17 Endonuclease Enzyme Example That You Should Know

Endonucleases are enzymes that break DNA into smaller fragments by cleaving the phosphodiester bond inside a polynucleotide chain. Let us see some of its examples.

  1. RecBCD endonuclease
  2. T7 endonuclease
  3. T4 endonuclease II
  4. Bal 31 endonuclease
  5. Endonuclease I
  6. Micrococcal nuclease
  7. Endonuclease II
  8. S1 nuclease
  9. P1-nuclease
  10. Mung bean nuclease I
  11. DNase I Enzyme (P00639)
  12. AP endonuclease
  13. BamHI 
  14. EcoRI 
  15. EcoRV 
  16. HindIII
  17. HaeIII

RecBCD endonuclease

RecBCD endonuclease is produced in E. coli cell. It is partially ATP-dependent and works in recombination and repair. The RecBCD enzyme performs the dual roles of a nuclease and a helicase, which deflates or separates the DNA strands and generates single-stranded nicks in the DNA.

T7 endonuclease (P00641)

Phage T7 (gene 3) is the source of T7 endonuclease enzyme. Replication requires DNA with a propensity for single strands over the double strands. An enzyme that particularly binds to and cleaves four-way (Holliday) DNA junctions following viral genomic replication to resolve junctions.

T4 endonuclease II (P07059)

Phage T4 (denA) is the source of T4 endonuclease II . The 5′-dCMP- ended oligonucleotides produced by this enzyme are split from the -TpC- sequence; the length of the product’s chain varies depending on the situation. Aids in the degradation of host DNA, enabling the creation of phage DNA by scavenging nucleotides from the host.

Bal 31 endonuclease

P. espejiana is the source of Bal 31 endonuclease . Additionally, the 3′ and 5′ ends of duplex DNA are altered by this endonuclease. At least two nucleases, combined with both fast and slow enzymes.

Endonuclease I (endo I; P25736)

E. coli (endA) is the source of Endonuclease I. Endo I mutants continue to develop properly despite being in the periplasm, exhibiting an average chain length of seven, would be inhibited by tRNA, causing double-stranded Dna adducts, and generating nicks when complexed with tRNA.

Micrococcal nuclease (P00644)             

Staphylococcus is the source of Micrococcal nuclease. Creates 3′-P termini, favors single-stranded DNA and AT-rich regions, requires calcium, and affects RNA. An enzyme that disintegrates the 5′ phosphodiester bonds in both DNA and RNA.

Endonuclease II (endo VI, exo III; P09030)

Coli (xthA) is the source of Endonuclease II. Near the cleavage site, there is also a 3′–>5′ exonuclease, and the 3′-P termini have phosphomonoesterase. The primary RE in E. coli is apurinic-apyrimidinic endonuclease.

S1 nuclease (P24021)

Aspergillus oryzae is the source. RNA is also affected. Only degrades single-stranded DNA and RNA; no apparent preference for bases. The end products of endonucleolytic cleavage are 5′ -phosphomononucleotide and 5′-phosphooligonucleotide.

P1-nuclease (P24289)

Penicillium citrinum is the source. RNA is also affected. Only degrades single-stranded DNA and RNA; no apparent preference for bases. End-products produced by endonucleolytic cleavage include 5′-phosphomononucleotide and 5′-phosphooligonucleotide.

Mung bean nuclease I

Mung bean sprouts is the source. RNA is also affected. However, double-stranded DNA, DNA/RNA hybrids, or double-stranded RNA are not broken down by the enzyme. It only produces nucleoside 5′-monophosphates when single-stranded DNA or RNA is broken down.

DNase I Enzyme (P00639)

Bovine pancreas is the source. The product has a four-link chain on average, and Mn2+ results in a double strand break. Serum endonuclease is produced by numerous exocrine and endocrine organs and is found in bodily fluids.

AP endonuclease

Nucleus and mitochondria are the sources. It involves the DNA Base Excision Repair pathway. The DNA-BER uses the AP endonuclease enzyme (base excision repair pathway).


BamHI, a type II restriction endonuclease generated by Bacillus amyloliquefaciens, can detect short (6 bp) DNA sequences and cut them precisely at a target location.


EcoRI is a restriction endonuclease enzyme that is a component of the restriction modification system and breaks down DNA double helices into fragments at certain locations.


EcoRV is a type II restriction endonuclease that goes by the name Eco32I. It is an extensively utilized restriction enzyme in molecular biology.


The Haemophilus influenzae type II site-specific deoxyribonuclease restriction enzyme hydrolyzes the cofactor Mg2+ to break the DNA palindromic sequence, AAGCTT.

Image Credits: HindIII Restriction Site by Helixitta (CC BY-SA 4.0)


HaeIII is an endonucleases that shields organisms from unidentified, external DNA. It is utilized in molecular biology labs. It was the third endonuclease discovered in the bacteria Haemophilus aegyptius


Enzymes called endonucleases breakdown the phosphodiester bond found in polynucleotide chains. While many DNA-cutting enzymes cleave at extremely specific nucleotide sequences, others, such as deoxyribonuclease I, break DNA somewhat randomly (without regard to sequence).

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