Country: United States
Date: June 2006
Why are most restriction site palindromic?
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
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.
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Update: June 2012