Question

a) Write the palindromic nucleotide for the following DNA segment $5'$- GAATTC-$3'$
b) Name the restriction endonuclease that recognizes the sequence.
c) How are sticky-ends produced? Mention their role.

Answer 1

Hint:-A double helix nucleic acid has one strand that reads in $5'$to $3'$direction and a complementary strand that reads in $3'$to $5'$ direction. In palindromic nucleotide sequences, the nucleotides present in one strand are the same as the complementary strand, provided the direction of the reading is kept the same ($5'$to $3'$ direction for both strands). For single-stranded nucleic acids, if its reverse complement, is the same only then it is called a palindromic sequence.

Complete Answer:-
a) The DNA segment: $5'$- GAATTC-$3'$
The Complementary DNA strand is $3'$-CTTAAG- $5'$
When read keeping the same direction, both the DNA segment and complement are the same. This nucleotide sequence is a palindrome.
b) Restriction enzymes or restriction endonucleases are enzymes present in bacterial cells that protect the bacteria from foreign pathogenic DNA. They cleave the foreign DNA into smaller fragments that are no longer functional. The restriction enzyme does this without harming its own DNA.
In laboratories, the most common restriction enzyme used is EcoR$1$. It scans the entire DNA and binds to specific sequences on the DNA. These are known as restriction sites. EcoR$1$ recognizes a specific sequence, which is a palindromic sequence.
The enzyme breaks the bond between two adjacent nucleotides on both the strands. The arrow shows the site where the EcoR$1$ cuts the DNA strands, to give:
$5' - G$ $AATTC - 3'$
$3' - CTTAA$ $G - 5'$
The cut in the double-stranded DNA is always neat and gives two uneven ends or overhangs.
c) Two DNA strands have the same overhangs because they have been cut by the same restriction enzyme. The overhangs can stick together by base pairing. These overhangs or uneven ends are called sticky ends. Sticky ends can be used to get recombinant DNA. A DNA fragment with a particular trait can be introduced in a vector DNA, forming a recombinant DNA.

Note:- Because the restriction enzymes recognize the same unique sequences in every DNA, it can be used to cleave a long DNA molecule into various fragments. The smaller fragments can be amplified and cloned as well. Certain restriction enzymes cut the DNA strand in a way that they leave no overhangs. Such ends are called blunt ends.