Final answer:
Agarose gel electrophoresis separates DNA based on size and shape, with ERCs treated with Topoisomerase I showing a change in their mobility due to relaxation of supercoiling. This is visualized as distinct bands, which can be analyzed with stains like ethidium bromide to confirm the treatment's effect.
Step-by-step explanation:
Topoisomerase I is an enzyme that alters the supercoiling of DNA by making single-stranded breaks and facilitating the relaxation of the molecule. When treating extrachromosomal ribosomal circles (ERCs) with Topoisomerase I and analyzing the results via agarose gel electrophoresis, the observed pattern is due to changes in the DNA's shape affecting its mobility through the gel matrix. Agarose gel electrophoresis separates DNA based on size and shape because the agarose matrix creates pores through which the negatively charged DNA molecules move, with smaller and less supercoiled molecules migrating faster towards the positive electrode. After treating with Topoisomerase I, the ERCs, which are typically supercoiled, will have a relaxed conformation and thus migrate differently compared to their untreated, more compact form. This can be visualized as distinct bands on the gel, each representing DNA fragments of different sizes, with linear DNA migrating less compared to supercoiled DNA due to its larger effective size in the gel matrix.
The results from such electrophoresis experiments can be used not only for analytic purposes—to confirm molecular changes like cleavage or relaxation—but also for preparative goals, such as isolating desired DNA fragments post-treatment. Stains such as ethidium bromide can be used to visualize the bands under UV light, providing a practical way to quantify and analyze DNA samples post-treatment.