Restriction enzymes, also known as restriction endonucleases, are proteins that act as molecular scissors, cutting DNA at specific sequences called restriction sites. These enzymes are naturally produced by bacteria as a defense mechanism against invading viruses (bacteriophages) by recognizing and cutting foreign DNA while leaving their own DNA unharmed, usually through methylation. Each restriction enzyme has a specific recognition sequence, typically 4 to 8 base pairs long, which it scans for in the DNA molecule.
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A restriction enzyme cleaves DNA at or near recognized sequence patterns. Many type II systems produce reproducible fragments useful in genetic engineering, while a corresponding DNA modification system protects the host sequence. Different recognition patterns and cut positions can produce blunt ends or single-stranded overhangs. Thus recognition specificity and the physical end structure are separate properties important for assembling DNA fragments. [ref]
