proper controls.

Final Answer:
A protein binding site protected from nuclease digestion