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Enzymes are essential for almost all of the chemical reactions in a living organism. There are many enzymes that originate from microorganisms that are utilized in molecular biology. Currently enzymes are also derived from recombinant microorganisms that are used as manipulating tools in molecular biology.

Polynucleotide kinase or PNK is an enzyme that catalyzes the transfer of a phosphate group from Adenosine triphosphate (ATP) to the 5'OH end of DNA, RNA or an oligonucleotide. It is a derivative of the bacteriophage T4 and commercial preparations are generally the cloned phage gene products expressed in Escherichia coli. The above catalytic reaction can be reversed as the enzyme is also a homotetramer and a 3'-phosphatase. The T4 polynucleotide kinase is utilized in the laboratory as a buffer for restriction enzymes in molecular techniques such as Polymerase Chain Reaction (PCR) and in the labeling of the 5’-terminus of nucleic acids (DNA and RNA) which can be utilized as probes for hybridization, markers for gel electrophoresis and transcript mapping. They can also be utilized as enzymes that cleave the 3’-phosphate.

S1 nuclease is a specific endonuclease enzyme derived from Aspergillus oryzae. The enzyme is employed to cleave ssDNA (single stranded DNA) and RNA into mono or oligonucleotides. Even though the primary substrates of S1 nuclease are single-stranded nucleic acids, it can also sometime introduce single-stranded breaks in double-stranded DNA or RNA, or hybrid molecule of DNA-RNA. The enzyme also hydrolyses single stranded regions of duplex DNA such as gaps or loops. Nuclease S1 that is derived from Aspergillus is utilized in the laboratory in the nuclease assays as a reagent. In molecular biology, it is utilized to cleave single stranded tails from DNA molecule to generate products with the blunt ends. Also it is used in opening hairpin loops that are produced during the synthesis of double stranded complimentary DNA (cDNA).