Definition
Restriction endonucleases are enzymes that cut DNA at specific sequences, acting as molecular scissors.
These enzymes are naturally found in bacteria, where they protect against foreign DNA (e.g., viral DNA) by cutting it.
Types of Restriction Enzymes
Type I
Cut DNA at random locations, often hundreds of base pairs away from their recognition site.
Less useful for precise genetic engineering.
Type II
The most commonly used type in laboratories.
Cut within or at short distances from their recognition sites, producing predictable and reproducible fragments.
Recognition sites are often palindromic (the same sequence read 5′→3′ on both strands).
Type III
Cut DNA at sites a short distance away (about 20–30 base pairs) from the recognition site.
Less frequently used in routine cloning compared to Type II.
Common Restriction Enzymes and Their Recognition Sites
EcoRI → Recognizes 5'-GAATTC-3' and produces sticky ends.
HindIII → Recognizes 5'-AAGCTT-3' and produces sticky ends.
HaeIII → Recognizes 5'-GGCC-3' and produces blunt ends.
Types of DNA Ends After Cutting
Sticky Ends (Cohesive Ends)
The enzyme cuts the two DNA strands at offset positions, leaving overhanging single-stranded regions.
These overhangs can base-pair (anneal) with complementary overhangs cut by the same enzyme.
Blunt Ends
The enzyme cuts both DNA strands at the same position, leaving no single-stranded overhang.
While this creates more stable DNA ends, blunt-end ligations can be less efficient compared to sticky-end ligations.
A) Sticky Ends → Single-stranded overhangs that help in DNA ligation.
B) Blunt Ends → No overhangs, making ligation less efficient.
