5. (5 points) Both non-homologous end joining (NHEJ) and single-strand annealing (SSA) lead to imperfect joining of DNA ends. What striking structural difference would you expect to find between ends joined by NHEJ and ends joined by SSA?
The answer I was looking for is that, when ends are joined by SSA, all of the DNA between the two homologous repreated segments is deleted. In contrast, deletions produced by NHEJ are usually only a few nucleotides, as in the example shown in our lecture notes.
However, the answers that some of you gave made me realize that this question was ambiguous. It could refer to the structure of the ends before joining. In that case, there are several possible answers. First, the ends joined by SSA must have large (several hundred bp) homologous regions located not too far away (exactly what's "too far" isn't clear) from the ds break; there's no such requirement for NHEJ. Second, after processing, the ends joined by SSA will transiently have long 3' single-stranded tails, whereas ends joined by NHEJ will have transient single-stranded tails that are much shorter. These will most likely be 5' tails rather than 3' tails.
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