Methyltranferases (methylases)
They add methyl groups (--CH3) to adenine or cytosine bases within the recognition sequence, which is thus modified and protected from the endonuclease.

Restriction-modification system
The restriction enzyme and its corresponding methylase constitute the restriction-modification system of a bacterial species

Blunt End
Some enzymes make strand incisions immediately opposite one another.These ends are called as "blunt" (meaning "not sharp") or "flush" (meaning "level or even").

Control Proteins
Some Restriction-Modification Systems are found to have an additional gene that encodes a protein involved in the control of expression of the restriction gene. These genes serve as transcriptional activators, preventing the expression of the restriction gene following transfer of the system into naïve hosts, until such time as Control Protein has accumulated and the methylation is sufficient to provide protection against what would otherwise be the deterious action of restriction endonucleases

Homing enzymes
They are site-specific DNases, encoded by introns or inteins. They specifically cleave intron - or intein - alleles of their genes and, thereby, facilitate homing of the introns or inteins that encode them.

Isoschizomers
They are pairs of restriction enzymes specific to the same recognition sequence and cut in the same location. For example, Sph I (CGTAC^G) and Bbu I (CGTAC^G) are isoschizomers of each other.

Prototype
The first enzyme to recognize and cut a given sequence is known as the prototype

Neoschizomer
An enzyme that recognizes the same sequence but cuts it differently is a neoschizomer

Nicking Enzymes
These are altered restriction enzymes that hydrolyze only one strand of the duplex, to produce DNA molecules that are "nicked", rather than cleaved

Orphan methyltransferases
In prokaryotic genomes, some DNA methyltransferases form a restriction-modification gene, but some others are present by themselves. These methyltransferases have no known cognate restriction enzyme, and are involved in methyl-directed mismatch DNA repair as well as ensuring that multiple origins of chromosomal replication within the cell fire synchronously

Star Activity
There are some restriction enzymes which cleave partially different base sequence than recognition sequence as a result of reduced specificity when used in a large excess to substrate DNA. This phenomenon is called Star Activity

Recognition Sequence
A nucleotide sequence-composed typically of 4, 6, or 8 nucleotides--that is recognized by a restriction endonuclease.

Endonucleases
A class of enzymes capable of hydrolyzing (breaking) the interior phosphodiester bonds of DNA or RNA chains. As opposed to cleavage (by exonucleases) at the terminal bonds (ends) of the molecular chain.

Hydrolysis
Literally, means "cleaved by water." It is used for a chemical reaction in which the chemical bond attaching an atom, or group of atoms to the (rest of the) molecule is cleaved, followed by attachment of a hydrogen atom at the same chemical bond.


Palindrome
A DNA molecule sequence that is the same when one strand of the molecule is read left to right and the other strand is read right to left.

Base (nucleotide)
A segment of the DNA (and RNA) molecules--- one of the four (repeating) chemical units that comprise DNA/RNA that, according to their order and pairing (i.e., on the parallel strands of DNA/RNA molecules), represent the different amino acids (i.e., within the protein molecule that each gene in the DNA codes-for). The four bases that comprise DNA are adenine (A), cytosine (C), guanine (G), and thymine (T).

Sequencing (of DNA molecules)
The process used to obtain the sequential arrangement of nucleotides in the DNA backbone. The cleavage into fragments (followed by separation of those fragments, which can then be sequenced individually) of DNA molecules by one of several methods: (1) a chemical cleavage method followed by polyacrylamide gel electrophoresis (PAGE) or capillary electrophoresis, (2) a method consisting of controlled interruption of enzymatic replication methods followed by PAGE, (3) a didexyl method utilizing fluorescent "tag" atoms attached to the DNA fragments, followed by use of spectrophotometry to identify the respective DNA fragments by their differing "tags" (which fluoresce at different wavelengths). This (fluorescent tag) variant of the dideoxy method can be automated to "decipher" large DNA molecules (i.e., genomes). Such automated machines are sometimes called "gene machines".

Double helix
Describes the coiling of the antiparallel strands of the DNA molecule, resembling a spiral staircase in which the paired bases form the steps and the sugar-phosphate backbones form the rails.

Splicing
The removal of introns and joining of exons in RNA (e.g., genes). Thus, introns are spliced out, while exons are spliced together.

Ligase
An enzyme used to catalyze the joining-together (i.e., "ligating") of two separate molecules, in an energy-requiring process. For example, the joining-together of two single-stranded DNA segments.

Unambiguous restriction enzymes
Enzymes that have a specific recognition sequence are called ambiguous Example: BamHI recognizes the sequence GGATCC and no others

Ambiguous restriction enzymes
Enzymes having slight variation in their recognition sequences are called unambiguous restriction enzymes. Example: HinfI recognizes a 5 bp sequence starting with GA, ending in TC, and having any base between (in the table, "N" stands for any nucleotide)