Restriction enzymes are specialized proteins, often called molecular “scissors,” that precisely cut DNA molecules. These enzymes were first discovered in the late 1960s as a defense mechanism in bacteria against invading viruses, specifically bacteriophages. Scientists like Werner Arber, Daniel Nathans, and Hamilton O. Smith received the Nobel Prize in 1978 for their foundational work characterizing these enzymes. Their discovery provided a powerful tool for manipulating DNA, transforming the field of molecular biology.
What Are Recognition Sequences?
Recognition sequences are short, specific stretches of DNA that restriction enzymes identify and bind to before making a cut. Each unique restriction enzyme recognizes a particular sequence of nucleotides, typically ranging from four to eight base pairs in length. This precise identification ensures DNA is cut only at designated locations.
These sequences commonly exhibit a palindromic nature. This means they read the same forwards on one DNA strand (from 5′ to 3′ direction) as they do on the complementary strand when read in the same direction. For example, if one strand reads 5′-GAATTC-3′, the complementary strand reads 3′-CTTAAG-5′, but when read 5′ to 3′ it is also GAATTC. This symmetrical arrangement allows the enzyme to interact with both strands of the DNA double helix, facilitating accurate cleavage.
The BamHI Recognition Sequence and Its Action
The restriction enzyme BamHI, isolated from the bacterium Bacillus amyloliquefaciens, recognizes a specific six-base pair DNA sequence: 5′-GGATCC-3′. This sequence is a palindrome. BamHI performs its cut within this specific recognition site, precisely between the two guanine (G) nucleotides on both DNA strands.
This staggered cut by BamHI results in “sticky ends,” also known as “cohesive ends.” These sticky ends are short, single-stranded overhangs of four nucleotides. For BamHI, the resulting overhangs are 5′-GATC-3′. These protruding ends are complementary to each other, allowing them to readily pair with other DNA fragments that have been cut with the same enzyme or another enzyme that produces compatible sticky ends.
How BamHI Is Used in Science
The sticky ends generated by BamHI are useful in molecular biology, enabling the joining of DNA fragments from different sources. This capability forms the basis of recombinant DNA technology and gene cloning. When DNA fragments with complementary sticky ends come together, they can temporarily bind through base pairing. An enzyme called DNA ligase then forms stable phosphodiester bonds, permanently joining the fragments to create a new, hybrid DNA molecule.
This process is used in gene cloning, where a specific gene of interest is cut from one organism’s DNA using BamHI and then inserted into a bacterial plasmid that has also been cut with BamHI. The plasmid, now containing the foreign gene, is introduced into bacteria. These bacteria then replicate the plasmid along with the inserted gene, allowing scientists to produce multiple copies of a gene or express the gene to synthesize desired proteins, such as human insulin.
Beyond gene cloning, BamHI and other restriction enzymes contribute to various other scientific applications. They are used in DNA fingerprinting, a technique that generates unique fragment patterns from an individual’s DNA, useful in forensic science and paternity testing. Restriction enzymes also play a role in mapping genes on chromosomes by creating predictable DNA fragments, and in constructing genetic libraries, which are collections of an organism’s entire genome broken into manageable, clonable pieces.