Palindromic DNA

The DNAs of several eukaryotes are shown to have Palindromic sequences, in which nucleotides of one strand going in one direction are the same as the nucleotides of the other strand going in the other direction, e.g.:



Thus DNA contains regions with an axis of two fold rotational symmetry which reads the same in both directions. The term Palindromic DNA ws first used by Wilson and Thomas. The sequences given above would transcribe the same RNA if RNA polymerase started from either side.

Palindromic regions may be relatively short (3-10 bases) e.g. those recognized by restriction enzymes, or may be long and consists of hundreds of base pairs. Eukaryotic DNA, in contrast to prokaryotic DNA, has many large Palindromic regions, which may contain up to several thousand base pairs. The two regions containing the inverted sequences may be very close to each other or may be separated by spacer regions more than a thousand bases long.

In eukaryotes the ribosomal DNA (rDNA) which codes for rRNA is associated with the nucleolus. The linear rDNA molecule is actually a gaint palindrome with its two halves virtually indentical. The symmetry continues right to the middle of the molecule. The linear rDNA form can be converted to a cruciform structure. Denaturation of the cruciform structure by heat or alkali treatment, and subsequent self-association upon renaturation (snap-back) results in the formation of a hairpin structure instead of the original double helix. Short palindromes may function as recognition sites of DNA for proteins which also have a two-fold rotational symmetry, e.g. lac repressor protein, CRP protein and many bacterial restriction enzymes. Binding of proteins to DNA is due to interaction between specific regions of the DNA and protein. Restriction enzymes of bacteria serve a protective function against foreign DNA by destroying it. These enzymes are specific for a Palindromic sequence in double stranded DNA, which is cleave is only a few locations.



Palindromes may also give structural strength to the transcribed RNA by hydrogen bonding in the hairpin loops. If the Palindromic sequences are not perfectly symmetrical, imperfect loops may results.

Long plaindromic DNA molecules from some lower evkaryotes have been shown to contain genes coding for ribosomal RNA. Extranuclear rDNA palindromes may have arisen by the process of copying of rRNA genes during gene amplification.