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Topic: Exonucleases

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Endonuclease

DNA polymerase

DNA replication

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	Exonuclease
		Exonucleases may also be called "restriction enzymes" because they split the DNA molecules only at recognized subunits.
		Exonucleases are also called phosphoesterases, and hydrolyze phosphodiester bonds from the 3' or 5' terminus of polynucleotide molecules.
		Because exonucleases break the bond at the 3' or 5' terminus, the entire nucleotide can be removed from start to finish and separated out from the DNA, to be modified, replaced, or borrowed by the researcher as necessary.
	www.iscid.org /encyclopedia/Exonuclease (262 words)

	Patent 7,011,958
		The present invention concerns a method for improving the stability of linear short DNA towards exonucleases in cell-free in vitro transcription/translation systems using lysates containing exonucleases or in cellular systems containing exonucleases, wherein the stability of the linear short DNA is improved by adding unspecific linear DNA.
		The present invention concerns a method for improving the stability of linear short DNA from degradation by exonucleases in cell-free in vitro transcription/translation systems using lysates containing exonucleases or in cellular systems, wherein the stability of the linear short DNA is improved by adding unspecific linear DNA.
		In this method a plasmid is cleaved with restriction enzymes and the resulting double-stranded non-covalently closed molecules are then modified to form dumbbell-shaped constructs by digesting the ends with a restriction endonuclease that forms single-stranded overhangs and subsequently ligating matching hairpin oligomers onto the resulting single-strand overhangs.
	www.pharmcast.com /Patents100/Yr2006/Mar2006/031406/7011958_DNA031406.htm (3052 words)

	Anticarsia gemmatalis multicapsid nucleopolyhedrovirus v-trex gene encodes a functional 3' to 5' exonuclease -- Slack ...
		Exonuclease reactions were fractionated by electrophoresis in a denaturing 13 % acrylamide/urea gel.
		be predicted for a 3' to 5' exonuclease and are the converse
		Exonuclease reactions were fractionated by electrophoresis in a denaturing acrylamide/urea gel.
	vir.sgmjournals.org /cgi/content/full/85/10/2863 (3483 words)

	Identification and Expression of the TREX1 and TREX2 cDNA Sequences Encoding Mammalian 3'right-arrow5' Exonucleases -- ... (Site not responding. Last check: 2007-11-03)
		5' exonucleases catalyze the excision of nucleoside monophosphates from the 3' termini of DNA.
		and expression of the cDNA encoding this exonuclease.
		Exonuclease reactions (50 µl) were prepared containing a partial duplex with a paired 3' terminus (lanes 1-4) and with one mispair (lanes 5-8), two mispairs (lanes 9-12), three mispairs (lanes 13-16), and five mispairs (lanes 17-20) at the 3' terminus.
	www.jbc.org /cgi/content/full/274/28/19655 (4580 words)

	2002 Molecular Parasitology Meeting: Abstract Book Online (Site not responding. Last check: 2007-11-03)
		RRP45 is one of the enzymes that we have shown to be critical for the stability of some other components of the exosome and, perhaps the complex as a whole (see Estévez Abstract).
		This, to our knowledge, is the first reported in vivo evidence for the role of 3' exonucleases and/or the exosome in any organism where the 3' degradation pathway predominates over the 5' degradation pathway.
		We are currently disrupting various other 3' and 5' exonucleases in bloodstream forms to study their role in mRNA degradation.
	www.mbl.edu /mpm/mpm-2002/abstracts/abstract.php?id=80 (192 words)

	Biocompare - Product Literature Center
		After a 16-hour incubation at the appropriate temperature, the banding pattern from these overdigested samples is compared to the signature-banding pattern produced by the enzyme in 1 hour.
		If the restriction endonuclease preparation is free from contaminating endonuclease and exonuclease activities, the overdigested reactions will exhibit the identical banding pattern characteristic of the 1-hour reactions.
		If the ends of the digested DNA have been compromised by contaminating exonucleases or phosphatases, the recognition site will no longer be intact, and the cut product will not ligate efficiently or, when recut, yield a banding pattern identical to the initial digest.
	www.biocompare.com /techart.asp?id=105 (952 words)

	Susan Lovett, Brandeis University Biology faculty member
		Mutational hotspots, exonucleases and mutation avoidance: The mismatch repair pathway contributes to replication fidelity in all organisms.
		Our studies also suggest that the single-strand DNA exonucleases in E. coli abort wide variety of strand mispairing events that lead to mutations or genetic rearrangements.
		Redundant exonuclease involvement in Escherichia coli methyl-directed mismatch repair.
	www.bio.brandeis.edu /faculty01/lovett.html (590 words)

	ARS \| Publication request: The V-Trex Gene of the Anticarsia Gemmatails Multicapsid Nucleopolyhedrovirus Encodes for a ... (Site not responding. Last check: 2007-11-03)
		Soluble lysates contained 3' to 5' exonuclease activity that was 2000 fold above that of wt virus infected cells.
		The exonuclease activity was inhibited by EDTA and was activated in the presence of Mg+2 and to a lesser extent, in the presence of Mn+2.
		From this study, the AgMNPV v-trex gene is concluded to encode for an independently active 3' to 5' exonuclease.
	www.ars.usda.gov /research/publications/Publications.htm?seq_no_115=163291&pf=1 (351 words)

	RNA/DNA Modification Enzymes (Site not responding. Last check: 2007-11-03)
		Absence of 5’ exonucleases and 5’ phosphatases :
		The enzyme is screened for the absence of nickase, endo- and exonucleases.
		Calf intestine alkaline phosphatase (CIP) hydrolyzes 5’-terminal monophosphate groups of DNA and RNA and 5’-di- and triphosphate groups of RNA This enzyme is widely used for removing 5’ phosphates from fragments of DNA or RNA prior to labeling the 5’ end with polynucleotide kinase, or to prevent self-ligation of cloning vectors.
	www.qbiogene.com /products/enzymes/RNADNAmod_enz_index.shtml (1198 words)

	University of Miami Department of Biochemistry and Molecular Biology (Site not responding. Last check: 2007-11-03)
		These exonucleases processively degrade DNA and, when untamed, inhibit recombination by destroying the substrate.
		exonuclease were found in the genomes of over 80 viruses that infect bacteria, plants or animals (6); many of these genomes contain Synaptase genes, too.
		exonuclease (9), and have isolated and partially characterized another novel recombination nuclease from a plant (G. Tolun and R. Myers, unpublished).
	molbio.med.miami.edu /index.php?option=content&task=view&id=19&Itemid=26 (1273 words)

	Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, ...
		The presence of many 3' exonucleases raises several questions, such as whether individual exonucleases are required for the processing of specific RNA species, and if so, what the specific roles of each exonuclease are.
		A second class of interesting 3' exonucleases consists of five related yeast proteins that are part of a large family of proteins that includes known 3' exoribonucleases [i.e.
		This assembly of mutant phenotypes for various (putative) exonuclease mutants allows several points to be made concerning the interaction of 3' trimming enzymes and their substrates.
	www.nature.com /cgi-taf/DynaPage.taf?file=/emboj/journal/v19/n6/full/7592248a.html (7153 words)

	Molecular Detail
		Browse By Molecule < E >: Exonuclease III
		Exonucleases are enzymes that cleave terminal nucleic acids (RNA or DNA).
		Exonucleases may be specific for the 5Æ or 3Æ end of the nucleotide strand.
	www.rndsystems.com /molecule_detail.aspx?m=1412 (33 words)

	Functions of Multiple Exonucleases Are Essential for Cell Viability, DNA Repair and Homologous Recombination in recD ...
		Functions of Multiple Exonucleases Are Essential for Cell Viability, DNA Repair and Homologous Recombination in recD Mutants of Escherichia coli -- Ðermic 172 (4): 2057 -- Genetics
		Articles by Ðermic, D. Functions of Multiple Exonucleases Are Essential for Cell Viability, DNA Repair and Homologous Recombination in recD Mutants of Escherichia coli
		exonucleases in a recD derivative of a nuclease-deficient recB1067
	www.genetics.org /cgi/content/full/172/4/2057 (5457 words)

	Chromosomes Are "Nibbled" Before They Fuse, Researchers Report
		Then, Hackett studied the engineered chromosomes in yeast missing an enzyme called exonuclease that normally recognizes and chews up broken chromosomes one strand of DNA at a time.
		To prove that fusion does indeed result in a random pattern of marker loss, Hackett made an artificial fused, or di-centric, chromosome, complete with genetic markers to identify which segments were destroyed.
		If so, identifying other proteins that work with exonucleases may offer a target to block the process and push cells in cancer toward death instead of genomic instability.
	www.hopkinsmedicine.org /Press_releases/2003/12_02_03.html (749 words)

	Single-Strand DNA-Specific Exonucleases in Escherichia coli: Roles in Repair and Mutation Avoidance -- Viswanathan and ... (Site not responding. Last check: 2007-11-03)
		Single-Strand DNA-Specific Exonucleases in Escherichia coli: Roles in Repair and Mutation Avoidance -- Viswanathan and Lovett 149 (1): 7 -- Genetics
		RecJ exonuclease, Exonuclease I (ExoI), and Exonuclease VII
		The 3'right-arrow5' Exonucleases of DNA Polymerases delta and varepsilon and the 5'right-arrow3' Exonuclease Exo1 Have Major Roles in Postreplication Mutation Avoidance in Saccharomyces cerevisiae
	www.genetics.org /cgi/content/abstract/149/1/7 (961 words)

	The roles of endonucleolytic cleavage and exonucleolytic digestion in the 5'-end processing of S. cerevisiae box C/D ...
		3' exonucleases Xrn1p and Rat1p are inactivated (xrn1
		The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation.
		Johnson, A.W. Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively.
	www.rnajournal.org /cgi/content/full/9/11/1362 (4200 words)

	Fred W. Perrino
		Our hypothesis is that 3'-->5' exonucleases repair the aranucleotides from DNA and contribute to reduced chemosensitivity in leukemic cells.
		We are exploring the contributions of each subunit toward the accurate replication of DNA and measuring the cooperative interactions between the subunits.
		Mazur, D.J. and Perrino, F.W. Structure and expression of the TREX1 and TREX2 3'-->5' exonuclease genes.
	www1.wfubmc.edu /molecular_genetics/Faculty+Members/Cancer/Perrino (576 words)

	Structure and Expression of the TREX1 and TREX2 3'right-arrow5' Exonuclease Genes -- Mazur and Perrino 276 (18): 14718 ... (Site not responding. Last check: 2007-11-03)
		exonuclease motifs in the WRN protein (27, 28), and biochemical
		III, exonuclease I, and the recently described exonuclease X (34).
		The gene for TREX1 encodes the major 3' exonuclease activity measured in extracts prepared from mammalian cells.
	www.jbc.org /cgi/content/full/276/18/14718 (5474 words)

	Bechhofer Laboratory - The Dorothy H. and Lewis Rosenstiel Department of Pharmacology and Biological Chemistry - Mount ... (Site not responding. Last check: 2007-11-03)
		We have shown that the 5' end of a message plays an important role in determining mRNA half-life, and are currently looking at specific sites on the mRNA at which decay initiates.
		In order to understand the function of these exonucleases, we are analyzing decay of endogenous mRNAs in mutant strains lacking one or more of these genes.
		Another major goal is to identify other exoribonuclease activities, since a mutant strain missing all four of the currently known exonucleases is viable and clearly contains one or more other 3'-to-5' exonuclease activities.
	www.mssm.edu /labs/bechhofer/research.shtml (406 words)

	Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases -- Feschenko et al. 100 (3): ... (Site not responding. Last check: 2007-11-03)
		Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases -- Feschenko et al.
		Exonuclease degradation of DNA displaced during the deletion process
		Functions of Multiple Exonucleases Are Essential for Cell Viability, DNA Repair and Homologous Recombination in recD Mutants of Escherichia coli
	www.pnas.org /cgi/content/abstract/100/3/1134 (451 words)

	Division of Genomic Medicine - University of Sheffield
		A novel helical arch discovered in a 5'-3' exonuclease could explain how this class of essential replicative enzymes digest their nucleic acids substrates.
		We have cloned and expressed a number of exonucleases from bacteria including the human pathogen Haemophilus influenzae.
		In collaboration with Dr. Dietrich Suck and Dr. Tom Ceska at the EMBL (Heidelberg) a structural model is emerging for this interesting group of enzymes.
	www.shef.ac.uk /dgm/fg/auii/people/js.htm (1211 words)

	Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes -- ... (Site not responding. Last check: 2007-11-03)
		Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes -- Raghavendra and Rao 31 (7): 1888 -- Nucleic Acids Research
		Functional cooperation between exonucleases and endonucleases—basis for the evolution of restriction enzymes
		Exonuclease activity is essential for multiple rounds of DNA cleavage by EcoP15I restriction enzyme
	nar.oxfordjournals.org /cgi/content/full/31/7/1888 (6099 words)

	Properties of Exonucleases and Endonucleases, New England Biolabs
		Not all reported activities and properties for each exonuclease or endonuclease are listed.
		Exonuclease I releases dNMP from ss DNA, except at the last hydrolytic step where a dinucleotide is produced.
		Exonuclease T can be used to make 3' extensions blunt, but it was 2-4 fold less efficient than Klenow polymerase plus dNTP on a test substrate.
	www.neb.com /nebecomm/tech_reference/dna_rna/prop_exonucleases_endonucleases.asp (372 words)

	Processing of the Precursors to Small Nucleolar RNAs and rRNAs Requires Common Components -- Petfalski et al. 18 (3): ... (Site not responding. Last check: 2007-11-03)
		Accumulation of excised pre-rRNA fragments in exonuclease mutants.
		55 is envisaged to be followed by exonuclease digestion by Rat1p to the 5' ends of the snoRNAs and 3' trimming.
		Following intron debranching, processing is envisaged to consist of exonuclease digestion by Rat1p to the 5' end of the snoRNA and 3' trimming.
	mcb.asm.org /cgi/content/full/18/3/1181 (6013 words)

	Yeast Exosome Mutants Accumulate 3'-Extended Polyadenylated Forms of U4 Small Nuclear RNA and Small Nucleolar RNAs -- ... (Site not responding. Last check: 2007-11-03)
		The exosome is a protein complex consisting of a variety of 3'-to-5' exonucleases that functions both in 3'-to-5' trimming
		Rrp6p is an exonuclease associated with the exosome
		The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex.
	mcb.asm.org /cgi/content/full/20/2/441 (7943 words)

	Choristoneura fumiferana nucleopolyhedrovirus encodes a functional 3'-5' exonuclease -- Yang et al. 85 (12): 3569 -- ... (Site not responding. Last check: 2007-11-03)
		Barnes, M. H., Spacciapoli, P., Li, D. and Brown, N. The 3'–5' exonuclease site of DNA polymerase III from Gram-positive bacteria: definition of a novel motif structure.
		Bronstein, J. and Weber, P. Purification and characterization of herpes simplex virus type 1 alkaline exonuclease expressed in Escherichia coli.
		Taft-Benz, S. and Schaaper, R. Mutational analysis of the 3'-5' proofreading exonuclease of Escherichia coli DNA polymerase III.
	vir.sgmjournals.org /cgi/content/full/85/12/3569 (2140 words)

	dgl9 (Site not responding. Last check: 2007-11-03)
		Prokaryotes have had to evolve a wide array of restriction endonucleases (to linearize and thus restrict double-stranded DNAs from entry),that work together with the highly efficient recBCD exonucleases (see last lecture) to protect themselves against phage infection.
		The recBCD exonucleases rapidly and efficiently degrade linear DNA; therefore linear DNA cannot be used to transform most prokaryotes.
		However, covalently closed, circular DNA can transform prokaryotes efficiently, provided the recipient strain is lacking restriction endonucleases or the covalently closed circular DNA lacks restriction endonuclease cleavage sites for those endonucleases that are produced in the recipient strain.
	www.biotech.ufl.edu /gabriel/dgl9.htm (866 words)

	Who ya gonna call? Germbusters!
		As the Mutagens and the Exonucleases pranced around the stage, advancing toward the inevitable capture, the enthusiastic catcalls from the kids in their chairs threatened to drown out the actors' voices.
		Eventually, the Exonucleases discovered and conquered the Mutagens, restoring the DNA code to normal.
		Of course, the tainted DNA was the secret of Watson's purple hair, so he reappeared at the end of the play with his head restored to normal.
	www.jhu.edu /~newslett/03-12-98/Features/7.html (711 words)

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