25+ Restriction Enzyme Examples: Detailed Facts


With the advancement in biotechnology, restriction enzyme has become an indispensable tool for recombinant DNA technology.

A restriction enzyme also known as molecular scissors is a site-specific endonuclease encoded by bacteria and archaea. This article accounts for detailed facts about different restriction enzyme examples.

Different types of restriction enzymes:

Restriction enzyme examples and its recognition sites are listed below.

EcoRI

SourceEscherichia coli

Recognition sequence – 5’-GAATTC-3′ 3’-CTTAAG-5′ ; sticky ends

restriction enzyme example
EcoRI From Wikipedia

EcoRII

Source Escherichia coli

Recognition sequence 5’-CCWGG-3′ 3’-GGWCC-5′; sticky ends

restriction enzyme example
EcoRII From Wikipedia

BamHI

Source-Bacillus amyloliquefaciens

Recognition sequence – 5’-GGATCC-3′ 3’-CCTAGG-5′: sticky ends

restriction enzyme example
BamHI From Wikipedia

TaqI

Source –Thermus aquaticus

Recognition sequence- 5’ TCGA-3′ 3’-AGCT-5′

HindIII

Source – Haemophilus influenzae

Recognition sequence – 5’ AAGCTT-3′ 3’-TTCGAA -5′

restriction enzyme example
HindIII From Wikipedia

Sau3AI

Source – Staphylococcus aureus

Recognition sequence 5′ GATC-3′ 3′-CTAG-5′;

NotI

Source –Nocardia otitidis

Recognition sequence – 5′-GCGGCCGC-3′ 3′-CGCCGGCG-5′

PvuII

Source –Proteus vulgaris

Recognition sequence – 5′-CAGCTG-3′ 3′-GTCGAC-5′

HaeIII

Source – Haemophilus aegyptius

Recognition sequence- 5′ GGCC-3′ 3′-CCGG-5′

restriction enzyme example
HaeIII From Wikipedia

AluI

Source – Arthrobacter luteus

Recognition sequence- 5’-AGCT-3′ 3’-TCGA-5′

EcoRV

SourceEscherichia coli

Recognition sequence- 5′-GATATC- 3′ 3′-CTATAG- 5′

restriction enzyme example
EcoRV From Wikipedia

SalI

SourceStreptomyces albus

Recognition sequence – 5′ -GTCGAS-3′ 3′-CAGCTG -5′

ScaI

Streptomyces caespitosus

Recognition sequence- 5′-AGTACT-3′ 3′-TCATGA-5′

SmaI

Source Serratia marcescens

Recognition sequence – 5′-CCCGGG-3′ 3′-GGGCCC-5′

HinFI

Source Haemophilus influenzae

Recognition sequence- 5′-GANTC-3′ 3′-CTNAG-5′

HaeIII

Source Haemophilus aegyptius

Recognition sequence- 5′-GGCC-3′ 3′- CCGG-5′

HgaI

Source Haemophilus gallinarum

Recognition sequence- 5’GACGC-3′ 3′-CTGCG-5′

EcoP15I

Source Escherichia coli

Recognition sequence- 5′-CAGCAGN25NN-3′ 3′-GTCGTCN25NN-5′

KpnI

Source – Klebsiella pneumoniae

Recognition sequence– 5’GGTACC-3′ 3′-CCATGG-5′

PstI

Source – Providencia stuartii

Recognition sequence– 5′-CTGCAG-3′ 3′-GACGTC-5′

SacI

Source – Streptomyces achromogenes

Recognition sequence- 5′-GAGCTC-3′ 3′-CTCGAG-5′

SpeI

Sorurce –Sphaerotilus natans

Recognition sequence- 5′-ACTAGT-3′ 3′-TGATCA-5′

SphI

Source – Streptomyces phaeochromogenes

Recognition sequence- 5′-GCATGC-3′ 3′-CGTACG-5′

StuI

Source- Streptomyces tubercidicus

Recognition sequence- 5′-AGGCCT-3′ 3′-TCCGGA-5′

XbaI

Source –Xanthomonas badrii

Recognition sequence – 5′-TCTAGA-3′ 3′-AGATCT-5′

Restriction enzymes cut the DNA strands in two different ways.

Some restriction endonuclease cut the DNA at the same point. Such straight-cut within the recognition site creates blunt ends with no over-hanging ends. These ends are often ligated by DNA ligase enzymes. Examples: PvuII, Haelll, Alul.

Contrastingly, the second class of restriction endonuclease undergoes staggered cut resulting in complementary single-stranded over-hanging ends. Such ends are called sticky or cohesive ends. Examples EcoR1, BamH1, Taq1. These are frequently used for cloning purposes in biotechnology.

restriction enzyme example
Restriction enzyme cleaves DNA strand in two different ways

Types of restriction enzymes

Restriction enzymes can be classified into four groups depending upon the composition, type of cofactors requirements, the target site, and cleavage position.

Type I

This type of restriction enzyme are multifunctional proteins that cleave only one DNA strand at random as well as distant sites and also performs methylase activities. The target sequence is about 15 bp in length and cleaves non-specifically away from the recognition site. For catalytic activity, it requires Mg2+, ATP, and S-adenosyl – L- methionine. Examples – EcoK, EcoB.

Type II

This group comprises most orthodox restriction enzymes which are used in recombinant DNA technology. These enzymes are the most stable endonucleases which cleave DNA at specific sites. Thus, these generate desirable fragments of DNA. The recognition sequences are palindromic in nature of 4-8 bp and for catalytic activity, only Mg2+ ions are required. These enzymes can perform the nucleolytic activity only. Examples – Hinfl, EcoRI, PvuII, Alul, Haelll.

restriction enzyme example
Type II restriction enzyme
(EcoRI in cyan and green color with two magnesium ions in magenta color) From Wikipedia

Type III

This group is an intermediate type between type I and type II. The length of the recognition sequence is 24-26 bp. They require both Mg2+ and ATP for their activity and cleave DNA sequences in close vicinity of target sites. Eg. Hinf III, EcoP1.

Type IV

The target DNA for this group is different from the rest of the types. It recognizes modified DNA sequences such as methylated, hydroxy-methylated, and also glycosylated bases. Eg., McrBC.

Restriction enzyme nomenclature

Restriction enzymes have unique nomenclature. Each enzyme is named after the bacterium from where it is isolated. The name contains the genus, species, and the strain of the bacterium.

The nomenclature of restriction enzymes follows a pattern

1. The first capital letter is the name of the genus from which bacterium is discovered.

2. The first two letters of the species name are written after the first initial.

3. Next is the strain identified which is written in subscript.

4. The number of enzymes produced by the bacterium.

5. Generally all restriction enzymes are prefixed with the general symbol R. This is used to distinguish from the methylases that are obtained from the same strains.

Example:  EcoRI name

Abbreviation                                Meaning

E                                                       Escherichia genus

co                                                     coli species

R                                                       RY13 strain

I                                                        First identified order of identification in the bacterium

What is a restriction enzyme?

The term restriction enzyme was derived from the studies of lambda bacteriophages where it was observed that these bacterial protein enzymes cleave the phage DNA and thus, restrict the activity. The own target sites of the bacterial cell are high methylated i.e., the addition of methyl groups to the adenosine and cytosine bases within the recognition sites. This methylation protects from cleavage.

A restriction enzyme is an endonuclease that enables site-specific cleavage of DNA sequence. These sites are called restriction sites or recognition sequences or target sites. These are usually synthesized by bacteria for defense mechanisms against invading bacteriophages. The mechanism comprising methylation along with restriction enzyme activity constitutes the restriction-modification system.

restriction enzyme example
Palindrome sequence From Wikipedia

DNA strand contains two strands. 5’ end-3’ end depicts the forward strand while the 3’ end – 5’ end is denoted as a reverse strand. At first, restriction enzymes recognize the specific DNA sequences and then make two incisions on each strand of DNA sequence. This specific sequence is called recognition sites. The sequences of recognition sites are palindrome sequences which reads the same on forward and reverse strands when read in the same orientation. The recognition sequences usually contain 4-8 nucleotides, mostly palindromic in nature.

Restriction enzyme structure

The most convenient restriction endonuclease enzymes belong to the type II enzyme.

The recognition sites are typically a short palindromic sequence of 4-8 bp and catalytic activity requires Mg2+ ions. It consists of two homodimers each 30kDa molecular mass, that recognize the palindromic sequences. The structural core of these enzymes consists of four β-strands and one α-helix. For this nucleolytic activity, it doesn’t require ATP hydrolysis.

As restriction enzymes are target-specific, 15-20 hydrogen bonds are formed between the dimers and bases of the target site.  In addition to hydrogen bonds, Van der Waals interaction also takes place. Due to these interactions, the enzyme undergoes conformational change leading to the activation of the catalytic center of the restriction enzyme. The catalytic center contains two carboxylates which are necessary for the binding of cofactor Mg2+. The resultants of the catalysis are DNA fragments with 5’-P and 3’-OH.

Summary

Restriction enzyme is a site- specific endonuclease that cleaves DNA strands at specific recognition sites. These are synthesized by bacteria as a part of their defense mechanism. For its activity some requires magnesium ions while others required ATP and S-adenosyl – L- methionine. Due to its nucleolytic activity these enzymes are extensively used in recombinant DNA technology.

Paurabi Das

I am a doctoral student of CSIR- CIMAP, Lucknow. I am devoted to the field of plant metabolomics and environmental science. I have completed my graduation from the University of Calcutta with expertise in Molecular Plant Biology and Nanotechnology. I am an ardent reader and incessantly developing concepts in every niche of biological sciences. I have published research articles in peer-reviewed journals of Elsevier and Springer. Apart from academic interests, I am also passionate about creative things such as photography and learning new languages. Let’s connect over Linkedin https://www.linkedin.com/in/paurabi-das-cimap26/

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