Question

Which of the following enzymes under appropriate conditions produce single-stranded nicks in DNA?

• A. S1 nuclease \
• B. Exonuclease III \
• C. DNase I \
• D. Terminal transferase

Hint:

DNase I + Magnesium ($\text{Mg}^{2+}$) = Independent single-strand nicks. DNase I + Manganese ($\text{Mn}^{2+}$) = Full double-strand breaks. The metal cofactor completely changes how it cuts!

Answer 1

The Correct Option is C

Step 1: Concept Nucleases are specialized enzymes that cleave the phosphodiester bonds holding nucleic acid backbones together. They vary in their preference for single-stranded or double-stranded substrates and can act either internally or from the ends of strands.

Step 2: Meaning A "single-stranded nick" is a clean break in the phosphodiester backbone of just one strand within a double-stranded DNA molecule, leaving the opposing template strand completely intact.

Step 3: Analysis * S1 nuclease (A): Specifically targets and degrades single-stranded DNA or RNA molecules, meaning it does not create clean individual nicks in double-stranded helices. * Exonuclease III (B): Chews along DNA sequentially from the ends of strands (5' to 3' or 3' to 5'), meaning it cannot cut internally to make a nick. * DNase I (C): An endonuclease that cleaves internally. In the presence of magnesium ions ($\text{Mg}^{2+}$), it cuts each strand independently, making random single-stranded nicks along double-stranded DNA. * Terminal transferase (D): An enzyme that adds nucleotides to the ends of strands without using a template; it does not cut DNA backbones.

Step 4: Conclusion Therefore, DNase I is the enzyme used to introduce random single-stranded nicks into double-stranded DNA templates. This corresponds to option C. Final Answer: (C)