In agarose gel electrophoresis, DNA fragments are separated from one another on the basis of their:
Answer & explanation
Correct answer: option 2
The correct answer is Option (2) → size
In gel electrophoresis, DNA fragments are made to move through an agarose gel by an electric field. DNA is negatively charged, so all fragments move towards the anode. The gel works like a sieve. Small fragments slip through it easily and move farther, while large fragments are held back. So the fragments end up in separate bands according to their size.
Option (1) palindromic recognition sequences — Incorrect. A palindromic recognition sequence is the site where a restriction enzyme cuts the DNA. It decides where the cuts are made, not how far a fragment moves in the gel.
Option (2) size — Correct. The agarose gel has a sieving effect. The smaller the fragment, the farther it moves, so fragments are separated by size.
Option (3) type of sticky ends — Incorrect. Sticky ends are the short single-stranded ends left by some restriction enzymes. They help in joining DNA pieces with DNA ligase, not in separating them on a gel.
Option (4) base sequence — Incorrect. Fragments of the same size move to the same place even if their base sequences differ. The gel cannot tell sequences apart.
NCERT Extract:
Separation and Isolation of DNA Fragments – “… Since DNA fragments are negatively charged molecules they can be separated by forcing them to move towards the anode under an electric field through a medium/matrix. Nowadays the most commonly used matrix is agarose which is a natural polymer extracted from sea weeds. The DNA fragments separate (resolve) according to their size through sieving effect provided by the agarose gel. Hence, the smaller the fragment size, the farther it moves.”
Figure 9.3 A typical agarose gel electrophoresis showing migration of undigested (lane 1) and digested set of DNA fragments (lane 2 to 4)