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Name: Alina
Status: Other
Grade:  Other
Location: CA
Country: United States
Date: June 2006


Question:
Why are most restriction site palindromic?



Replies:
There are two theories: 1) palindromic sequences "feel" the same when approached from either direction by restriction endonucleases (enzymes that cut DNA at specific sites), thus increasing the probability of finding these sites. Recall that restriction endonucleases were evolved by bacteria to protect them against infection by bacteriophage DNA. 2) Palindromic sequences might form hairpin loops that would make them easy to recognize by restriction endonucleases. Notice that if you unwind the two strands of DNA in a palindromic region, the left end of one strand can form Watson-Crick base pairs with the right end of the same strand forming a loop out in the shape of a hairpin. This could occur in both DNA strands forming a double loop out which be quite noticeable at the molecular level.

Ron Baker, Ph.D.


The "usual" definition of a "palindrome" is a word or number that reads the same "left to right" as it does "right to left". This is a 1- dimensional palindrome. There are phrase palindromes, musical palindromes, numerical palindromes, etc. and palindromes can be generalized to include multi-dimensional palindromes. What is "left" and what is "right" obviously depends upon the context. The concept also appears in molecular sequencing.

A simple "reason" why palindromic sites are restrictive is a matter of combinations. Consider this example: Suppose that a restrictive sequence is 3 units (sites) long, and that there are 2 letters A, B(molecules) to choose from. Now for a palindrome "order matters". Combinatorially, that means the letters A and B are selected "with replacement", i.e. for any of the three positions there is a 50/50 chance of selecting an A or a B. The palindromic sequences must have mirror symmetry.

The possibilities are: AAA, BAA, ABA, AAB, BBA, ABB, BAB, BBB (I think I snagged them all.). In addition, there may be other limitations such as "there must be exactly 2 "A's". So of the 8 possibilities, only one, ABA fill all the restrictions of symmetry and composition (exactly 2 "A's").

This example is obviously contrived, but it is intended to illustrate the principle. As the palindrome length increases, and the number of components increases, and the number of other constraints are imposed, the number of palindromic possibilities becomes a small fraction of the total number of possibilities.

Vince Calder



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