|MadSci Network: Molecular Biology|
Dear Kimberly, A good way to think about this is that a restriction enzyme is basically a pair of "DNA scissors" with a targeting module attached to them. The enzyme knows where to cut the DNA strands (they actually cut both strands of the DNA double helix) because the targeting module finds the place where it prefers to bind, and then the scissors cut a fixed distance from that. So, the real question you are asking is, how does the targeting module decide where to bind? As you have probably just learned, DNA is a string of four bases (A,C,G,T) connected together like the links in a chain. For instance, one chain could be TATTCGAAATCGCTACGGG.... As you have also probably just learned, A pairs with T and G pairs with C, and so this chain will have a partner chain paired with it (they are intertwined like braided hair) that will have the "partner" base present at every position (if one chain has A at a certain point, the other chain will have T paired with it at that point, etc). So the two chains twined together could be "read" from one end to the other by reading the linear sequence of the bases on both strands. A restriction enzyme's targeting module decides where to bind by reading along the chains and finding the linear sequence of 4 or 6 or 8 base pairs to which it wants to bind and attaching to them, for instance, GAATTC. Then when it is stuck to them, the DNA scissors module cuts at a fixed position away. Hope this helps. Remember that most recognition of DNA by proteins involves the proteins reading along the strands until they find a short region of 4-8 bases pairs that have a certain sequence, and then binding to them and only them.
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