Restriction endonucleases: Which statements accurately describe what these enzymes do in bacteria and in vitro?

Introduction:
Restriction endonucleases recognize specific DNA sequences and cleave phosphodiester bonds, forming the basis for many cloning and mapping techniques. In bacteria, they function as part of restriction–modification systems to defend against phage. This question evaluates your understanding of their biological role and cutting patterns.

Given Data / Assumptions:

• Type II restriction enzymes recognize palindromic sites and cut at or near those sites.
• Cleavage can generate either cohesive (overhang) or blunt ends.
• Host DNA is typically protected by methylation at recognition sites.

Concept / Approach:
Restriction enzymes curtail phage infection by degrading unmodified foreign DNA while sparing methylated host DNA. In vitro, they are chosen for the type of ends they generate: staggered cuts with 5′ or 3′ overhangs facilitate directional cloning; blunt cutters are useful for end-agnostic ligations though often less efficient. Many different enzymes exist, each with defined recognition sites and cut patterns.

Step-by-Step Solution:

Verification / Alternative check:
Enzyme datasheets (e.g., EcoRI, HindIII for sticky ends; EcoRV, SmaI for blunt ends) explicitly state overhangs versus blunt termini, confirming diverse cut modes and uses.

Why Other Options Are Wrong:

• “Only nick one strand” is false for standard restriction endonucleases; specialized nicking variants exist but classic enzymes cleave both strands to generate double-strand breaks.

Common Pitfalls:
Assuming all enzymes make sticky ends; selection of enzyme determines end type and cloning strategy.

Final Answer:
All of the above