Question

A \(9.2\) kb plasmid DNA shown below has four BamHI sites \((p), (q), (r), (s)\). If a mutation results in the loss of BamHI site \((r)\), assuming the complete digestion by BamHI, the number of DNA fragments seen in agarose gel after electrophoresis will be _ _ _. (in integer)

Hint:

In agarose gel electrophoresis, DNA fragments of the same size migrate together and appear as one band.

Answer 1

Correct Answer: 2

Step 1: Understand digestion of circular plasmid DNA.
For a circular plasmid, if there are \(n\) restriction sites for an enzyme, complete digestion gives \(n\) DNA fragments.

Step 2: Identify the original BamHI sites.
Initially, the plasmid has four BamHI sites:
\[ p,\ q,\ r,\ s \]

Step 3: Apply the mutation condition.
The mutation causes loss of BamHI site \(r\).
So, the remaining BamHI sites are
\[ p,\ q,\ s \]

Step 4: Determine the number of physical fragments.
Since three BamHI sites remain on the circular plasmid, complete digestion produces three physical fragments.

Step 5: Find the fragment sizes.
From the figure:
\[ p\to q=2.4\ \text{kb} \] \[ q\to r=1.2\ \text{kb}, \quad r\to s=2.2\ \text{kb} \] Since \(r\) is lost, the fragment from \(q\) to \(s\) becomes
\[ 1.2+2.2=3.4\ \text{kb} \] Also,
\[ s\to p=3.4\ \text{kb} \]

Step 6: Identify bands seen on agarose gel.
The fragments are
\[ 2.4\ \text{kb},\quad 3.4\ \text{kb},\quad 3.4\ \text{kb} \] The two \(3.4\ \text{kb}\) fragments migrate together and appear as a single band.

Step 7: Final conclusion.
Thus, the number of distinct DNA fragments seen on agarose gel is
\[ \boxed{2} \]