Let us make an in-depth study of the palindromes. After reading this article you will learn about: 1. Introduction to Palindromes 2. Palindromes in DNA and 3. Role of Palindromes.
Introduction to Palindromes:
RNA is a single stranded molecule but it can also form double stranded regions in its structure like DNA. When a sequence of bases is followed by a complementary sequence nearby in the same molecule, the chain may fold back upon itself to generate an antiparallel double stranded hairpin like structure. The hair pin structure consists of a double stranded base paired region called stem and a loop of unpaired bases which is the region between complementary base sequences. Therefore, single stranded RNA has secondary structure.
These complementary sequences are formed of inverted repeats called palindromes.
Secondary structure formed after pairing of complementary strands shows inverted repeats in a single stem.
In the palindrome, hydrogen bonds are formed between complementary bases.
Palindrome structure can be twisted to form a double helical structure like the DNA as the complementary bases are hydrogen bonded. The two strands are also antiparallel like DNA.
Palindromes in DNA:
Palindromes can also be present in DNA. One strand of DNA can also have similar secondary structure because primary structure of DNA is the same as that of RNA.
The double stranded DNA molecule can also have complementary sequence but these lie in the opposite strands. It consists of two copies of an identical sequence present in reverse orientation but in separate opposite strands. These are formed of inverted repeats or palindromes. In double stranded DNA it is also called dyad symmetry.
This sequence of double helix DNA is the same when read in the opposite direction. When either strand is read in 5′ —> 3′ direction, it generates the sequences 5’GACCTAGGTC3′. This is left to right in one strand and right of left in the other strand. The vertical line in the centre is the axis of symmetry. The two inverted repeats may be separated by a spacer having many different bases.
Here the axis of symmetry has been shifted into the centre of additional bases or spacer that separates the two repeats.
The two strands of DNA can form two hairpins opposite to each other to form a cruciform as it represents the junction of four duplex regions. In this way, palindromes produce an intrastrand double helical hairpin. Inverted repeats having spacers between them produce stem and loop structure.
Role of Palindromes:
In lac operon, the structure of operator is a palindrome having inverted repeats. The repressor recognizes the operator by its palindromes.
Palindromes cause joining of two DNA molecules.
Plasmid vectors join the chromosome of other bacteria by palindromes. Palindromes are present at the ends of plasmid as well as the chromosome it joins. Restriction enzymes Eco R1 recognize and make staggered cuts in both molecules producing short complementary sticky ends. These sticky ends are palindromes. These two DNA molecules with palindromes will join and combine (anneal) with each other.
Ribosomal RNA (rRNA) has extensive stems and loops formed by palindromes.
Transposoms or Jumping genes often have inverted repeats at either end.