The below mentioned article provides notes on palindromic DNA.
In the DNA molecule a variety of base sequences have been observed. Most of them do not have special features. The repeated sequences are of particular interest because they are the site of enzymatic activity and, sometimes give special features to the nucleic acid. For the first time Wilson and Thomas (1974) used the term palindromic DNA.
The palindromic DNA or palindromes are the inverted repeats and region of dyad symmetry. The length of palindromes may be short by about 3-10 bases or long by about 50-100 base pairs. As compared to prokaryotic DNA, the eukaryotic DNA contains a large palindrome of about several thousand base pairs. Sometimes a spacer separates the two inverted repeats (Fig. 5.9A).
The DNA molecules containing palindromes and inverted repeats may exist in alternative forms. After separation of complementary strands, the intra-molecular base pairing may result in a double stranded stretch formed between adjacent complementary sequences. This is known as cruciform structure (Fig. 5.9 B).
The cruciform structures have been produced in laboratory but not detected in the DNA isolated from cells. Moreover, if repeats are present in the same orientation, it is called direct repeats. They neither exist in alternative form of dsDNA nor have effect on the single advanced molecule.
In addition, if both the palindromes and inverted repeats are present they affect the ssDNA or RNA. They form intra-strand hydrogen bonding between adjacent or nearly complementary sequences.
Consequently a palindrome produces an intrastrand double stranded structure which is known as hairpin (Fig 5.10 A). The interrupted inverted repeats result in a structure consisting of a double stranded segment with a terminal single-stranded loop. This structure is called stem and loop (B).
Several possible functions of palindrome have been suggested such as:
(i) Its action as recognition sites of DNA for protein and many bacterial restriction enzymes,
(ii) Its action as bacterial restriction enzyme against destruction by foreign DNA,
(iii) Providing structural strength to the transcribed RNA by hydrogen bonding in the hairpin loops,
(iv) Possible involvement of cruciform structure in genetic recombination, and
(v) Its possession of genes on long palindrome of some lower eukaryotes that code for ribosomal RNA.