RNA polymerase IV is an enzyme which synthesizes small interfering RNA siRNA in plants. ref name Herr2005 cite journal author Herr, A. J. , M. B. Jensen, T. Dalmay, and D. C. Baulcombe title RNA Polymerase IV Directs Silencing of Endogenous DNA doi 10.1126 science.1106910 journal Science year 2005 volume 308 pmid 15692015 ref Polymerase IV is specific to plants genomes and is required for the synthesis of over 90 of 24 nt heterochromatic siRNA. ref name Zhang2007 cite journal author Zhang, Xiaoyu , Ian R. Henderson,Cheng Lu,Pamela J. Green, and Steven E. Jacobsen title Role of RNA polymerase IV in plant small RNA metabolism journal Proc Natl Acad Sci USA year 2007 volume 104 doi 10.1073 pnas.0611456104 ref Function RNA polymerase silences the transposons and repetitive DNA in the siRNA pathway. ref name Herr2005 The siRNA plays a major role in defending the genome against the invading viruses and transposable elements by RNA directed DNA methylation. ref name Zhang2007 Polymerase IV and ROS1 demethylase unlocks and recondenses the 5S rDNA chromatin , which is present in seed and used for the development of adult features in plants. ref name Douet2008 cite journal author Douet, Julien , Bertrand Blanchard, Claudine Cuvillier, and Sylvette Tourmente title Interplay of RNA Pol IV and ROS1 During Post Embryonic 5S rDNA Chromatin Remodeling journal Plant and Cell Physiology year 2008 volume 49 ref Polymerase IV is involved in setting the methylation patterns in the 5S genes during plant maturation. ref name Douet2008 In Arabidopsis thaliana arabidopsis polymerase IV works with binding protein DCL3 and a RNA polymerase II RDR2 in a silencing pathway which Polymerase IV would produce RNA, which is changed to dsRNA by RDR2 then converted to siRNA by DCL3. ref name Herr2005 References Reflist Polymerases Category Enzymes pt RNA polimerase RNA polimerase IV ... more details
Image T7 RNA polymerase.jpg thumb right T7 RNA Polymerase blue producing mRNA light blue from a double stranded DNA template orange . T7 RNA Polymerase is an RNA polymerase from the T7 phage T7 bacteriophage that catalyzes the formation of RNA in the 5 3 direction. Activity T7 polymerase is extremely Promoter biology promoter specific and transcribes only DNA downstream of a T7 promoter. The T7 polymerase also requires a DNA template and Mg sup 2 sup ion as cofactor for the synthesis of RNA. It has a very low error rate. T7 polymerase has a molecular weight of 99 kDa. Structure T7 polymerase has been crystallised in several forms and the structures placed in the Protein Data Bank PDB . The different structures are http www.ebi.ac.uk pdbe searchResults.html?display pdb&search type advanced&sort column reverse release date&Uniprot P00573&term UniProt 20P00573 listed here . These explain how T7 polymerase binds to DNA and transcribes it. Related proteins Related family members include phage T3 and SP6 RNA polymerase s, but this family is also related to the mitochondrial RNA polymerase. The T7 family of RNA polymerases is structurally and evolutionarily distinct from the multi subunit ... RNA polymerases, T7 polymerase is not inhibited by the antibiotic rifampicin . Nevertheless, many common ..., T7 RNA polymerase is commonly used to transcribe DNA that has been cloned into vectors ..., Theis K, Gong P title Structure and function in promoter escape by T7 RNA polymerase journal Prog ... 6603 05 80008 X url Cite journal author Sousa R, Mukherjee S title T7 RNA polymerase journal Prog ... T7 RNA polymerase or, the virtues of simplicity journal Cell. Mol. Biol. Res. volume 39 issue 4 pages ... of T7 RNA polymerase and the heterogeneity of transcription elongation complexes journal J. Biol ... T7 RNA Polymerase Enzymology http openwetware.org wiki In vitro transcription with T7 RNA polymerase OpenWetWare polymerases Category RNA Molecular cell biology stub Enzyme stub de T7 RNA Polymerase ... more details
Unreferenced stub auto yes date December 2009 This article is about the DNA Polymerase. For the RNA Polymerase, see RNA polymerase II DNA polymerase II also known as DNA Pol II or Pol II is a prokaryote prokaryotic DNA polymerase most likely involved in DNA repair . The enzyme is 90 kDa in size and is coded by the POLB polB gene . DNA Pol II can synthesize DNA new base pairs at an average rate of between 40 and 50 nucleotides second. Strains lacking the gene show no defect in growth or replication. Synthesis of Pol II is induced during the stationary phase of cell growth. This is a phase in which little growth and DNA synthesis occurs. It is also a phase in which the DNA can accumulate mutation damage such as short gaps, which act as a block to DNA Pol III . Under these circumstances, Pol II helps to overcome the problem because it can reinitiate DNA synthesis downstream of gaps. Pol II has a low error rate but it is much too slow to be of any use in normal DNA synthesis. Pol II differs from Pol I in that it lacks a 5 3 exonuclease activity, and cannot use a nicked duplex template. See also DNA replication . DEFAULTSORT Dna Polymerase Ii Category DNA replication Category EC 2.7.7 Category Enzymes Transferase stub cs DNA polymer za II it DNA polimerasi II ... more details
polymerase and, indeed, the first known of any kind of polymerase . It was initially characterized ... molecular biology 5 3 forward DNA Dependent DNA polymerase activity, requiring a 3 Primer molecular ... . A Directionality molecular biology 5 3 forward RNA Dependent DNA polymerase activity. Pol I operates ... DNA polymerase I as a reverse transcriptase author Ricchetti M, Buc H year 1993 month February journal Embo Journal volume 12 issue 2 pages 387 396 pmc 413221 ref In the replication process, DNA Polymerase ... that Polymerase I was not the enzyme responsible for most DNA synthesis &mdash DNA replication ... by Polymerase I averages only between 10 and 20 nucleotides second. Moreover, its cellular abundance ... was proven when, in 1969, John Cairns biochemist John Cairns isolated a viable Polymerase I mutant that lacked the polymerase activity. ref cite journal journal Nature volume 224 issue 5225 pages ... Strain with a Mutation affecting DNA Polymerase author Paula de Lucia coauthors John Cairns ref Cairns ... them for DNA polymerase activity. The 3,478th clone contained the polA mutant, which was named ... The eureka enzyme the discovery of DNA polymerase author Errol C. Friedberg ref It was not until the discovery of DNA polymerase III that the main replicative DNA polymerase was finally identified. Research applications DNA polymerase I obtained from E. coli is used extensively for molecular biology ... molecule called the Klenow fragment , widely used in molecular biology . Exposure of DNA polymerase ... the DNA polymerase and proofreading activities. See also DNA polymerase II DNA polymerase III References Reflist Polymerases DNA replication DEFAULTSORT Dna Polymerase I Category EC 2.7.7 Category DNA ... more details
Image RNA polymerase II.fcgi.png thumb 300px right RNA polymerase II of Saccharomyces cerevisiae consisting of all 12 subunits. Credit Meyer PA, Ye P, Zhang M, Suh MH, Fu J, Phasing RNA polymerase II using ... Meyer cite journal author Meyer PA, Ye P, Zhang M, Suh MH, Fu J title Phasing RNA polymerase II ... this url http www.ncbi.nlm.nih.gov Structure mmdb mmdbsrv.cgi?uid 39591. RNA polymerase II also ... type of RNA polymerase . A wide range of transcription factors are required for it to bind to its promoter ... core RNA polymerase II was first purified using transcription assays. ref name Sawadogo cite journal author Sawadogo M, Sentenac A title RNA polymerase B II and general transcription factors ... RA title RNA polymerase II holoenzymes and subcomplexes journal J. Biol. Chem. volume 273 issue ... C, Vigneron M title Interactions between the human RNA polymerase II subunits journal J Biol Chem. month ... directed RNA polymerase II subunit RPB1 an enzyme that in human s is encoded by the POLR2A gene . RPB1 is the largest subunit of RNA polymerase II. It contains a C terminus carboxy terminal domain CTD composed of up to 52 heptapeptide repeats YSPTSPS that are essential for polymerase activity. ref ... studies of the carboxy terminal repeat domain of Drosophila RNA polymerase II in vivo journal ... with several other polymerase subunits, it forms the DNA binding domain of the polymerase, a groove ... web title Entrez Gene POLR2A polymerase RNA II DNA directed polypeptide A, 220kDa url http www.ncbi.nlm.nih.gov ... two other polymerase subunits forms a structure within the polymerase that maintains contact ... cite web title Entrez Gene POLR2B polymerase RNA II DNA directed polypeptide B, 140kDa url http ... POLR2C the third largest subunit. Exists as a heterodimer with another polymerase subunit, POLR2J forming a core subassembly. RPB3 strongly interacts with RPB1 5, 7, 10 12. ref name Acker RNA polymerase ... RNA polymerase II pol II subunit hsRPB4 with its partner hsRPB7 and with pol II journal Mol Cell Biol ... more details
Pol III can also refer to HNoMS Pol III , a Norwegian guard vessel from WWII DNA polymerase III holoenzyme ... Name Bacterial DNA polymerase III alpha subunit image width caption crystal structure of the catalytic alpha subunit of e. coli replicative dna polymerase iii Pfam PF07733 Pfam clan InterPro IPR011708 ... pol3 delta Name DNA polymerase III, delta subunit image PDB 1xxh EBI.jpg width caption atpgs bound ... polymerase III, delta subunit, C terminal image PDB 1xxi EBI.jpg width caption adp bound e. coli clamp ... family OPM protein CAZy CDD Infobox protein family Symbol DNA pol3 tau 4 Name DNA polymerase III subunits ... 5 Name DNA polymerase III tau subunit V interacting with alpha image width caption solution structure of the c terminal 14 kda domain of the tau subunit from escherichia coli dna polymerase iii Pfam ... Infobox protein family Symbol DNA pol3 theta Name DNA polymerase III, theta subunit image PDB 2ido ... protein family Symbol DNA pol3 chi Name DNA polymerase III chi subunit, HolC image PDB 1em8 EBI.jpg .... the subunit has the polymerase activity. the subunit as 3 5 exonuclease activity. the subunit ... the polymerase bound to the DNA. 2 units which acts to dimerize two of the core enzymes , , and ... DNA polymerase III synthesizes base pairs at a rate of around 1000 nucleotides per second. ref ... stranded DNA, is synthesized by primase an RNA polymerase for RNA , for DNA , for polymerase RNA ribose sugar phosphate backbone G U A U Polymerase Pol RNA primer hydrogen bonding C A T A G C A T C ... progresses and the replisome moves forward, DNA polymerase III arrives at the RNA primer ... G U A U Polymerase Pol RNA primer III hydrogen bonding C A T A G C A T C C DNA template ss DNA single stranded DNA deoxyribose sugar phosphate backbone Synthesis of DNA DNA polymerase III will then synthesize ... or lagging strand Okazaki fragment of the DNA. DNA polymerase III has a high processivity and therefore ... onto the DNA strands. DNA deoxyribose sugar phosphate backbone G U A U C G T A G G Polymerase Pol ... more details
Touchdown polymerase chain reaction or touchdown style polymerase chain reaction is a method of polymerase chain reaction by which primer molecular biology primers will avoid amplifying nonspecific sequences. The Annealing biology annealing temperature during a polymerase chain reaction determines the specificity of primer annealing. The Denaturation biochemistry melting point of the primer sets the upper limit on annealing temperature. At temperatures just below this point, only very specific base pairing between the primer and the template will occur. At lower temperatures, the primers bind less specifically. Nonspecific primer binding obscures polymerase chain reaction results, as the nonspecific sequences to which primers anneal in early steps of amplification will swamp out any specific sequences because of the exponential growth exponential nature of polymerase amplification. The earliest steps of a touchdown polymerase chain reaction cycle have high annealing temperatures. The annealing temperature is decreased in increments for every subsequent set of cycles the number of individual cycles and increments of temperature decrease is chosen by the experimenter . The primer will anneal at the highest temperature which is least permissive of nonspecific binding that it is able to tolerate. Thus, the first sequence amplified is the one between the regions of greatest primer specificity it is most likely that this is the sequence of interest. These fragments will be further amplified during subsequent rounds at lower temperatures, and will out compete the nonspecific sequences to which the primers may bind at those lower temperatures. If the primer initially during the higher temperature phases binds to the sequence of interest, subsequent rounds of polymerase chain reaction can be performed upon the product to further amplify those fragments. References cite journal ... Amplifiers Category Polymerase chain reaction it Touchdown PCR vi Touchdown PCR zh ... more details
RNA polymerase I also called Pol I is, in eukaryotes , the enzyme that only Transcription genetics transcribes ribosomal RNA but not 5S ribosomal RNA 5S rRNA , which is synthesized by RNA Polymerase III , a type of RNA that accounts for over 50 of the total RNA synthesized in a cell. ref cite journal author Russell J, Zomerdijk JC title The RNA polymerase I transcription machinery journal Biochem. Soc. Symp. issue 73 pages 203 16 year 2006 pmid 16626300 ref Pol I consists of 8 14 protein subunits polypeptides . All 12 subunits have identical or related counterparts in RNA polymerase II Pol II and RNA polymerase III Pol III . rDNA transcription is confined to the nucleolus where several hundreds of copies of rRNA genes are present, arranged as tandem head to tail repeats. Pol I transcribes one large transcription genetics transcript , encoding an rDNA gene over and over again. This gene encodes the 18S, the 5.8S, and the 28S RNA molecules of the ribosome in eukaryotes . The transcripts are cleaved by snoRNA . The 5S ribosomal RNA is transcribed by RNA polymerase III Pol III . Because of the simplicity of Pol I transcription, it is the fastest acting polymerase. Regulation of rRNA transcription The rate of cell growth is directly dependent on the rate of protein synthesis, which, itself, is intricately linked to ribosome synthesis and rRNA transcription. Thus, intracellular signals must coordinate the synthesis of rRNA with that of other components of protein translation. Two specific mechanisms have been identified, ensuring proper control of rRNA synthesis and Pol I mediated ... of Transcription genetics transcription by any polymerase , there are three main stages Initiation the construction of the RNA polymerase complex on the gene s promoter biology promoter with the help ... polymerase complex. Initiation Initiation the construction of the polymerase complex on the promoter ... elucidated. See also RNA polymerase RNA polymerase II RNA polymerase III References Reflist ... more details
Polymerase cycling assembly or PCA , also known as Assembly PCR is a method for the assembly of large DNA oligonucleotide s from shorter fragments. The process uses the same technology as polymerase chain reaction PCR , but takes advantage of DNA hybridization and annealing as well as DNA polymerase to amplify a complete sequence of DNA in a precise order based on the single stranded oligonucleotides used in the process. It thus allows for the production of synthetic gene s and even entire synthetic genome s. PCA principles Image PCA polymerase cycling assembly.jpg right 400px thumbnail Much like how primers are designed such that there is a forward primer and a reverse primer capable of allowing DNA polymerase to fill the entire template sequence, PCA uses the same technology but with multiple oligonucleotides. While in PCR the customary size of oligonuleotides used is 18 base pairs, in PCA lengths of up to 50 are used to ensure uniqueness and correct hybridization. Each oligonucleotide is designed to be either part of the top or bottom strand of the target sequence. As well as the basic requirement of having to be able to tile the entire target sequence, these oligonucleotides must also have the usual properties of similar melting temperatures, hairpin free, and not too GC rich to avoid the same complications as PCR. During the polymerase cycles, the oligonucleotides anneal to complementary fragments and then are filled in by polymerase. Each cycle thus increases the length of various fragments randomly depending on which oligonucleotides find each other. It is critical that there is complementarity between all the fragments in some way or a final complete sequence will not be produced as polymerase requires a template to follow. After this initial construction phase, additional primers encompassing both ends are added to perform a regular PCR reaction, amplifying the target ... DEFAULTSORT Polymerase Cycling Assembly Category Genetic engineering Category Laboratory techniques ... more details
to pol , and thought to be the main polymerase involved in leading strand synthesis ref cite journal author Pursell, Z.F. et al. date 2007 title Yeast DNA Polymerase Participates in Leading Strand ... Scott D McCulloch Thomas A Kunkel 148 161 . POLH , POLI , POLK , DNA polymerase eta , , POLK , and Rev1 are Y family DNA polymerases and Pol is a B family DNA polymerase. These polymerases are involved ... polymerase References reflist Polymerases DNA replication Category EC 2.7.7 Category DNA replication ... more details
File Journal pone 0008430 g001.png thumb Journal pone 0008430 g001 Polymerase endonuclease amplification reaction PEAR is a DNA amplification technology for the amplification of oligonucleotides ref name Wang2010 cite journal last Wang first Xiaolong coauthors Deming Gou, Shuang yong Xu title Polymerase Endonuclease Amplification Reaction PEAR for Large Scale Enzymatic Production of Antisense Oligonucleotides journal PLoS ONE date January 1, 2010 year 2010 month January volume 5 issue 1 pages 7 doi 10.1371 journal.pone.0008430 pmid 20062528 url http www.plosone.org article info doi 10.1371 journal.pone.0008430 accessdate 22 August 2011 pmc 2797076 ref . A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease PspGI cleavage releases monomeric duplex oligonucleotides. PEAR has the potential to be a useful tool for Large scale production of oligonucleotides. PEAR is a minimal DNA replication system, so it can be considered as a minimal life system. it is of therectical interests to study the origin and evolution of repetitive DNA. The repetitive DNA products can be transferred directly into cells or organisms to study the function of the repetitive DNA. References Reflist Category DNA replication ... more details
RNA polymerase II holoenzyme is a form of Eukaryote eukaryotic RNA polymerase II that is recruited to the promoters ... RA title RNA polymerase II holoenzymes and subcomplexes journal J. Biol. Chem. volume 273 issue ... cgi reprint 273 43 27757.pdf ref It consists of RNA polymerase II , a subset of general transcription ... polymerase II main RNA polymerase II RNA polymerase II also called RNAP II and Pol II is an enzyme found ... of a Transcription preinitiation complex preinitiation complex , which, together with RNA polymerase ... author Orphanides G, Lagrange T, Reinberg D title The general transcription factors of RNA polymerase ... ref The cluster of RNA polymerase II and various transcription factors is known as a basal ... of protein coding gene s in eukaryote s and archaea . The PIC helps position RNA polymerase II over ... polymerase II active site for transcription. ref name Lee The typical PIC is made up of six general ... , and TFIIH . The construction of the polymerase complex takes place on the gene promoter biology promoter ... downstream BRE sup d sup of the TATA box. ref cite web title Polymerase II url http www.als.lbl.gov ... journal author Ossipow V, Fonjaliaz P, Schibler U title An RNA Polymerase II Complex Containing All ... into proper position for entry into the active site of RNA polymerase II . TFIIB binds partially ... recruits RNA polymerase II and TFIIF. ref name Ossipow Transcription Factor II F TFIIF two ... polymerase II Pol II enter the complex together. TFIIF helps to speed up the polymerization process ... DNA. ref name Lee Transcription Factor II E TFIIE helps to open and close the RNA polymerase II Pol ... II at the amino acid serine. This switches the RNA polymerase to start producing RNA . ref name Pierce ... to the C terminal domain CTD of RNA polymerase II holoenzyme , acting as a bridge between this enzyme ... of POLR2A . The carboxy terminal domain CTD of RNA polymerase II is that portion of the polymerase ... of Drosophila RNA polymerase II in vivo journal Genetics. volume 140 issue 2 pages 599 613 year 1995 ... more details
In eukaryote cells, RNA polymerase III also called Pol III Transcription genetics transcribes DNA to synthesize ribosomal 5S rRNA , tRNA and other small RNAs. This enzyme complex has a more limited role than the DNA polymerase III holoenzyme Pol III in prokaryote cells. The genes transcribed by RNA Pol III fall in the category of housekeeping genes whose expression is required in all cell types and most environmental conditions. Therefore the regulation of Pol III transcription is primarily tied to the regulation of cell growth and the cell cycle , thus requiring fewer regulatory proteins than RNA polymerase II . In the process of Transcription genetics transcription by any polymerase there are three main stages Initiation requiring construction of the RNA polymerase complex on the gene s promoter biology promoter . Elongation the writing of the RNA transcript. Termination the finishing of RNA writing and disassembly of the RNA polymerase complex. Initiation Initiation the construction of the polymerase complex on the promoter. Pol III is unusual compared to Pol II requiring no control sequences upstream of the gene, instead normally relying on internal control sequences sequences within ... also termed class I gene initiation TFIIIA T ranscription F actor for polymerase III A binds to the intragenic ... TFIIIC T ranscription F actor for polymerase III C binds to two intragenic lying within the transcribed ... of the start site of transcription. TFIIIB T ranscription F actor for polymerase III B , consists ... and Bdp1. ref name tfiiib cite journal title Essential roles of Bdp1, a subunit of RNA polymerase ... that TFIIIB containing Brf2 also plays a role in promoter opening. Termination Polymerase III ..., as it is in prokaryotes. Transcribed RNAs The types of RNAs transcribed from RNA polymerase ..., Teichmann M, Pagano A title The expanding RNA polymerase III transcriptome journal Trends Genet. volume ... 17274687 pmc 1790723 doi 10.1371 journal.pgen.0030001 ref See also DNA polymerase III holoenzyme ... more details
PBB geneid 27343 DNA polymerase lambda , also known as POLL , is a protein that, in humans, is encoded by the POLLA gene . ref name entrez cite web title Entrez Gene POLL polymerase DNA directed , lambda url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 27343 accessdate ref ref name pmid10982892 cite journal author Aoufouchi S, Flatter E, Dahan A, Faili A, Bertocci B, Storck S, Delbos F, Cocea L, Gupta N, Weill JC, Reynaud CA title Two novel human and mouse DNA polymerases of the polX family journal Nucleic Acids Res. volume 28 issue 18 pages 3684 93 year 2000 month September pmid 10982892 pmc 110747 doi 10.1093 nar 28.18.3684 url issn ref Function Pol is a member of the DNA polymerase Family X X family of DNA polymerase s. It is thought to resynthesize missing nucleotides during non homologous end joining , a pathway of DNA repair Double strand breaks DNA ... A, Wilson TE title DNA joint dependence of pol X family polymerase action in nonhomologous end joining ... al. title Implication of DNA polymerase lambda in alignment based gap filling for nonhomologous DNA ... with the 5 phosphate of the downstream DNA strand. This allows the polymerase to stabilize the two ... L, Kunkel TA, Pedersen LC title A structural solution for the DNA polymerase lambda dependent repair ... participate in base excision repair , where it provides backup activity in the absence of DNA polymerase ... EK, Prasad R, Shock DD, Hou EW, Beard WA, Wilson SH title DNA polymerase lambda mediates a back ... url ref Besides its catalytic polymerase domain, pol has an 8 kDa domain and a BRCT domain . The 8 ... Identification of an intrinsic 5 deoxyribose 5 phosphate lyase activity in human DNA polymerase ... Pol is structurally and functionally related to DNA polymerase mu pol , another member of the X ... kappa light chain gene rearrangement is impaired in mice deficient for DNA polymerase mu ... cite journal author Maga G, Villani G, Ramadan K, et al. title Human DNA polymerase lambda ... more details
PBB geneid 27434 DNA polymerase mu is a human protein encoded by the POLM gene . ref name entrez cite web title Entrez Gene POLM polymerase DNA directed , mu url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 27434 accessdate ref Function Pol is a member of the DNA polymerase Family X X family of DNA polymerase DNA polymerases . It participates in resynthesis of damaged or missing nucleotides during the non homologous end joining non homologous end joining NHEJ pathway of DNA repair . ref name pmid15964833 cite journal author Daley JM, Laan RL, Suresh A, Wilson TE title DNA joint dependence of pol X family polymerase action in nonhomologous end joining journal J. Biol. Chem. volume 280 issue 32 pages 29030 7 year 2005 month August pmid 15964833 doi 10.1074 jbc.M505277200 url ref Pol interacts with Ku protein Ku and LIG4 DNA ligase IV , which also participate in NHEJ. ref name pmid12077346 cite journal author Mahajan KN, Nick McElhinny SA, Mitchell BS, Ramsden DA title Association of DNA polymerase mu pol mu with Ku and ligase IV role for pol mu in end joining double strand break repair journal Mol. Cell. Biol. volume 22 issue 14 pages 5194 202 year 2002 month July pmid 12077346 pmc 139779 doi 10.1128 MCB.22.14.5194 5202.2002 url ref It is structurally and functionally related to DNA polymerase lambda pol , and, like pol , pol has a BRCT domain that is thought to mediate interactions with other DNA repair proteins. ref name pmid15242403 cite journal author Nick McElhinny SA, Ramsden DA title Sibling rivalry competition between Pol X family members in V D J recombination and general double strand break repair journal Immunol. Rev. volume 200 issue pages 156 64 year 2004 month August pmid 15242403 doi 10.1111 j.0105 2896.2004.00160.x ... deoxynucleotidyl transferase TdT , a specialized DNA polymerase that adds random nucleotides to DNA ... is impaired in mice deficient for DNA polymerase mu journal Immunity volume 19 issue 2 pages ... more details
PCR inhibitors usually affect PCR through interaction with DNA or interference with the DNA polymerase . Inhibitors can escape removal during the DNA purification procedure by binding directly to single or double stranded DNA. ref name promega cite web url http www.promega.com profiles 1001 ProfilesinDNA 1001 09.pdf title An Introduction to PCR Inhibitors Promega Corporation accessdate 2007 12 15 format PDF work ref Alternatively, by reducing the availability of Cofactor biochemistry cofactors such as Mg sup 2 sup or otherwise interfering with their interaction with the DNA polymerase, PCR is inhibited. ref name promega In a multiplex PCR reaction, it is possible for the different sequences to suffer from different inhibition effects to different extents, leading to disparity in their relative amplifications. ref name promega Types of inhibitors Inhibitors may be present in the original sample, such as blood, fabrics, tissues and soil but may also be added as a result of the sample processing and DNA extraction techniques used. ref name promega Excess salts including KCl and NaCl, ionic detergents such as sodium deocycholate , sarkosyl and sodium dodecyl sulfate SDS , ethanol, isopropanol and phenol among others, all contribute via various inhibitory mechanisms, to the reduction of PCR efficiency. ref name promega Quantifying extent of inhibition In order to try to assess the extent of inhibition that occurs in a reaction, a control can be performed by adding a known amount of a template to the investigated reaction mixture based on the sample under analysis . By comparing the amplification of this template in the mixture to the amplification observed in a separate experiment in which the same template is used in the absence of inhibitors, the extent of inhibition in the investigated ... and increasing the concentration of the chosen DNA polymerase also confers some resistance to polymerase ... scientist wiki References Reflist DEFAULTSORT Polymerase Chain Reaction Inhibitors Category DNA ... more details
The T7 DNA polymerase of the T7 phage T7 bacteriophage is a DNA dependent DNA polymerase responsible for the fast rate of T7 phage DNA replication in vivo . The polymerase consists of a 1 1 complex of the viral T7 gene 5 protein 80kDA and the E. coli thioredoxin 12kDA . It lacks a 5 3 exonuclease domain, but the 3 5 exonuclease activities are approximately 1000 fold greater than that of Klenow fragment . ref Cite journal author Sambrook, J., Russell, D.W. title Molecular Cloning A Laboratory Manual, Third edition journal Cold Spring Harbor Laboratory Press location Cold Spring Harbor, New York, 2001. year 2001 ref The exonuclease activity appears to be responsible for the high fidelity of this enzyme and prevents strand displacement synthesis ref Cite journal author LECHNER, R. L. AND RICHARDSON, C. C. journal J. Biol. Chem. title A preformed, topologically stable replication fork. volume 258 year 1983 pages 11185 11196 pmid 6885816 issue 18 ref This polymerase is unique due to its considerable processivity , or ability to stay on DNA for a greater than average number of base pairs. It is also suitable for site directed mutagenesis ref Cite journal author BEBENEK, K. et al. journal Nucl. Acids Res. title The use of native T7 DNA polymerase for site directed mutagenesis. volume 17 year 1989 pages 5408 doi 10.1093 nar 17.13.5408 pmid 2668888 issue 13 pmc 318147 ref but is not recommended for DNA sequencing applications. ref Cite journal author Doublie S., Tabor S., Long A., Richardson C., and Ellenberger T. journal Nature title Crystal Structure of a Bacteriophage T7 DNA Replication complex at 2.2 A Resolution. volume 391 year 1998 pages 251 258 doi 10.1038 34593 pmid 9440688 issue 6664 ref References references Refbegin 2 PBB Further reading citations Refend The PBB Controls template provides controls for Protein Box Bot, please see Template PBB Controls for details. PBB Controls update page yes require manual inspection no update protein box yes update summary no update ... more details
edit Polymerase DNA directed , beta , also known as POLB , is an enzyme that, in humans, is encoded by the POLB gene . ref name entrez cite web title Entrez Gene POLB polymerase DNA directed , beta ... ref Function In Eukaryote eukaryotic cells, DNA polymerase beta POLB performs base excision repair ... , and drug resistance. ref name entrez Regulation of expression DNA polymerase beta maintains genome ... of DNA polymerase beta in cell results in a mutator phenotype and a decreased sensitivity ... Deregulated DNA polymerase beta induces chromosome instability and tumorigenesis journal Cancer Res ... polymerase beta in human ovarian tumor cells impact on sensitivity towards antitumor agents journal ... SH title DNA polymerase beta expression differences in selected human tumors and cell lines journal .... ref name pmid12674496 cite journal author He F, Yang XP, Srivastava DK, Wilson SH title DNA polymerase ... author Narayan S, He F, Wilson SH title Activation of the human DNA polymerase beta promoter by a DNA ... structure within the 3 UTR of DNA polymerase beta mRNA acts as a post transcriptional regulatory element ... to be determined. Interactions DNA polymerase beta has been shown to Protein protein interaction ... with DNA polymerase beta and has a potential role in cellular phenotype journal Cancer Res. volume ... DNA polymerase beta and the XRCC1 protein journal EMBO J. volume 15 issue 23 pages 6662 70 publisher ... of a DNA polymerase beta variant journal Biochemistry volume 40 issue 30 pages 9005 13 publisher ... laysummary laysource laydate quote doi 10.1021 bi0028789 ref See also Polymerase DNA directed , alpha ... journal author Date T title Two regions in human DNA polymerase beta mRNA suppress translation in Escherichia ... U, Ghosh L, Banerjee S title DNA polymerase beta mutations in human colorectal cancer journal Cancer ... of DNA polymerase beta by in vitro phosphorylation with protein kinase C journal J. Biol ... SenGupta DN title Sequence of human DNA polymerase beta mRNA obtained through cDNA cloning journal ... more details
Multiplex polymerase chain reaction Multiplex PCR is a modification of polymerase chain reaction in order to rapidly detect Deletion genetics deletions or Gene duplication duplications in a large gene . This process DNA replication amplifies genomic DNA samples using multiple primer molecular biology primers and a temperature mediated DNA polymerase in a thermal cycler . Multiplex PCR was first described in 1988 as a method to detect deletions in the dystrophin gene. ref cite journal journal Nucleic Acids Research title Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification authors Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT year 1988 volume 16 issue 23 pages 11141 11156 PMID 3205741 pmc 339001 pmid 3205741 doi 10.1093 nar 16.23.11141 ref It has also been used with the steroid sulfatase gene. ref cite journal title Screening for steroid sulfatase STS gene deletions by multiplex DNA amplification journal Human Genetics authors Ballabio A, Ranier JE, Chamberlain JS, Zollo M, Caskey CT volume 84 issue 6 pages 571 573 year 1990 PMID 2338343 doi 10.1007 BF00210812 ref In 2008, multiplex PCR was used for analysis of Microsatellite genetics microsatellite s and single nucleotide polymorphism SNPs . ref cite journal author Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ title Multiplex ready PCR a new method for multiplexed SSR and SNP genotyping journal BMC Genomics volume 9 pages 80 year 2008 pmid 18282271 pmc 2275739 doi 10.1186 1471 2164 9 80 ref Multiplex PCR consists of multiple primer sets within a single PCR mixture to produce amplicon s of varying sizes that are specific to different DNA sequences. By targeting multiple genes at once, additional information may be gained from a single test run that otherwise would require several times the reagents and more time to perform. Annealing temperatures for each of the primer ... Category Polymerase chain reaction de Multiplex PCR ... more details
Ikhtiyar al Din Ai Taq was an influential amir in western Greater Khorasan Khurasan following the decline of the Seljuks , and the ruler of Gurgan and Dihistan from 1161 until 1165 . ref Bosworth, pps. 156 & 188 ref Career Ai Taq had originally been one of the Seljuks Seljuk sultan Sanjar Sanjar s ghilman ghulams . When Sanjar was captured by rebellious Oghuz Turks Ghuzz bands in 1153 , Ai Taq built up an army and quickly established his influence in the western regions of Sanjar s empire. Ai Taq had not been the only individual to take advantage of Sanjar s overthrow. In Nishapur another of Sanjar s former ghulams, Mu ayyid al Din Ai Aba , had taken power and had gained control of a significant portion of Khurasan. Relations between Ai Taq and Ai Aba quickly soured and by 1158 warfare had broken out among them. ref Bosworth, p. 185 ref Ai Taq received military assistance from Shah Ghazi Rustam, the Bavandid ruler of Tabaristan . Despite this, his forces were defeated by Ai Aba and Sultan Mahmud Khan Karakhanid Mahmud Khan and he was forced to flee to Tabaristan. In the end he was compelled to sue for peace and had to pay off his opponents. ref Al E Bavand ref In around 1160 Ai Taq was attacked by a force of Ghuzz under their chief Yaghmur . Despite Bavandid support, he was defeated and was forced to flee. He made his way to Khwarezm , where the Khwarezmshah Il Arslan supplied him with assistance. ref Il Arslan ref This enabled him to establish himself in Gurgan and Dihistan, where he acknowledged the suzerainty of Il Arslan. ref Bosworth, p. 186 ref Unfortunately for him, however, he eventually lost the support of the shah, and a Khwarezmid army expelled him from Dihistan in 1165 . Notes Reflist References Al E Bavand. Encyclopaedia Iranica Online. Encyclopaedia Iranica. 2 February 2008. http www.iranicaonline.org articles al e bavand Bosworth, C.E. The Political and Dynastic ... 2008. http www.iranicaonline.org articles il arslan DEFAULTSORT Ikhtiyar Al Din Ai Taq Category ... more details
Pfam box Symbol RNA pol flaviviral Name RNA directed RNA polymerase, flaviviral Pfam PF00972 InterPro IPR000208 PROSITE PDB RNA dependent RNA polymerase RdRP , RDR , or RNA replicase , is an enzyme EC number 2.7.7.48 that catalyzes the Self replication replication of RNA from an RNA template. This is in contrast to a typical DNA dependent RNA polymerase , which catalyzes the transcription genetics transcription of RNA from a DNA template. RNA dependent RNA polymerase RdRp is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage that have sense negative RNA. ref name pmid2759231 cite journal author Koonin EV, Gorbalenya AE, Chumakov KM title Tentative identification of RNA dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral polymerases journal FEBS Lett. volume 252 issue 1 2 pages 42 6 year 1989 month July pmid 2759231 doi 10.1016 0014 5793 89 80886 5 ref ref name pmid8709232 cite journal author Zanotto PM, Gibbs MJ, Gould EA, Holmes EC title A reevaluation of the higher taxonomy of viruses based on RNA polymerases ... protein to initiate polymerase activity. The viral protein genome linked VPg primer is covalently bound ... polymerase complexes with VPg journal Biochemistry Mosc. volume 74 issue 10 pages 1132 41 year 2009 ... SC title Structure of the RNA dependent RNA polymerase of poliovirus journal Structure volume 5 issue ... JD, Andino R, Cameron CE title Poliovirus RNA dependent RNA polymerase 3Dpol structural, biochemical ... dependent RNA polymerase structure and function as guided by known polymerase structures and computer ... dengue type 1 virus NS5 protein expressed in Escherichia coli exhibits RNA dependent RNA polymerase activity. This RNA directed RNA polymerase possesses a number of short regions and motifs homologous ... coli exhibits RNA dependent RNA polymerase activity journal Virology volume 216 issue 2 ... InterPro content IPR000208 DEFAULTSORT Rna Dependent Rna Polymerase Category Gene expression ... more details
Digital Polymerase Chain Reaction digital PCR, DigitalPCR, dPCR, or dePCR is a refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify nucleic acids including DNA , cDNA or RNA . The key difference between dPCR and traditional PCR lies in the method of measuring nucleic acids amounts, with the former being a more precise method than PCR. PCR carries out one reaction per single sample. dPCR also carries out a single reaction within a sample, however the sample is separated into a large number of partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid amounts. The method has been demonstrated as useful for studying variations in gene sequences such as copy number variants and point mutations and it is routinely used for clonal amplification of samples for next generation sequencing . PCR Basics The polymerase chain reaction method is used to quantify nucleic acids by amplifying a nucleic acid molecule with the enzyme DNA polymerase . Conventional PCR is based on the theory that amplification is exponential. Therefore, nucleic acids may be quantified by comparing the number of amplification cycles and amount of PCR end product to those of a reference sample. However, many factors complicate this calculation, creating uncertainties and inaccuracies. These factors include the following initial amplification cycles may not be exponential PCR amplification eventually plateaus after an uncertain number of cycles and low initial concentrations of target nucleic acid molecules may not amplify to detectable levels. However, the most significant limitation of PCR is that PCR amplification efficiency in a sample of interest may be different from that of reference samples. Since PCR is an exponential process, only ... Polymerase chain reaction Category Laboratory techniques ... more details
ligase III LigIII , DNA polymerase beta pol , and scaffolding proteins such as X ray cross ... year 2008 title Deficiency in Poly ADP ribose Polymerase 1 PARP 1 Accelerates Aging and Spontaneous ... ADP ribose polymerase 1 activity regulates JP 8 induced sustained cytokine expression in alveolar macrophages ... zinc finger s and will recruit XRCC1 , DNA ligase III, DNA polymerase beta, and a kinase to the nick ... ADP ribose polymerase at inotekcorp.com http parplink.u strasbg.fr index.html The PARP Link Homepage at parplink.u strasbg.fr MeshName Poly ADP Ribose Polymerase http www.parp inhibitors.com Parp Inhibitors ... more details
Infobox settlement official name Taq Rezaleh ye Mohammad Aqa native name settlement type village pushpin map Iran mapsize 150px coordinates region IR subdivision type List of countries Country subdivision name flag Iran subdivision type1 Provinces of Iran Province subdivision name1 Lorestan Province Lorestan subdivision type2 Counties of Iran County subdivision name2 Pol e Dokhtar County Pol e Dokhtar subdivision type3 Bakhsh subdivision name3 Mamulan District Mamulan subdivision type4 Rural Districts of Iran Rural District subdivision name4 Afrineh Rural District Afrineh leader title leader name established title established date area total km2 area footnotes population as of 2006 population total 130 population density km2 auto timezone Iran Standard Time IRST utc offset 3 30 timezone DST Iran Daylight Time IRDT utc offset DST 4 30 coordinates display latd 33 latm 17 lats 42 latNS N longd 47 longm 54 longs 28 longEW E elevation m area code website footnotes Taq Rezaleh ye Mohammad Aqa lang fa , also Romanize d as q Rez leh ye Mo ammad q also known as q e Re leh and q e Re l ref GEOnet3 3794356 Taq Rezaleh ye Mohammad Aqa ref is a village in Afrineh Rural District , Mamulan District , Pol e Dokhtar County , Lorestan Province , Iran . At the 2006 census, its population was 130, in 21 families. ref IranCensus2006 15 ref References reflist Pol e Dokhtar County Category Populated places in Pol e Dokhtar County Lorestan geo stub ... more details
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