Q.44 The plasmid DNA was subjected to restriction digestion using the enzyme EcoRI and analysed on
an agarose gel. Assuming digestion has worked (the enzyme was active), match the identity of the
DNA bands shown in the image in Group I with their identity in Group II.
Group I Group II
P. Bands labeled as A 1. Nicked
Q. Band labeled as B 2. Supercoiled
R. Band labeled as C 3. Concatemers
S. Band labeled as D 4. Linear
(A) P-3, Q-1, R-2, S-4 (B) P-1, Q-4, R-3, S-2
(C) P-4, Q-3, R-1, S-2 (D) P-4, Q-1, R-2, S-3
Introduction
Understanding plasmid DNA conformations on agarose gel electrophoresis is a core concept in molecular biology and a frequently tested topic in competitive exams. When plasmid DNA is run on a gel in uncut and restriction enzyme–digested forms, different structural conformations migrate differently, producing distinct banding patterns.
In this article, we analyze a plasmid DNA sample digested with EcoRI, match the observed DNA bands with their correct identities, and explain all options step by step to clearly justify the correct answer.
Correct Answer
Option (A): P-3, Q-1, R-2, S-4
Background: How Plasmid DNA Migrates on Agarose Gel
Plasmid DNA can exist in multiple structural forms, each migrating differently during electrophoresis:
| DNA Form | Structural Property | Migration Speed |
|---|---|---|
| Concatemers | Multimeric plasmid forms | Slowest |
| Nicked (Open Circular) | Single-strand break | Slow |
| Linear | One double-strand break | Intermediate |
| Supercoiled | Tightly coiled intact plasmid | Fastest |
Analysis of the Gel Image
The gel contains two lanes:
-
Uncut plasmid DNA
-
EcoRI-digested plasmid DNA
EcoRI makes one cut in the plasmid, converting it into a linear DNA molecule.
Matching Group I with Group II
🔹 Band A (P → 3: Concatemers)
-
Appears highest on the gel
-
Moves the slowest
-
Represents large multimeric plasmid forms
✔ Correctly identified as Concatemers
🔹 Band B (Q → 1: Nicked)
-
Migrates slower than linear DNA
-
Represents open circular plasmid with single-strand breaks
✔ Correctly identified as Nicked DNA
🔹 Band C (R → 2: Supercoiled)
-
Migrates fastest in the uncut lane
-
Compact and tightly wound structure
✔ Correctly identified as Supercoiled DNA
🔹 Band D (S → 4: Linear)
-
Present only after EcoRI digestion
-
Single distinct band
-
Represents plasmid cut once
✔ Correctly identified as Linear DNA
Explanation of All Options
Option (B): P-1, Q-4, R-3, S-2
Incorrect because:
-
Concatemers are mislabeled as nicked
-
Linear DNA is wrongly assigned to uncut bands
Option (C): P-4, Q-3, R-1, S-2
Incorrect because:
-
Concatemers cannot be linear
-
Supercoiled DNA is incorrectly labeled as nicked
Option (D): P-4, Q-1, R-2, S-3
Incorrect because:
-
EcoRI digestion produces linear, not concatemer DNA
Final Conclusion
EcoRI digestion of a plasmid with a single restriction site produces one linear DNA band, while the uncut plasmid shows multiple conformations. Correct identification of these forms depends on understanding DNA topology and migration behavior.
✔ Final Correct Match:
P-3 (Concatemers), Q-1 (Nicked), R-2 (Supercoiled), S-4 (Linear)
➡ Answer: Option (A)
