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a nuclease that cleaves nucleic acids at interior bonds and so produces fragments of various sizes

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2014/12/18 09:52:39」(JST)

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Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as Deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences.^[1]

Restriction enzymes are endonucleases from eubacteria and archea that recognize a specific DNA sequence.^[2] The nucleotide sequence recognized for cleavage by a restriction enzyme is called the restriction site. Typically, a restriction site will be a palindromic sequence of about four to six nucleotides long. Most restriction endonucleases cleave the DNA strand unevenly, leaving complementary single-stranded ends. These ends can reconnect through hybridization and are termed "sticky ends". Once paired, the phosphodiester bonds of the fragments can be joined by DNA ligase. There are hundreds of restriction endonucleases known, each attacking a different restriction site. The DNA fragments cleaved by the same endonuclease can be joined together regardless of the origin of the DNA. Such DNA is called recombinant DNA; DNA formed by the joining of genes into new combinations.^[3] Restriction endonucleases (restriction enzymes) are divided into three categories, Type I, Type II, and Type III, according to their mechanism of action. These enzymes are often used in genetic engineering to make recombinant DNA for introduction into bacterial, plant, or animal cells, as well as in synthetic biology.^[4]^:375–390

Notations

The commonly used notation for restriction endonucleases is of the form "vwxyz", where "vwx" names the life form (bacteria) where this restriction endonuclease may be found, "y" names the strain (and is optional), and "z" (in Roman numerals) indicates different restriction endonucleases in the same life form (bacteria). Thus for example, "EcoRI" means that the restriction endonuclease is found in Escherichia coli ("Eco"); strain RY13 ("R"), restriction endonuclease number "I". Another example: "HaeII" and "HaeIII" refer to bacterium Haemophilus aegyptius, number II and number III, respectively.^[5]^:64-64 The restriction enzymes used in molecular biology usually recognize short target sequences of about 4 – 8 base pairs. For instance, the EcoRI enzyme recognizes and cleaves the sequence 5' – GAATTC – 3'.^[6]

Restriction enzyme Eco RI

Restriction endonucleases come in several types. A restriction endonuclease typically requires a recognition site and a cleavage pattern (typically of nucleotide bases: A, C, G, T). If the recognition site is outside the region of the cleavage pattern, then the restriction endonuclease is referred to as Type I. If the recognition sequence overlaps with the cleavage sequence, then the restriction endonuclease restriction enzyme is Type II.

Further discussions

Restriction endonucleases may be found that cleave standard dsDNA (double-stranded DNA), or ssDNA (single-stranded DNA), or even RNA. This discussion is restricted to dsDNA, however, the discussion can be extended to the following:

Standard dsDNA
Non-standard DNA

Holliday junctions Holliday junction
Triple-stranded DNA, quadruple-stranded DNA (G-quadruplex)
Double-stranded hybrids of DNA and RNA (one strand is DNA, the other strand is RNA)^[5]^:72–73
Synthetic or artificial DNA (for example, containing bases other than A, C, G, T, refer to the work of Eric T. Kool). Research with synthetic codons, refer to the research by S. Benner, and enlarging the amino acid set in polypeptides, thus enlarging the proteome or proteomics, see the research by P. Schultz.^[5]^{:chapter 3}

In addition, research is now underway to construct synthetic or artificial restriction endonucleases, especially with recognition sites that are unique within a genome.

Restriction endonucleases or restriction enzymes typically cleave in two ways: blunt-ended or sticky-ended patterns. An example of a Type I restriction endonuclease.^[5]^:64

DNA repair

Endonucleases play a role in DNA repair. AP endonuclease, specifically, catalyze the incision of DNA exclusively at AP sites, and therefore prepare DNA for subsequent excision, repair synthesis and DNA ligation. For example, when depurination occurs, this lesion leaves a deoxyribose sugar with a missing base.^[7] The AP endonuclease recognizes this sugar and essentially cuts the DNA at this site and then allows for DNA repair to continue.^[8] E. coli cells contain two AP endonucleases: endonuclease IV (endoIV) and exonuclease III (exoIII). While in Eukaryotes, there is only one AP endonuclease.^[9]

Common endonucleases

Below are tables of common prokaryotic and eukaryotic endonucleases.^[10]

Prokaryotic Enzyme	Source	Comments
RecBCD enonuclease	E. coli	Partially ATP dependent; also an exonuclease; functions in recombination and repair
T7 endonuclease	phage T7 encoded (gene 3)	Essential for replication; preference for single stranded over double stranded DNA
T4 endonuclease IV	phage T4 encoded (denA)	Splits -TpC- sequence to yield 5'-dCMP- terminated oligonucleotides; chain length of product varies with conditions
Bal 31 endonuclease	Alteromonas espejiana	Also an exonuclease; nibbles away 3' and 5' ends of duplex DNA
EndonucleaseI (endo I)	E. coli (endA)	Periplasmic location; average chain length of product is 7; inhibited by tRNA; produces double stranded DNA break; proudces nick when complexed with tRNA; endo I mutants grow normally
Micrococcal nuclease	Staphylococcus	Produces 3'-P termini; requires Ca2+; also acts on RNA; prefers single stranded DNA and AT-rich regions
Endonuclease II (endo VI, exo III)	E. coli (xth)	Cleavage next to AP site; also a 3'-->5' exonuclease; phosphomonoesterase on 3'-P termini

Eukaryotic Enzyme	Source	Comments
Neurospora endonuclease	Neurospora crassa	Also acts on RNA
S1-nuclease	Aspergillus oryzae	Also acts on RNA
P1-nuclease	Penicillium citrinum	Also acts on RNA
Mung bean nuclease I	mung bean sprouts	Also acts on RNA
Ustilago nuclease (Dnase I)	Ustilago maydis	Also acts on RNA
Dnase I	Bovine pancreas	Average chain length of product is 4; produces double strand break in presence of Mn2+
AP endonuclease	Nucleus, mitochondria	Involved in DNA Base Excision Repair pathway
Endo R	HeLa cells	Specific for GC sites

Mutations

Xeroderma pigmentosa is a rare, autosomal recessive disease caused by a defective UV-specific endonuclease. Patients with mutations are unable to repair DNA damage caused by sunlight.^[11]

Sickle Cell anemia is a disease caused by a point mutation. The sequence altered by the mutation eliminates the recognition site for the restriction endonuclease MstII that recognizes the nucleotide sequence.^[12]

tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia. Pontocerebellar hypoplasias (PCH) represent a group of neurodegenerative autosomal recessive disorders that is caused by mutations in three of the four different subunits of the tRNA-splicing endonuclease complex.^[13]

References

^ Cox M, Nelson DR, Lehninger AL (2005). Lehninger principles of biochemistry. San Francisco: W.H. Freeman. p. 952. ISBN 0-7167-4339-6.
^ Stephen T. Kilpatrick; Jocelyn E. Krebs; Lewin, Benjamin; Goldstein, Elliott (2011). Lewin's genes X. Boston: Jones and Bartlett. ISBN 0-7637-6632-1.
^ Cox M, Nelson DR, Lehninger AL (2005). Lehninger principles of biochemistry. San Francisco: W.H. Freeman. p. 307. ISBN 0-7167-4339-6.
^ Simon M (2010). Emergent computation: Emphasizing Bioinformatics. New York: Springer. p. 437. ISBN 1441919635.
^ ^a ^b ^c ^d ^e Cox M, Nelson DR, Lehninger AL (2005). Lehninger principles of biochemistry. San Francisco: W.H. Freeman. p. 1100. ISBN 0-7167-4339-6.
^ Losick R, Watson JD, Baker TA, Bell S, Gann S, Levine MW (2008). Molecular biology of the gene. San Francisco: Pearson/Benjamin Cummings. ISBN 0-8053-9592-X.
^ Ellenberger T, Friedberg EC, Walker GS, Wolfram S, Wood RJ, Schultz R (2006). DNA repair and mutagenesis. Washington, D.C: ASM Press. ISBN 1-55581-319-4.
^ Alberts B (2002). Molecular biology of the cell. New York: Garland Science. ISBN 0-8153-3218-1.
^ Nishino T, Morikawa K (December 2002). "Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors". Oncogene 21 (58): 9022–32. doi:10.1038/sj.onc.1206135. PMID 12483517.
^ Tania A. Baker; Kornberg, Arthur (2005). DNA replication. University Science. ISBN 1-891389-44-0.
^ Medical Biochemistry at a Glance. New York: Wiley. 2012. ISBN 0-470-65451-1.
^ Ferrier DR, Champe PC, Harvey RP (2008). Biochemistry. Philadelphia: Wolters Kluwer/Lippincott Williams & Wilkins. ISBN 0-7817-6960-4.
^ Budde BS, Namavar Y, Barth PG, Poll-The BT, Nürnberg G, Becker C, van Ruissen F, Weterman MA, Fluiter K, te Beek ET, Aronica E, van der Knaap MS, Höhne W, Toliat MR, Crow YJ, Steinling M, Voit T, Roelenso F, Brussel W, Brockmann K, Kyllerman M, Boltshauser E, Hammersen G, Willemsen M, Basel-Vanagaite L, Krägeloh-Mann I, de Vries LS, Sztriha L, Muntoni F, Ferrie CD, Battini R, Hennekam RC, Grillo E, Beemer FA, Stoets LM, Wollnik B, Nürnberg P, Baas F (September 2008). "tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia". Nat. Genet. 40 (9): 1113–8. doi:10.1038/ng.204. PMID 18711368.

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English Journal

Microarray-based fluorescence assay of endonuclease functionality and inhibition.

Ma L, Su M, Li T, Wang Z.SourceState Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. wangzx@ciac.jl.cn.
The Analyst.Analyst.2013 Jan 3. [Epub ahead of print]
Here, a double-strand (ds) DNA microarray-based fluorescence assay has been deployed for studying endonuclease functionality and inhibition. The dsDNA microarrays are fabricated by hybridization of the Cy5-labeled oligonucleotides with the immobilized complementary oligonucleotide probes on the glas
PMID 23282850

Endonuclease-responsive aptamer-functionalized hydrogel coating for sequential catch and release of cancer cells.

Li S, Chen N, Zhang Z, Wang Y.SourceProgram of Biomedical Engineering, School of Engineering, University of Connecticut, Storrs, CT 06269-3222, USA.
Biomaterials.Biomaterials.2013 Jan;34(2):460-9. doi: 10.1016/j.biomaterials.2012.09.040. Epub 2012 Oct 17.
Rare circulating tumor cells are a promising biomarker for the detection, diagnosis, and monitoring of cancer. However, it remains a challenge to develop biomedical devices for specific catch and nondestructive release of circulating tumor cells. The purpose of this study was to explore a unique sys
PMID 23083933

Japanese Journal

Prospecting cold deserts of north western Himalayas for microbial diversity and plant growth promoting attributes(ENVIRONMENTAL BIOTECHNOLOGY)

Journal of bioscience and bioengineering 119(6), 683-693, 2015-06
NAID 110009970759

マウス個体でのゲノム編集(1)効率よく正確なゲノム改変を施すには (AYUMI ゲノム編集 : 基礎から応用へ)

医学のあゆみ 252(2), 159-163, 2015-01-10
NAID 40020320282

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