Restriction Endonucleases

Since a large number of restriction enzymes were discovered, it was necessary to adopt a uniform naming system for them. Smith and Nathans, in 1973, proposed a system to name the restriction endonucleases and we use a simplified version of it today. Few important points, in naming the restriction enzymes are listed below:

·        The first letter represents the genus of the host organism and is in uppercase.

·        The next two alphabets are the species name in the lowercase

·        Sometimes strain designation is added. For example, R in EcoRI or the serotype of the host bacterium such as d in HindIII.

·        Roman numerals represent the order of characterization of different restriction enzymes from the same organism. The first restriction enzyme from an organism is designated I, the second as II and so on. For example, HpaI and HpaII are the enzymes that were isolated from the same organism i.e. Haemophilus parainfluenzae.

For example, the restriction enzyme EcoRI is isolated from Escherichia coli strain RY13 and it is the first enzyme isolated from this strain.

Restriction enzymes can cut the DNA in two ways. Some enzymes make double-stranded cuts giving a blunt or flush end while others cut few nucleotides apart such that they produce short, single stranded overhangs at each end. Such ends are called sticky or cohesive ends because under annealing conditions base-pairing occurs between them which can stick the DNA molecules back together again (Figure 1).

Results of cleavage with different types of restriction endonucleases

Some of the enzymes that produce sticky ends may produce 5' overhangs (Ex. Sau3AI, HinfI) while some may produce 3' overhangs (Ex. PstI) (Figure 2). Further, there are some enzymes which have different recognition sequences but they give the same sticky ends (Ex. Sau3AI and BamHI). Sau3AI has 4-bp recognition sequence while BamHI has a 6-bp recognition sequence and both give a 5' overhang as follows:

Types of overhangs