Question

Explain the significance of ‘palindromic nucleotide sequence’ in the formation of recombinant DNA.

Answer 1

Hint: A palindromic sequence is a nucleic acid sequence on double-stranded DNA or RNA that is the same when read from$5\prime \to 3\prime$on one strand and$3\prime \to 5\prime$on the other strand i.e., complementary strand.

Complete answer:
Recombinant DNA is formed by recombinant DNA technology in which the gene of interest is inserted into the host genome. This recombination process makes use of restriction enzymes i.e., restriction endonucleases that make cuts within the nucleotide sequence of the gene of interest as well as the host genome. The recognition site of these enzymes is a little away from the center of the palindromic sites, but between the same two bases on the opposite strands leaving behind sticky ends that facilitate the action of DNA ligase. Thus, the presence of palindromic nucleotide sequences helps in the recognition of the site of cleavage of the restriction endonucleases, thereby initiating the process of formation of recombinant DNA.

Additional information:
Enzymes that cleave the DNA into fragments at or near the restriction sites within the molecule are called restriction endonucleases. These enzymes are found in bacteria and archaea that provide a protective mechanism against invading viruses. These endonucleases do not cleave the DNA of bacteria and archaea that produces it because of the presence of a restriction-modification system (in which there is methylation of the restriction sites that are not recognized by the endonucleases) in these organisms.

Enzyme	Source	Recognition sequence	Cut
EcoR1	Escherichia coli	$5\prime -$GAATTC$3\prime - $CTTAAG	$5\prime - - -$G AATTC$ - - - 3\prime $$3\prime - - - $CTTAA G$ - - - 5\prime $
Taq1	Thermus aquaticus	$5\prime - $TCGA$3\prime - $AGCT	$5\prime - - - $T CGA$ - - - 3\prime $$3\prime - - - $AGC T$ - - - 5\prime $

Note: Palindromic nucleotide sequences have their significance in replication, transcription, and repair mechanisms which are directional. They are known for providing the restriction sites that are recognized by the restriction endonucleases to cleave the DNA.