Question at position 5 In two separate reactions you digestion a large piece of DNA (700 kB). One you digest with RsaI (a 4-base cutter), the other you digest with BamHI (a 6-base cutter). You then run them on an agarose gel but forgot which lane was which. The sample digested with RsaI (assume complete digestion) is most likely to be _____________.The lane with the larger fragmentsThe lane with the smaller fragmentsThere is no way to tellThe lane that has visible fragments rather than a smearThe lane with the least number of fragments

Question

Question at position 5 In two separate reactions you digestion a large piece of DNA (700 kB). One you digest with RsaI (a 4-base cutter), the other you digest with BamHI (a 6-base cutter). You then run them on an agarose gel but forgot which lane was which. The sample digested with RsaI (assume complete digestion) is most likely to be _____________.The lane with the larger fragmentsThe lane with the smaller fragmentsThere is no way to tellThe lane that has visible fragments rather than a smearThe lane with the least number of fragments

BlackTom AI · Accepted Answer

First, let's restate the setup to make the context clear: two separate digestions of a 700 kb DNA piece are performed—one with a 4-base cutter (RsaI) and one with a 6-base cutter (BamHI). After complete digestion, you run the fragments on an agarose gel but you don’t know which lane corresponds to which enzyme.
Option 1: 'The lane with the larger fragments' — This is unlikely because a 4-base cutter will cut DNA more frequently than a 6-base cutter, producing many smaller fragments. Therefore, the lane with larger fragments would correspond to less frequent cutting, not to RsaI, assuming complete digestion for both; this option contradicts the expectation of more fragmentation with a shorter recognition sequence.
Option 2: 'The lane with the smaller fragments' — This is the correct inference. A 4-base recognition site occurs more often in a genome than a 6-base site (on average every 4 bases vs every 6 bases), so digestion with RsaI will yield a much larger number of smaller DNA fragments than BamHI, assuming complete digestion and no supercoiling concerns. Hence, the lane with the smaller fragments most likely contains the RsaI-digested sample.
Option 3: 'There is no way to tell' — While gel interpretation can be tricky in some contexts, the fundamental difference in cutting frequency between a 4-base cutter and a 6-base cutter gives a predictable pattern: more fragments that are smaller with the 4-base cutter. Therefore, one can distinguish them based on fragment size distribution, making this option incorrect.
Option 4: 'The lane that has visible fragments rather than a smear' — Digestion tends to produce discrete bands corresponding to fragment sizes; however, a smear could still occur if fragments are numerous and varied in size or if the DNA is degraded. The presence of a smear is not a reliable indicator to identify which lane is which between these two complete digestions, so this option isn’t a dependable criterion for assignment.
Option 5: 'The lane with the least number of fragments' — Since the 4-base cutter cuts more frequently, it will produce more fragments, not fewer. Therefore, the lane with the least number of fragments would more likely belong to BamHI, making this option inconsistent with the expected outcome for RsaI digestion.
In summary, the logic hinges on the relative frequency of cutting: a 4-base cutter generates many more, smaller fragments than a 6-base cutter, so the lane with the smaller fragments is the one that contains the RsaI-digested sample. This aligns with the principle that shorter recognition sequences yield higher fragmentation density.

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