A DNA fragment isolated from an EcoRI digest of genomic DNA was combined with a plasmid vector linearized by EcoRI digestion so that sticky ends could anneal. Phage \(T 4\) DNA ligase was then added to the mixture. List all possible products of the ligation reaction.

EcoRI is a type of restriction enzyme that is commonly used in molecular biology for DNA manipulation. It specifically recognizes a unique sequence of DNA, 'GAATTC,' and cuts within this sequence, resulting in 'sticky ends.' These ends are single-stranded overhangs that facilitate the binding of another DNA molecule with a complementary sequence. During the EcoRI digest, both the plasmid vector and DNA fragment were treated with the EcoRI enzyme, generating sticky ends that are identical for each DNA molecule. This process is crucial for the next step, which involves annealing of these sticky ends to form a recombinant DNA molecule.

A plasmid vector is a small, circular piece of DNA that is often used as a vehicle to artificially carry foreign genetic material into another cell. In the exercise, the plasmid vector was linearized by the EcoRI digest to create sticky ends that are receptive to the foreign DNA fragment with complementary sticky ends. Once the foreign DNA is inserted into the plasmid, it can be introduced into a bacterial cell to replicate, making numerous copies of the foreign DNA in the form of recombinant DNA.

Selection of the right plasmid vector is critical for the success of cloning experiments, as vectors come with various features such as antibiotic resistance genes, which can be used to select for bacteria that have successfully taken up the plasmid.

The term 'sticky ends annealing' refers to the process where complementary sticky ends of DNA molecules come together and become temporarily attached via hydrogen bonds. After the EcoRI digest produces DNA fragments and plasmid vectors with compatible overhangs, these molecules can anneal. The annealing occurs because of base pairing rules, with A pairing with T and C pairing with G. This annealing is reversible and not covalently bonded yet, which makes it necessary to introduce an enzyme to permanently link the DNA strands.

By maintaining optimal conditions such as the right temperature and ionic strength, the efficiency of sticky ends annealing can be maximized, ensuring a higher likelihood of successful ligation in the next step of the reaction.

Phage T4 DNA ligase is an enzyme that catalyzes the formation of a phosphodiester bond between adjacent nucleotides in DNA. It is instrumental in the DNA ligation reaction, where it 'seals' the nicks in the sugar-phosphate DNA backbone. When T4 DNA ligase is added to the annealed molecules of DNA fragments and a plasmid vector, it creates a stable, covalently linked molecule, which is essential for a successful genetic engineering experiment.

DNA ligases like T4 DNA ligase are often used in the lab in various processes including DNA cloning, molecular cloning, and repair of DNA strands. Their ability to join DNA ends is a cornerstone of modern biotechnology and is commonly exploited in the construction of recombinant DNA.