MadSci Network: Molecular Biology

Re: How does the restriction enzyme know where to cut the DNA strand?

Date: Tue Apr 20 20:08:27 1999
Posted By: Chris Larson, Post-doc/Fellow Laboratory of Genetics
Area of science: Molecular Biology
ID: 924571178.Mb

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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