Restriction enzymes — which type cuts within its recognition site? Restriction endonucleases are grouped into Types I, II, and III based on structure and cleavage behavior. Which type typically cuts the DNA within its specific recognition sequence, yielding predictable fragments for cloning?

Introduction / Context:
Restriction enzymes revolutionized molecular cloning by enabling precise DNA cutting at defined sequences. The operational differences among Types I, II, and III determine how useful an enzyme is for mapping and cloning applications. The question focuses on the type that cleaves directly at its recognition site.

Given Data / Assumptions:

• Type II enzymes recognize palindromic sequences and cut at or near those sites.
• Type I and III enzymes are multi-subunit, ATP-dependent, and cut away from the recognition sequence.
• Cloning requires predictable, reproducible overhangs or blunt ends.

Concept / Approach:

Type II restriction endonucleases (e.g., EcoRI, HindIII, BamHI) bind defined sequences and cleave at specific positions within them, producing consistent sticky or blunt ends ideal for ligation. Types I and III have more complex activities and cleave at variable distances, which is less practical for routine cloning.

Step-by-Step Solution:

Verification / Alternative check:

Standard cloning protocols and maps list Type II restriction sites exactly at cut positions, confirming their utility and behavior.

Why Other Options Are Wrong:

Type I and III cleave at variable distances from the site; “All” is incorrect; Type IV refers to modification-dependent endonucleases and is not relevant here.

Common Pitfalls:

Confusing recognition with cleavage location; only Type II reliably cuts within the sequence.

Final Answer:

Type II