DNA Structure and Replication

ID #1708

Does it matter that base pairs of one strand are complementary to another strand in reannealing, even though the strands are both in the 5' to 3' direction? Or is antiparallel strand pairing more important in reannealing?

Let's create some hypothetical molecules. Molecule #1 has this sequence:




Molecule #2 has this sequence:




Clearly, these molecules won't anneal if their 5' ends are lined up together, because the bases aren't even complementary. But they will anneal in an antiparallel fashion, because they "fit" and are complementary.


Now consider Molecule #3:




Will Molecule #3 anneal with Molecule #1? NO! It might look like the bases line up, but the strands must be antiparallel when the molecules form a double helix, AND the bases have to be complementary. If you put the 5' end of Molecule #3 near the 3' end of Molecule #1, you'll see that now you've got T's across from C's, and this pairing won't work.

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