Palindromic Sequences

Palindromes are the group of words that read the same, forward and backward. E.g. β€œmadam”.

In molecular biology, palindromic sequences are referred to as the sequence of nucleotides in the DNA duplex or RNA, where the sequence in one strand is the same as the complementary sequence of the other strand when read from the same direction on both the strands, either 5’ to 3’ or 3’ to 5’.

5′ β€”β€” GAATTC β€”β€” 3′
3′ β€”β€” CTTAAG β€”β€” 5′

The DNA double helix consists of two complementary strands running antiparallel to each other. The adenine always pairs with the thymine (or uracil in RNA) and guanine pairs with the cytosine. A strand is said to have a palindromic sequence if the sequence of nucleotides is the same as the reverse of its complement. E.g. ACCTAGGT is a palindrome. The complementary strand will have TGGATCCA and if it is reversed then it will be the same as the original sequence. That means if read from backwards, it is the complement of the forward nucleotide sequence. The two halves of a palindrome sequence are complementary to each other. The longer palindromic sequences have a tendency to form a hairpin loop.

When the nucleotide sequences are almost palindromic with few mismatches, it is called near palindrome. When complementary sequences are interrupted by a gap sequence, it is known as inverse repeat.

Some of the examples of palindromic sequences and the role they play in cellular mechanisms are given below:

Restriction Enzyme Recognition Site

Many restriction enzymes or restriction endonucleases identify a specific palindrome site and cut the DNA strands. They mostly cut the DNA, slightly away from the centre of the palindrome and between the same two nitrogenous bases in both the strands. They form identical overhanging single strands at both ends of the strand. They are known as β€œsticky ends” due to their tendency to easily pair with the complementary strand and form hydrogen bonds.

Restriction enzymes are used in the recombinant DNA technology to insert the desired DNA fragment into the vector forming recombinant DNA molecule. When the same restriction enzyme is used to cut DNA from both sources, then both the DNA fragments produce the same sticky ends. Sticky ends facilitate the joining of strands by the enzyme DNA ligase.

The recognition sequence of few restriction enzymes is given below:

Restriction Enzyme Source Recognition Sequence Cut
EcoR1 Escherichia coli 5′–GAATTC–3’


5′—G AATTC—3′

3′—CTTAA G—5′

BamH1 Bacillus amyloliquefaciens 5′–GGATCC–3’


5′—G GATCC—3′

3′—CCTAG G—5′

DNA Replication, Gene Regulation and Expression

Palindromic sequences have great significance. Palindromic sequences are found in abundance in the genome of most organisms. The human genome has many palindromic sequences distributed throughout.

They play an important role in DNA replication, gene expression and regulation. Palindromic sequences account for major deletions and insertions during DNA replication. They also promote interchromosomal recombination and translocation. Shorter palindromic sequences (>50 bp long) provide stability to DNA but a longer palindromic sequence makes DNA vulnerable to mutations and makes it unstable.

The hairpin formed by palindromic sequences is vulnerable to breakage and translocation. They can inhibit translation by interfering with the ribosomal translocation on mRNA. Thus, inhibiting the expression of genes.

Palindrome sequences also have a role to play in gene expression by methylation. Methylation sites can be found in the palindrome sequences. Methylation makes a gene inactive.

Palindromic mutations are linked to many diseases, such as various cancers, neuronal disorders, mental retardation, etc. They are important with regard to evolution. The beneficial mutations are retained during the course of evolution.

This was all about the Palindromic Sequences. Learn more about other related concepts for NEET, only at BYJU’S.

Frequently Asked Questions onΒ Palindromic Sequences

  1. What is the palindromic nucleotide sequence?

Palindromic sequences are read the same forward and backwards, both ways and are significant. Enzymes identify the sequences regardless of the side to approach the DNA. DNA sequences are double-stranded and by reading these base pairs, the palindromes can be found. Typically, these sequences are 3 to 5 bases in length.

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