A nuclease is an enzyme capable of cleaving the phosphodiester bond s between the nucleotide subunits of nucleic acid s. Older publications may use terms such as polynucleotidase or nucleodepolymerase . ref Avery, O.T., MacLeod, C.M., McCarty, M. 1944 . Studies on the chemical nature of the substance inducing transformation of pneumococcal types Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus type III. J. Exp. Med. 79 137 158. ref Nucleases are usually further divided into endonuclease s and exonuclease s, although some of the enzymes may fall in both categories. Introduction In the late 1960s, scientists Stuart Linn and Werner Arber isolated examples of the two types of enzymes responsible for phage growth restriction in Escherichia coli E. coli bacteria. ref Linn S., Arber, W. 1968 . Host specificity of DNA produced by Escherichia coli, X. In vitro restriction of phage fd replicative form. Proc. Natl. Acad. Sci. USA. 59 1300 1306 ref ref Arber ... type of enzyme was called a methylase and the other a restriction nuclease . These enzymatic tools ... way. Site specific nuclease Structure specific nuclease For details see flap endonuclease . Sequence specific nuclease This important development came when H.O. Smith, K.W. Wilcox, and T.J. Kelley ... nuclease whose functioning depended on a specific DNA nucleotide sequence. Working with Haemophilus ... strain Rd. Numbers following the nuclease names indicate the order in which the enzymes were ... that break nucleic acid chains somewhere in the interior, rather than at the ends, of the molecule. A nuclease .... For example, the nuclease EcoRI has the following recognition sequence class wikitable Enzyme Source ... has given birth to the genetic engineering technology. See also Nuclease protection assay Micrococcal nuclease S1 nuclease P1 nuclease HindIII PIN domain References reflist External links http www.accessexcellence.org ... Nukleasen fr Nucl ase it Nucleasi he nl Nuclease ja oc Nucleasa pl Nukleazy pt Nuclease ... more details
P1 nuclease is a nuclease that works on single stranded DNA as well as RNA. P1 nuclease cleaves at every position yielding nucleoside 5 monophosphates. It is useful at removing single stranded strands hanging off the end of double stranded DNA and at completely cleaving melted DNA for simple DNA composition analysis. The enzyme does not recognize or act on double stranded DNA. enzyme stub Category Enzymes ... more details
Unreferenced stub auto yes date December 2009 S1 nuclease is an endonuclease that is active against single stranded DNA and RNA molecules. It is five times more active on DNA than RNA. Its reaction products are oligonucleotide s or single nucleotide s with 5 phosphorylation phosphoryl groups. Although its primary substrate is single stranded, it can also occasionally introduce single stranded breaks in double stranded DNA or RNA, or DNA RNA hybrids. It is used in the laboratory as a reagent in nuclease protection assay s. In molecular biology, it is used in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA. DEFAULTSORT S1 Nuclease Category Enzymes Enzyme stub ... more details
infobox enzyme Name Micrococcal nuclease EC number 3.1.31.1 CAS number 9013 53 0 IUBMB EC number 3 1 31 1 GO code image Staph nuclease 3h6m ribbon.jpg width caption Ribbon schematic of micrococcal nuclease 3D structure, with Ca sup 2 sup and TdtP inhibitor Micrococcal Nuclease S7 Nuclease or MNase is an endonuclease endo exonuclease that preferentially digests single stranded nucleic acids .The rate of cleavage is 30 times greater at the 5 side of A or T than at G or C and results in the production of mononucleotides and oligonucleotides with terminal 3 phosphates . The enzyme is also active against double stranded DNA and RNA and all sequences will be ultimately cleaved. Characteristics The enzyme has a molecular weight of 16.9kDa. The pH optimum is reported as 9.2. The enzyme activity is strictly dependent on Ca sup 2 sup and the pH optimum varies according to Ca sup 2 sup concentration. ref cite journal author Heins JN, Suriano JR, Taniuchi H, Anfinsen CB title Characterization of a nuclease produced by Staphylococcus aureus journal J. Biol. Chem. volume 242 issue 5 pages 1016 20 year 1967 pmid 6020427 doi ref The enzyme is therefore easily inacitvated by EGTA chemical EGTA . Source This enzyme is the extracellular nuclease of Staphylococcus aureus . Two strains, V8 and Foggi, yield almost identical enzymes. ref cite journal author Cusumano CL, Taniuchi H, Anfinsen CB title Staphylococcal nuclease Foggi strain . I. Order of cyanogen bromide fragments and a fourth histidine ... extracellular nuclease micrococcal nuclease . Structure The 3 dimensional structure of micrococcal nuclease then called Staphyloccal nuclease was solved very early in the history of protein x ray crystallography ... Resolution Structure of an Inhibitor Complex of the Extracellular Nuclease of Staphylococcus aureus ... diagram above, the nuclease molecule has 3 long alpha helix alpha helices and a 5 stranded, barrel shaped ... 22 A material and safety data sheet for the product External links MeshName Micrococcal Nuclease EC ... more details
Orphan date February 2009 Chimeric nucleases are an example of Protein engineering engineered proteins which must comprise a DNA binding domain to give sequence specificity and a nuclease domain for DNA cleavage. DNA binding domains details DNA binding domain DNA binding domains including the basic helix loop helix , zinc finger , helix turn helix and leucine zipper motifs have been used in construction of sequence specific nucleases. Of these, zinc fingers have been suggested the most important due to their modularity, allowing construction of a tailor made DNA binding domain. ref name durai2005 cite journal author Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, Chandrasegaran S title Zinc finger nucleases custom designed molecular scissors for genome engineering of plant and mammalian cells journal Nucleic Acids Res. volume 33 issue 18 pages 5978 90 year 2005 pmid 16251401 doi 10.1093 nar gki912 url http nar.oxfordjournals.org cgi pmidlookup?view long&pmid 16251401 pmc 1270952 ref Nuclease domain details Nuclease The nuclease domain is responsible for physical cleavage of DNA strands and may introduce either single stranded or double stranded breaks. FokI is an example of a sequence specific endonuclease whose non specific nuclease domain introduces double stranded breaks and has been used in a variety of experiments including identification of high and low affinity binding sites of transcription factors in vitro , to study recruitment of factors to promoter sites in vivo using protein position identification with a nuclease tail assay and to study proteins specific to interaction with DNA in the Z DNA conformation Durai et al., 2005 and references therein . See also DNA binding domain Nuclease Protein engineering Chimera protein References references Category Engineered proteins Category Protein engineering Category Genetics experiments hydrolase stub ... more details
Orphan date April 2010 Mung bean nuclease is a nuclease derived from mung bean s that removes nucleotides in a step wise manner from single stranded DNA molecules and is used to remove such ssDNA from a mixture also containing double stranded DNA dsDNA . Mungbean Nuclease is a singlestrand specific nuclease purified from sprouts of mung bean Vigna radiata. The enzyme degrades single stranded DNA or RNA to nucleoside 5 monophosphates, but does not digest double stranded DNA, double stranded RNA, or DNA RNA hybrids. Mung Bean Nuclease catalyzes the specific degradation of single stranded DNA or RNA, and produces mono and oligonucleotides carrying a 5 P terminus. Mung bean exonuclease is a nuclease derived from mung beans that removes nucleotides in a step wise manner from single stranded DNA ... . Molecular Weight Theoretical 39 kDa Mung bean nuclease has a stringent single stranded specificity ... by the restriction enzymes etc. Mung bean nuclease requires Zn2 . The addition of EDTA or SDS causes irreversible inactivation. Do not use at pH below 4.6. Mung bean nuclease should not be used at low .... Mung Bean Nuclease is a single strand specific nuclease purified from sprouts of the mung bean Vigna radiata . Because Mung Bean Nuclease has higher specificity for ssDNA and RNA than S1 Nuclease, it is the enzyme of choice for most applications requiring a single strand specific nuclease . Unlike S1 nuclease S1 Nuclease , Mung Bean Nuclease will not cleave the intact strand of nicked duplex DNA ... at ApN and at T U pN. It completely degrades ApA, but does not degrade G and C. Unlike S1 Nuclease, it does not cleave the strand opposite to that which has been nicked. Mung Bean Nuclease catalyzes .... Mung bean exonuclease is a nuclease derived from mung beans that removes nucleotides in a step wise ... double stranded DNA dsDNA . Unit Definition One unit of Mung Bean Nuclease converts 1 ... 1 Nuclease in TILLING. Unidirectional deletion of large DNA in combination with Exonuclease III ... more details
Orphan date April 2011 Crab duplex specific nuclease is a nuclease derived from Paralithodes camtschaticus kamchatka crab hepatopancreas that displays a strong preference for cleaving double stranded DNA and DNA in DNA RNA hybrid duplexes, compared to single stranded DNA. Moreover, the cleavage rate of short, perfectly matched DNA duplexes by this enzyme is essentially higher than that for non perfectly matched duplexes of the same length. It has been applied to Single nucleotide polymorphism SNP detection ref name pmid12466298 cite journal last Shagin first DA coauthors Rebrikov, DV, Kozhemyako, VB, Altshuler, IM, Shcheglov, AS, Zhulidov, PA, Bogdanova, EA, Staroverov, DB, Rasskazov, VA, Lukyanov, S title A novel method for SNP detection using a new duplex specific nuclease from crab hepatopancreas journal Genome Research date 2002 Dec volume 12 issue 12 pages 1935 42 pmid 12466298 doi 10.1101 gr.547002 pmc 187582 ref and RNA normalization. ref name pmid21472699 cite journal last Christodoulou first DC coauthors Gorham, JM, Herman, DS, Seidman, JG title Construction of Normalized RNA seq Libraries for Next Generation Sequencing Using the Crab Duplex Specific Nuclease journal Current Protocols in Molecular Biology date 2011 Apr volume Chapter 4 pages Unit 4.12 pmid 21472699 doi 10.1002 0471142727.mb0412s94 pmc 3152986 ref References Reflist Category King crabs Category EC 3.1 enzyme stub ... more details
Nuclease protection assay is a laboratory technique used in biochemistry and genetics to identify individual RNA molecules in a heterogeneous RNA sample extracted from cell biology cells . The technique can identify one or more RNA molecules of known sequence even at low total concentration . The extracted RNA is first mixed with antisense RNA or DNA probes that are complementary to the sequence or sequences of interest and the complementary strands are Hybridisation molecular biology hybridized to form double stranded RNA or a DNA RNA hybrid . The mixture is then exposed to ribonuclease s that specifically cleave only single stranded RNA but have no activity against double stranded RNA. When the reaction runs to completion, susceptible RNA regions are degraded to very short oligomer s or to individual nucleotide s the surviving RNA fragments are those that were complementary to the added antisense strand and thus contained the sequence of interest. Probe The probes are prepared by cloning part of the gene of interest in a vector under the control of any of the following promoters, SP6, T7 or T3. These promoters are recognized by DNA dependent RNA polymerases originally characterized from bacteriophages. The probes produced are radioactive as they are prepared by in vitro transcription using radioactive UTPs. Uncomplemented DNA or RNA is cleaved off by nucleases. When the probe is a DNA molecule, S1 nuclease is used when the probe is RNA, any single strand specific ribonuclease can be used. Thus the surviving probe mRNA complement is simply detected by autoradiography. Uses Nuclease protection assays are used to map intron s and 5 end 5 and 3 end 3 ends of transcribed gene ..., but also produces accurate information about the size of the target RNA. Nuclease protection assay ... RNA during the nuclease digestion step. References http www.nature.com nrg journal v8 n6 abs nrg2026.html ... Molecular biology techniques biochem stub th Nuclease protection assay ... more details
and specificity of the nuclease domain used in ZFNs. Directed evolution has been employed to generate ... is still a significant concern. ref Zinc finger Nuclease induced Gene Repair With Oligodeoxynucleotides ... more details
Transcription Activator Like Effector Nuclease s TALENs are artificial restriction enzyme s generated by fusing the TAL effector DNA binding domain to a DNA cleavage domain. Use These reagents enable efficient, programmable, and specific DNA cleavage and represent powerful tools for genome editing in situ . Synthetic transcription factors using TALE domain constructs can also be used for gene regulation by pairing the TALE DNA binding domain with an endogenous activation domain affecting expression at specific sites in complex genomes. ref name Morbitzer2010 Cite doi 10.1073 pnas.1013133107 ref ref name Miller2011 cite journal last Miller first Jeffrey coauthors et.al. title A TALE nuclease architecture for efficient genome editing journal Nature Biotechnology year 2011 month February volume 29 issue 2 pages 143 8 doi 10.1038 nbt.1755 pmid 21179091 ref ref name Zhang2011 cite journal last Zhang first Feng coauthors et.al. title Efficient construction of sequence specific TAL effectors for modulating mammalian transcription journal Nature Biotechnology year 2011 month February volume 29 issue 2 pages 149 53 doi 10.1038 nbt.1775 pmid 21248753 pmc 3084533 ref ref name Geissler2011 Cite doi 10.1371 journal.pone.0019509 ref Transcription activator like effectors TALEs can be quickly engineered to bind practically any DNA sequence. ref name Boch2011 cite journal last Boch first Jens title TALEs of genome targeting journal Nature Biotechnology year 2011 month February volume 29 issue 2 pages 135 6 doi 10.1038 nbt.1767 pmid 21301438 ref DNA binding domain TAL effector s are proteins ... from the end of the FokI endonuclease can be used to construct hybrid nuclease s that are active in a yeast ... engineered transcription activator like effector TALE hybrid nuclease with novel DNA binding specificity ..., target gene, and nuclease used, it should be monitored when designing new systems. A simple heteroduplex ... Cite doi 10.1038 nbt.1934 ref . See also Genome editing with engineered nucleases Zinc finger nuclease ... more details
ZFN is an acronym that may refer to Tulita Airport , an airport in Canada Zinc finger nuclease , a nuclease enzyme coupled to a zinc finger based DNA binding domain The Zero Configuration File Network , an open source network program disambig it ZFN ... more details
Unreferenced date December 2009 Orphan date February 2009 An HMG protein is a proteins involved with chromatin structure. They endow the chromosome with nuclease sensitivity. They also recruit transcription factor s to bind to Enhancer genetics enhancers . See High mobility group DEFAULTSORT Hmg Protein Category Proteins Protein stub ... more details
Endodeoxyribonucleases are enzymes which are both deoxyribonuclease s and endonuclease s. They are classified with Enzyme Commission number EC numbers 3.1.21 through 3.1.25. Examples include restriction enzymes DNA restriction enzymes micrococcal nuclease External links MeshName Endodeoxyribonucleases Category EC 3.1 enzyme stub ... more details
Unreferenced date December 2009 Hamilton O. Smith H.O. Smith , K.W. Wilcox, and T.J. Kelley, working at Johns Hopkins University in 1968, isolated and characterized the first restriction nuclease whose functioning depended on a specific DNA nucleotide sequence. Citation needed date September 2011 Working with Haemophilus influenzae bacteria, this group isolated an enzyme , called HindII, that always cut DNA molecules at a particular point within a specific sequence of six base pairs. Citation needed date September 2011 This sequence is 5 G T pyrimidine T or C purine A or G A C 3 P3 C A purine A or G pyrimidine T or C T G 5 They found that the HindII enzyme always cuts directly in the center of this sequence. Citation needed date September 2011 Wherever this particular sequence of six base pairs occurs unmodified in a DNA molecule, HindII will cleave both DNA backbones between the 3rd and 4th base pairs of the sequence. Moreover, HindII will only cleave a DNA molecule at this particular site. For this reason, this specific base sequence is known as the recognition sequence for HindII. See also Nuclease HindIII DEFAULTSORT Hindii Category Molecular biology Category Biotechnology Category Restriction enzymes Category EC 3.1 es HindII ... more details
Orphan date February 2009 A hypersensitive site is a short region of chromatin and is detected by its super sensitivity to cleavage by DNase I and other various nuclease s DNase II and micrococcal nuclease s . In a hypersensitive site, the nucleosomal structure is not organized in the usual fashion, which results in a 100 fold increase in sensitivity to enzyme attack than in bulk chromatin . Location Hypersensitive sites are found on every active gene, and many of these genes often have more than one hypersensitive site. Most often, hypersensitive sites are found only in chromatin of cells in which the associated gene is being expressed, and do not occur when the gene is inactive. In DNA being transcribed, 5 hypersensitive sites appear before transcription begins, and the DNA sequences within the hypersensitive sites are required for gene expression . Note hypersensitive sites precede active promoter s. Hypersensitive sites are generated as a result of the binding of transcription factor s that displace histone octamer s. They can also be located by indirect end labelling. A fragment of DNA is cut once at the hypersensitive site with Deoxyribonuclease DNase and at another site with a restriction enzyme . The distance from the known restriction site to the DNase cut is then measured to give the location. Category Genetics Category Molecular biology biochem stub ... more details
The CompoZr Zinc finger nuclease ZFN platform is a technology developed by Sigma Aldrich that allows researchers to target and manipulate the genome of living cells thereby creating cell lines or entire organisms with permanent and heritable gene deletions, insertions, or modifications. The technology was released in September 2008 ref cite web url http www.compozrzfn.com NewsDetail.aspx?id 17 title Sigma Aldrich Launches Breakthrough Genome Editing Tools ref . In December 2008, CompoZr ZFN Technology ranked third in The Scientist Magazine s Top Ten Innovations of 2008 ref cite web url http www.the scientist.com 2008 12 1 45 1 title The Scientist Top Ten Innovations of 2008 ref . In July 2009, the first genetically modified mammal was created through the use of CompoZr ZFN Technology ref cite web url http www.compozrzfn.com NewsDetail.aspx?id 20 title Researchers Create First Targeted Knockout Rats Using Zinc Finger Nuclease Technology ref . References reflist External links http www.compozrzfn.com Default.aspx CompoZr Homepage http www.compozrzfn.com Articles.aspx CompoZr Publications Category Engineered proteins Category Zinc proteins ... more details
Multiple issues unreferenced May 2009 orphan February 2009 context July 2009 First developed in the Barbara Ramsay Shaw Shaw lab in 1990, boranophosphates have great potential as therapeutic and diagnostic agent s, as the modification confers many unique properties. Sood 1990 The boranophosphate resembles the normal phosphate in that the negative charge is retained however, the polarity of the molecule changes because the negative charge is localized on the remaining non bridging oxygen . He 1998 Partitioning experiments have demonstrated that boranophosphates are more lipophilic than normal phosphates Shaw 2000 this could allow for increased cellular uptake and targeted delivery. In addition, boranophosphates have increased nuclease resistance without affecting activation of RNase H cleavage of RNA in RNA boranophosphate hybrids. Shaw 2000 Category Phosphates ... more details
Unreferenced stub auto yes date December 2009 Excision endonuclease , also known as excinuclease or UV Specific Endonuclease , is a nuclease enzyme which excises a fragment of nucleotides during DNA repair . The excinuclease cuts out a fragment by hydrolyzing two phosphodiester bonds, one on either side of the lesion in the DNA. This process is part of nucleotide excision repair , a mechanism that can fix specific damages to the DNA in the G1 phase of the eukaryotic cell cycle . Such damages can include the thymine dimers created by UV rays. A deficiency of excinuclease occurs in a rare autosomal recessive disease called xeroderma pigmentosum . Diagnosis of this disease is done by measuring the enzyme s level in white blood cells in a blood sample. Symptoms in children include extreme ultraviolet UV sensitivity, excessive freckle freckling , multiple skin cancer s and corneal ulcer ations. Typically, these symptoms are seen during a child s first sun exposure. Citation needed date November 2009 Category DNA repair Enzyme stub ca escinucleasa es escinucleasa ... more details
reveals fusion of a specific DNA binding domain with a nonspecific nuclease journal Proc. Natl. Acad ... domain The C terminal nuclease catalytic domain has a typical ref name pmid17369272 cite journal ... terminal domains. ref name Zhou 2004 See also EcoRI , another nuclease enzyme from Escherichia coli . EcoRV , another nuclease enzyme from Escherichia coli . B3 DNA binding domain from higher plants is evolutionary related to EcoRII BamHI , another nuclease enzyme from Bacillus amyloliquefaciens . HindIII , another nuclease enzyme from Haemophilus influenzae . HaeIII , another nuclease enzyme from Haemophilus aegyptius . TaqI , another nuclease enzyme from Thermus aquaticus . FokI , another nuclease ... Nuclease ru uk zh ... more details
domain. ref name Wah 1998 Activity When the nuclease is unbound to DNA, the endonuclease domain ... combination with a variety of DNA binding domains such as the zinc finger see zinc finger nuclease ... Zinc finger nuclease Category Bacterial enzymes Category Restriction enzymes es FokI pl FokI ... more details
also EcoRI , another nuclease enzyme from E. coli . EcoRII , another nuclease enzyme from E. coli . FokI , a nuclease enzyme from Flavobacterium okeanokoites References references Category EC 3.1.21 ... more details
A degradative enzyme is an enzyme in a broader sense a protein which degrades biological molecules . Some examples of degradative enzymes Lipase , which digests lipid s, ref cite journal author Svendsen A title Lipase protein engineering journal Biochim Biophys Acta volume 1543 issue 2 pages 223 228 year 2000 pmid 11150608 doi 10.1016 S0167 4838 00 00239 9 ref Carbohydrase s, which digest carbohydrate s e.g., sugars , ref cite journal journal Science year 1957 volume 125 issue 3236 pages 12 15 doi 10.1126 science.125.3236.12 title Mechanism of Carbohydrase Action url http www.sciencemag.org content 125 3236 12.short ref Protease s, which digest protein s, ref Barrett A.J., Rawlings ND, Woessner JF. The Handbook of Proteolytic Enzymes , 2nd ed. Academic Press, 2003. ISBN 0 12 079610 4. ref ref Hedstrom L. Serine Protease Mechanism and Specificity. Chem Rev 2002 102 4501 4523. ref Nuclease s, which digest nucleic acid s. References reflist 2 See also Hydrolase DEFAULTSORT Degradative Enzyme Category Enzymes Enzyme stub sr Degradativni enzim ... more details
automatic taxobox Syncephalastrum racemosum is a filamentous fungus. ref name pmid8489265 cite journal author Chen LY, Ho HC, Tsai YC, Liao TH title Deoxyribonuclease of Syncephalastrum racemosum enzymatic properties and molecular structure journal Arch. Biochem. Biophys. volume 303 issue 1 pages 51 6 year 1993 month May pmid 8489265 doi 10.1006 abbi.1993.1254 url http linkinghub.elsevier.com retrieve pii S0003 9861 83 71254 3 ref ref name pmid10191256 cite journal author Ho HC, Liao TH title Protein structure and gene cloning of Syncephalastrum racemosum nuclease journal Biochem. J. volume Pt 2 issue pages 261 7 year 1999 series 339 month April pmid 10191256 pmc 1220154 doi url http www.biochemj.org bj 339 0261 bj3390261.htm ref Clinical significance It can cause nail disease, ref name pmid16638375 cite journal author Pavlovi MD, Bulaji N title Great toenail onychomycosis caused by Syncephalastrum racemosum journal Dermatol. Online J. volume 12 issue 1 pages 7 year 2006 pmid 16638375 doi url http dermatology.cdlib.org 121 case reports syncephalastrum pavlovic.html ref especially in damaged nails. References Reflist Category Zygomycota Fungus stub Mycoses ja ... more details
Orphan date August 2011 Infobox protein family Symbol Endonuclease NS Name Endonuclease NS image PDB 1smn EBI.jpg width caption identification of the serratia endonuclease dimer structural basis and implications for catalysis Pfam PF01223 Pfam clan CL0263 InterPro IPR001604 SMART PROSITE PDOC00821 MEROPS SCOP 1smn TCDB OPM family OPM protein CAZy CDD In molecular biology, enzymes in the DNA RNA non specific endonuclease family of bacteria l and eukaryotic endonucleases EC number 3.1.30. share the following characteristics they act on both DNA and RNA , bond cleavage cleave double stranded and single stranded nucleic acid s and require a divalent ion such as magnesium for their activity. A histidine has been shown to be essential for the activity of the Serratia marcescens nuclease . This residue chemistry residue is located in a conserved sequence conserved region which also contains an aspartic acid residue that could be implicated in the binding of the divalent ion. ref name pmid8078761 cite journal author Friedhoff P, Gimadutdinow O, Pingoud A title Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment guided mutagenesis journal Nucleic Acids Res. volume 22 issue 16 pages 3280 7 year 1994 month August pmid 8078761 pmc 523719 doi 10.1093 nar 22.16.3280 url ref References reflist InterPro content IPR001604 Category Protein domains ... more details
Encyclopedia
top
