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Palindromic
DNA - A palindrome is a sentence that reads the same forwards and backwards, e.g. 'Madam I'm Adam'.
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. :
-A-A-T-T-G-C-A-A-T-T
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-T-T-A-A-C-G-T-T-A-A
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Thus DNA contains regions with an axis of two fold rotational symmetry which reads the same in both directions. The term palindromic DNA was first used by Wilson and Thomas (1974).
The sequence 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 consist of hund-reds of base pairs.
Eukaryotic DNA, in contrast to prokaryotic DNA, has-many large palindromic regions, which may contain up toseveral thousand base pairs.
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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. Short palindromes have been found in prokaryotes, e.g. the recognition sites for the lac repressor, the CAP- protein and restriction nucleases of bacteria.
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The lac operator of E. coli is protected from pancreatic deoxyribonuclease digestion by the lac repressor protein. This protected region consists of 27 base pairs of which 16 are arranged symmetrically.
The lac promoter gene of E. coli also contains palindromic sequences.
In eukaryotes the ribosomal DNA (rDNA) which codes for rRNA is associated with the nucleolus. In addition, extrachromosomal copies of rDNA have been found in the oocytes of many animals.
This DNA arises as a result of selective amplification of rDNA during early oogenesis and during conjugation in the protozoan Tetrahymena and the slime mould Physarum (Enberg and Klenow, 1978).
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The linear rDNA molecule is actually a giant palindrome with its two halves virtually identical. 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 hairpie-structure instead of the original double helix.
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Functions of palindromic DNA
The exact significance of palindromic DNA is not known, although several functions have been suggested.
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 palindromic sequences in double stranded DNA, which is cleaved in 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 result.
Protein-DNA interaction might take place through the cruciform structure, although this view has been challenged. The cruciform structures are also suggested to be involved in genetic recombination.
Long palindromic DNA molecules from some lower evkaryotes have been shown to contain genes coding for ribosomal RNA. Extra nuclear rDNA palindromes may have arisen by the process of copying of rRNA genes during gene amplification.
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 result.
Protein-DNA interaction might take place through the cruciform structure, although this view has been challenged. The cruciform structures are also suggested to be involved in genetic recombination.
Long palindromic DNA molecules from some lower evkaryotes have been shown to contain genes coding for ribosomal RNA. Extra nuclear rDNA palindromes may have arisen by the process of copying of rRNA genes during gene amplification.
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