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The experimental procedure involved the following steps:

Step 1: Separation of the two strands in the DNA sample.

Step 2: Annealing of the previously separated strands.

Step 3: Treatment of the double-stranded DNA with a 3' - 5' exonuclease.

Based on the results obtained from agarose gel electrophoresis, it was observed that the DNA from Step 3 exhibited a size smaller than 1kb.

To explain this outcome, the most possible reason is that the DNA in sample S possesses certain characteristics which could be:


Option: 1

It is palindromic.

Option: 2

It contains sequence repeats.

Option: 3

It experiences sequence inversion.


Option: 4

Each strand within the DNA sample contains a self-complementary sequence.

Answers (1)

  • The most probable reason for obtaining a DNA size smaller than 1kb in Step 3 is option (d) that is each strand within the DNA sample contains a self-complementary sequence. This means that the DNA strands have regions that can pair with themselves forming secondary structures like hairpins or stem-loops. 
  • When treated with a 3' - 5' exonuclease, these secondary structures can hinder the enzyme's ability to degrade the DNA efficiently, resulting in smaller DNA fragments observed on the agarose gel electrophoresis.
  • However, in Step 1, the DNA sample two strands are separated, and in Step 2, they are annealed or recombined.
  • But, in Step 3, the double-stranded DNA is treated with a 3' - 5' exonuclease, an enzyme that degrades DNA from the free ends. However, if the DNA strands contain self-complementary sequences, they can fold back on themselves and form stable secondary structures. These structures can impede the exonuclease's progression along the DNA, resulting in incomplete degradation and smaller DNA fragments. This is why the DNA from Step 3 appears to be smaller than the original 1kb size on the agarose gel.
  • Hence, the correct answer is option 4 
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