The image below shows the restriction map of a circular plasmid that is 2981 base pairs long. The recognition sites of 3 restriction endonucleases are shown in base pairs from the origin of replication (0 bp). Link to image.
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What is the size of the largest fragment in base pairs, produced by digestion of the plasmid with EcoR1?

Question

The image below shows the restriction map of a circular plasmid that is 2981 base pairs long. The recognition sites of 3 restriction endonucleases are shown in base pairs from the origin of replication (0 bp). Link to image.
Links to an external site.

What is the size of the largest fragment in base pairs, produced by digestion of the plasmid  with EcoR1?

BlackTom AI · Accepted Answer

To approach this problem, I first identify what digestion with EcoR1 does on a circular plasmid: it creates fragments between every EcoR1 site, and the sizes of those fragments correspond to the distances along the circle between consecutive EcoR1 recognition sites.

From the map, we see an EcoR1 site labeled at 701 bp. The origin of replication on circular DNA is defined as 0 bp, so we treat 0 bp as a potential EcoR1 site location unless specified otherwise. If EcoR1 sites exist at 0 bp and at 701 bp, the circle would be cut at these two positions, yielding two fragments whose sizes are the distances between the sites along the circle.

The total plasmid length is 2981 bp. The distance between the EcoR1 site at 0 bp and the EcoR1 site at 701 bp is 701 bp. The complementary fragment, which runs from 701 bp back to 0 bp around the circle, would then have length 2981 − 701 = 2280 bp.

Thus, after EcoR1 digestion, the two fragments would be 701 bp and 2280 bp in size. Of these two fragments, the largest is 2280 bp.

Why this matches the given answer: if the EcoR1 site positions are 0 bp and 701 bp, the larger fragment spans from 701 bp all the way around to the origin, totaling 2280 bp, which corresponds to the expected largest fragment size.

Why other plausible interpretations would fail here: if there were only a single EcoR1 site (as would be the case if there were no site at 0 bp), digesting a circular plasmid would linearize it and yield a single fragment equal to the full plasmid length (2981 bp), not 2280 bp. If EcoR1 sites were both at 701 bp or both clustered very near each other, the fragment sizes would differ from 2280. Since the example answer is 2280, the assumption that EcoR1 sites are at 0 bp and at 701 bp provides the consistent fragment pair of 701 bp and 2280 bp, with the latter being the largest.

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