Involving A Hydrolase (3.) Patents (Class 435/91.53)
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Publication number: 20100167942Abstract: Compositions, methods and related uses are provided relating to cleaving modified DNA. For example, a set of DNA fragments obtainable by enzymatic cleavage of a large DNA is described where at least 50% are similarly sized and have a centrally positioned modified nucleotide. In addition, an enzyme preparation is provided that includes one or more enzymes that recognize a modified nucleotide in a DNA and cleave the DNA at a site that is at a non-random distance from the modified nucleotide. The one or more enzymes are further characterized by an N-terminal conserved domain with greater than 90% amino acid sequence homology to WXD(X)10YXGD. The related uses include creating a methylome, methods of purifying DNA fragments containing a modified nucleotide and diagnostic applications.Type: ApplicationFiled: December 22, 2009Publication date: July 1, 2010Applicant: NEW ENGLAND BIOLABS, INC.Inventors: Yu Zheng, Richard J. Roberts
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Publication number: 20100159534Abstract: A protein is described that has an amino acid sequence characterized by at least 90% sequence identity with SEQ ID NO: 24, the protein being capable of recognizing a sequence consisting of 5?-GCCGAG-3? within the double-stranded DNA and cleaving the substrate predominantly at 21/19 nucleotides from the recognition site. A method is also described that utilizes the protein for creating a DNA tag for use as a unique identifier for paired end sequencing of DNA or serial analysis of gene expression.Type: ApplicationFiled: December 21, 2007Publication date: June 24, 2010Applicant: NEW ENGLAND BIOLABS, INC.Inventor: Richard D. Morgan
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Publication number: 20100129879Abstract: A method for partitioning a genome is provided. In certain embodiments, the method comprises: a) nicking a region of the genome using a sequence-specific nicking endonuclease to produce a nicked double-stranded genomic region; b) hybridizing the nicked double-stranded genomic region with an oligonucleotide comprising: i. an affinity tag; and ii. a nucleotide sequence that is complementary to the nucleotide sequence that is immediately adjacent to the nick site, to produce a duplex in which a terminal nucleotide of the oligonucleotide lies immediately adjacent to said a nucleotide of the nick site; c) ligating the terminal nucleotide of the oligonucleotide to the nucleotide of the nick site to produce a ligation product; and d) separating the ligation product from unligated products using the affinity tag. Compositions and kits for practicing the method are provided.Type: ApplicationFiled: November 21, 2008Publication date: May 27, 2010Inventors: Robert A. Ach, Brian J. Peter
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Publication number: 20100120101Abstract: A chamber in which an agent, like genomic DNA, may be harvested and optionally manipulated rapidly (e.g., on the order of a few hours), without shearing or fragmentation.Type: ApplicationFiled: January 8, 2008Publication date: May 13, 2010Applicant: U.S. Genomics, Inc.Inventors: Vishal Patil, Emilia Mollova, Rudolf Gilmashin
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Publication number: 20100093041Abstract: An improved method of preventing carryover contamination of an amplification reaction involves treating uracil-containing DNA with uracil-N-DNA glycosylase and heating the DNA in the presence of polyamines, such as spermidine, spermine and the like. Alternatively, after treatment with uracil-N-DNA glycosylase, the reaction is further incubated with an enzyme having AP lyase activity.Type: ApplicationFiled: June 16, 2009Publication date: April 15, 2010Applicant: ROCHE MOLECULAR SYSTEMS, INC.Inventors: Amar Gupta, Stephen Gordon Will, Roy Bohenzky, Janine Montiel
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Publication number: 20100081174Abstract: The invention provides methods for enriching methyl-CpG sequences from a DNA sample. The method makes use of conversion of cytosine residues to uracil under conditions in which methyl-cytosine residues are preserved. Additional methods of the invention enable to preservation of the context of me-CpG dinucleotides. The invention also provides a recombinant, full length and substantially pure McrA protein (rMcrA) for binding and isolation of DNA fragments containing the sequence 5?-CMeCpGG-3?. Methods for making and using the rMcrA protein, and derivatives thereof are provided.Type: ApplicationFiled: July 22, 2009Publication date: April 1, 2010Applicant: Brookhaven Science Associates, LLCInventor: John J. Dunn
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Publication number: 20100021974Abstract: It is an object of the present invention to provide a method for preparing a cRNA, the method being capable of preventing decrease in cRNA yield. In order to achieve the object, the method comprises (a) a step of performing a reaction for preparing a single-stranded cDNA by treating with RNaseH an mRNA-cDNA hybrid prepared by reverse transcription and a reaction for preparing a double-stranded cDNA from the single-stranded cDNA and then inactivating the RNaseH contained in the resultant reaction solution; (b) a step of contacting the reaction solution with a solid support having a cationic group on its surface under pH conditions where the cationic group is positively charged; (c) a step of separating the solid support from the reaction solution; (d) a step of eluting the double-stranded cDNA from the solid support; and (e) a step of performing a transcription reaction for preparing a cRNA from the double-stranded cDNA.Type: ApplicationFiled: December 5, 2006Publication date: January 28, 2010Inventors: Hideji Tajima, Masaaki Takahashi, Tomoyuki Hatano, Hisahiro Tajima
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Publication number: 20090269743Abstract: The present invention relates a sticker for DNA collection and a method for isolating DNAs using the same. Particularly, the sticker for DNA collection is covered with a paint solution comprising EDTA, Tris, SDS and peyonine to isolate keratins exclusively when attached onto human skin and detached. Further, the specific sticker for DNA collection separates DNAs efficiently to amplify genes by using a PCR technique. Therefore, the present invention can be applied to identify a real child and investigate a crime with a fingerprint and to screen genetic diseases.Type: ApplicationFiled: October 5, 2005Publication date: October 29, 2009Inventors: Jae-Song Ryu, Yong-Kil Yu
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Publication number: 20090246756Abstract: Isolated polypeptides having 5?-kinase and/or 3?-phosphatase activity and temperature optimum of at least 60° C. are described. The invention also relates to isolated nucleic acids encoding the polypeptides, nucleic acid constructs and host cells comprising the nucleic acid sequences as well as methods using the polypeptides and kits for practicing the methods.Type: ApplicationFiled: May 6, 2005Publication date: October 1, 2009Applicant: Prokaria EheInventors: Thorarinn Blondal, Arnthor Aevarsson, Gudmundur O. Hreggvidsson, Jakob Kristjansson
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Publication number: 20090203085Abstract: Methods and compositions are provided related to the amplification of target polynucleotide sequences as well as total RNA and total DNA amplification. In some embodiments, the methods and compositions also allow for the immobilization and capture of target polynucleotides with defined 3? and or 5? sequences to solid surfaces. The polynucleotides attached to the solid surfaces can be amplified or eluted for downstream processing. In some cases, nucleotides attached to solid surfaces can be used for high throughput sequencing of nucleotide sequences related to target DNA or target RNA.Type: ApplicationFiled: February 12, 2009Publication date: August 13, 2009Inventors: Nurith KURN, Shenglong Wang
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Publication number: 20090197307Abstract: The invention provides methods of preparing nucleic acids, such as RNA molecules, of a defined size or range of sizes. The invention provides compositions, methods and kits for use in the production and preparation of small RNA molecules (including without limitation micro-RNA, siRNA, d-siRNA and e-siRNA) and other nucleic acids of various sizes.Type: ApplicationFiled: August 11, 2008Publication date: August 6, 2009Applicant: INVITROGEN CORPORATIONInventors: Knut R. Madden, Adam N. Harris, Karl H. Hecker, Byung-in Lee
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Publication number: 20090155859Abstract: Methods and kits for generating contamination-free reagents and reagent solutions for use in nucleic acid amplification are provided. Methods include processing of polymerase solutions, nucleotide solutions and primer solutions to render contaminating nucleic acid inert. The methods employ the proofreading activity of the polymerase and/or exonucleases to de-contaminate the reagents and reagent solutions. Methods and kits for contamination-free nucleic acid amplification are provided.Type: ApplicationFiled: December 17, 2007Publication date: June 18, 2009Applicant: GENERAL ELECTRIC COMPANYInventors: John Richard Nelson, Robert Scott Duthie, Gregory Andrew Grossmann
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Publication number: 20090053698Abstract: The present invention provides a method for obtaining or amplifying a polynucleotide (a tester-specific polynucleotide), in which an amount existing in a sample (tester) is larger than the amount existing in another sample (driver), easily and within a short time as well as with high efficiency, a polynucleotide obtained (amplified) by such method, a method for identifying gene mutation in the tester, and a kit to be used in such methods.Type: ApplicationFiled: February 27, 2006Publication date: February 26, 2009Applicant: WAKO PURE CHEMICAL INDUSTRIES, LTD.Inventor: Yukinobu Hayashida
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Publication number: 20090042258Abstract: Methods and compositions are provided for generating a single-stranded extension on a polynucleotide molecule, the single-stranded extension having a desired length and sequence composition. Methods for forming single-stranded extensions include: the use of a cassette containing at least one nicking site and at least one restriction site at a predetermined distance from each other and in a predetermined orientation; or primer-dependent amplification which introduces into a polynucleotide molecule, a modified nucleotide which is excised to create a nick using a nicking agent. The methods and compositions provided can be used to manipulate a DNA sequence including introducing site specific mutations into a polynucleotide molecule and for cloning any polynucleotide molecule or set of joined polynucleotide molecules in a recipient molecule such as a vector of choice.Type: ApplicationFiled: August 15, 2008Publication date: February 12, 2009Applicant: NEW ENGLAND BIOLABS, INC.Inventor: Jurate Bitinaite
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Patent number: 7482125Abstract: The present invention features methods and compositions for the renaturation, hybridization, association, or reassociation of nucleic acids that combines both acceleration of the reaction rate and improved specificity.Type: GrantFiled: October 30, 2006Date of Patent: January 27, 2009Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Eugeni Namsaraev, Ronald W. Davis, George Karlin-Neumann
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Publication number: 20090011403Abstract: Described herein are methods for separating one or more analytes present in a fluid sample. The methods involve passing the fluid through or into a microporous material, wherein the analytes are localized near the surface of the microporous material. Additional processing steps such as hybridization and amplification can be performed once the analyte is localized. In one method, once the analyte is localized, the analyte can be detected, counted, and correlated in order to determine the concentration of the analyte in the sample. In another method, the localized analyte is destabilized to make the localized analyte more accessible for chemical manipulation. Modified microporous materials and composite materials are also disclosed that can be used in any of the methods and articles described herein. The composite is composed of a microporous material and a pigment, wherein the pigment is incorporated in the microporous material.Type: ApplicationFiled: May 17, 2005Publication date: January 8, 2009Applicant: UNIVERSITY OF UTAH RESEARCH FOUNDATIONInventors: Roger E. Smith, Karl V. Voelkerding, Marc G. Elgort, Jacob Durtschi
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Publication number: 20090011472Abstract: Provided herein are nucleic acid synthesis methods and agents that employ an endonuclease for example, endonuclease V, to introduce a nick into a target DNA including one or more inosine, and uses a DNA polymerase to generate amplicons of the target DNA.Type: ApplicationFiled: January 10, 2007Publication date: January 8, 2009Applicant: GENERAL ELECTRIC COMPANYInventors: JOHN RICHARD NELSON, ROBERT SCOTT DUTHIE, CARL WILLIAMS FULLER, GREGORY ANDREW GROSSMANN, ANURADHA SEKHER
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Publication number: 20090011471Abstract: Nucleic acid sequences encoding at least a portion of a polypeptide are directly incorporated into a plasmid by DNA polymerization or reverse transcription of a nucleic acid template. In particularly preferred embodiments, nucleic acid sequences encoding at least a portion of an antibody are directly incorporated into a plasmid by reverse transcription of messenger RNA (mRNA).Type: ApplicationFiled: June 12, 2007Publication date: January 8, 2009Inventors: Katherine S. Bowdish, Shana Frederickson, Ying-Chi Lin, Mark Renshaw, Martha Wild, John McWhirter
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Publication number: 20080311630Abstract: The invention relates to expression constructs for targeted inhibition of gene expression and methods for their production and which, after transfection thereof into eukaryotic cells, are suitable for inhibiting in a targeted manner these cells formation of defined proteins by RNA interference, wherein the method is a three step method requiring no PCR steps and is carried out in one reaction vessel in a few hours and are suitable for multiple gene expression inhibition.Type: ApplicationFiled: November 22, 2006Publication date: December 18, 2008Applicant: Mologen AGInventors: Matthias Schroff, Detlef Oswald
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Publication number: 20080286786Abstract: Methods of preparing nucleic acid from polysaccharide-containing samples for detection by providing one or more glycosidases to the sample to degrade polysaccharides are provided. The nucleic acids can further be extracted from the sample. The method is particularly useful for detecting nucleic acid in samples with high starch content.Type: ApplicationFiled: April 11, 2008Publication date: November 20, 2008Inventors: K. Yeon Choi, Michael S. Zwick, Kent McCue
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Patent number: 7435563Abstract: The present invention relates to a process for the preparation of enantiomerically pure (S)-3-methyl-amino-1-(thien-2-yl)propan-1-ol of the formula II-S by obtainment of (S)-3-hydroxy-3-thien-2-ylpropionitrile from its enantiomer mixture with the R isomer and the subsequent reaction of (S)-3-hydroxy-3-thien-2-ylpropionitrile with hydrogen and methylamine in the presence of a catalyst to give II-S.Type: GrantFiled: July 31, 2003Date of Patent: October 14, 2008Assignee: BASF AktiengesellschaftInventor: Rainer Stürmer
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Patent number: 6872816Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of nucleic acid from various viruses in a sample.Type: GrantFiled: March 24, 1998Date of Patent: March 29, 2005Assignee: Third Wave Technologies, Inc.Inventors: Jeff G. Hall, Victor I. Lyamichev, Andrea L. Mast, Mary Ann D. Brow, Robert W. Kwiatkowski, Stephanie H. Vavra
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Patent number: 6833260Abstract: The invention features methods and compositions for rapidly and effectively hydrolyzing lactose using recombinant lactic acid bacteria.Type: GrantFiled: April 4, 2000Date of Patent: December 21, 2004Assignee: Protein Scientific, Inc.Inventor: Frank E. Ruch
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Patent number: 6669963Abstract: A stable particle in liquid formulation comprising a discontinuous phase of microparticles is suspended in a continuous phase which is a non-aqueous liquid, preferably biocompatible in which the microparticles are insoluble. The microparticles comprise finely powdered sugar glass, such as trehalose, palatnit, glucopyranosyl sorbitol, glucopyranosyl mannitol, lactitol and monosaccharide alcohols, such as mannitol and inositol, holding at least one biomolecular product, the biomolecular product in the sugar glass either being in stable solid solution or being itself in suspension in the sugar glass.Type: GrantFiled: November 4, 1999Date of Patent: December 30, 2003Assignee: Elan Drug Delivery LimitedInventor: Jaap Kampinga
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Publication number: 20030175908Abstract: Methods of manipulation of nucleic acid, in particular amplification by means of the polymerase chain reaction (PCR), including use of oligonucleotides and combinations and kits comprising such oligonucleotides, also methods comprising use of nested PCR, allowing for improved results in methods wherein large numbers of nucleic acid fragments are manipulated by means of PCR and electrophoresis. Oligonucleotides are provided for use a size standards in electrophoresis, and internal controls allowing for calculation of relative amounts of material present. Improved results can be achieved in methods of profiling mRNA transcribed in a system under investigation.Type: ApplicationFiled: January 28, 2003Publication date: September 18, 2003Inventors: Sten Linnarsson, Patrik Ernfors, Goran Bauren, Ats Metsis, Arno Pihlak, Andreas Montelius
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Patent number: 6607901Abstract: An enzyme isolated from an organism that metabolizes alpha-galactosyl containing saccharides, comprising an alpha-galactosidase (E.C. 3.2.1.22, alpha-D-galactoside galatohydrolase) with optimal activity in the neutral to alkaline pH range, and which hydrolyzes a variety of alpha-galactose containing saccharides, in particular raffinose. The enzyme is preferably a protein monomer and an ex-alpha-galactosidase.Type: GrantFiled: April 25, 2001Date of Patent: August 19, 2003Assignee: State of Israel-Ministry of Agriculture, Volcani Research CenterInventors: Arthur Schaffer, Gao Zhifang
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Patent number: 6548250Abstract: The invention relates to a method of generating a signal indicative of the presence of a target nucleic acid sequence in a sample, where the method includes forming a cleavage structure by incubating a sample containing a target nucleic acid sequence with a nucleic acid polymerase and cleaving the cleavage structure with a FEN nuclease to generate a cleaved nucleic acid fragment. The invention also relates to methods of detecting or measuring a target nucleic acid sequence, where the method includes forming a cleavage structure by incubating a target nucleic acid sequence with a nucleic acid polymerase, cleaving the cleavage structure with a FEN nuclease and detecting or measuring the release of a fragment.Type: GrantFiled: August 30, 2000Date of Patent: April 15, 2003Assignee: StratageneInventor: Joseph A. Sorge
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Patent number: 6541226Abstract: A method for specifically cleaving a double-stranded DNA. The method comprises forming a three-stranded portion comprising the double-stranded DNA portion including the position to be cleaved or its vicinity and an oligonucleotide and treating the three-stranded protion with a nuclease.Type: GrantFiled: April 14, 2000Date of Patent: April 1, 2003Assignee: Aisin Seiki Kabushiki KaishaInventors: Yasushi Shigemori, Michio Oishi
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Patent number: 6531294Abstract: Pancreatic carboxypeptidase B or an isoform or a mutein of carboxypeptidase B may be prepared by (a) expressing a natural or unnatural enzymatically inactive precursor form of carboxypeptidase B in a microorganism by secretion, (b) purifying the precursor form expressed by secretion, and (c) converting the purified precursor form into the active form by an enzymatic treatment. A nucleic acid construct and a host cell containing the construct are useful for preparing pancreatic carboxypeptidase B or an isoform or a mutein thereof by this method.Type: GrantFiled: March 22, 2000Date of Patent: March 11, 2003Assignee: Aventis Pharma Deutschland GmbHInventor: Paul Habermann
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Patent number: 6504024Abstract: Propargylethoxyamino nucleosides are disclosed having the structure wherein R1 and R2 are —H, lower alkyl, or label; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; W1 is —H or —OH; W2 is —OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3′-position; and W3 is —PO4, —P2O7, —P3O10, phosphate analog, or —OH. Additionally, a primer extension method is provided employing the above propargylethoxyamino nucleosides.Type: GrantFiled: June 14, 2001Date of Patent: January 7, 2003Assignee: PE Corporation (NY)Inventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Patent number: 6458535Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.Type: GrantFiled: July 9, 1999Date of Patent: October 1, 2002Assignee: Third Wave Technologies, IncInventors: Jeff G. Hall, Victor I. Lyamichev, Andrea L. Mast, Mary Ann D. Brow
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Patent number: 6451563Abstract: A process to obtain linear double-stranded covalently closed DNA “dumbbell” constructs from plasmids by restriction digest, subsequent ligation with hairpin oligodesoxyribonucleotides, optionally in the presence of restriction enzyme, and a final digestion with endo- and exonucleolytic enzymes that degrade all contaminating polymeric DNA molecules but the desired construct. The invention also provides a process to obtain said dumbbell constructs employing endonuclease class II enzymes. Furthermore, the invention provides a process to obtain linear, covalently closed DNA molecules, such as plasmids, free from contamination by genomic DNA, by submitting the DNA preparation to a facultative endonucleolytic degradation step and an obligatory exonucleolytic degradation step.Type: GrantFiled: February 14, 2000Date of Patent: September 17, 2002Assignee: Mologen Forschungs-, Entwicklungs- und Vertriebs GmbHInventors: Burghardt Wittig, Claas Junghans, Matthias Schroff
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Patent number: 6416950Abstract: Disclosed herein are molecules that include a deoxyribonucleic acid (DNA) covalently bonded to a protein and uses thereof.Type: GrantFiled: December 2, 1999Date of Patent: July 9, 2002Assignee: Phylos, Inc.Inventors: Peter Lohse, Markus Kurz
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Patent number: 6391595Abstract: The invention provides a novel transferase that acts on a saccharide, as a substrate, composed of at least three sugar units wherein at least three glucose residues on the reducing end are linked &agr;-1,4 so as to transfer the &agr;-1,4 lingages to a &agr;-1,&agr;-1 linkages; a process for producing the transferase; a gene coding for the same; and a process for producing an oligosaccharide by using the same.Type: GrantFiled: April 26, 1999Date of Patent: May 21, 2002Assignee: Kirin Beer Kabushiki KaishaInventors: Masaru Kato, Yutaka Miura
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Publication number: 20020042112Abstract: Fast and highly accurate mass spectrometry-based processes for detecting a particular nucleic acid sequence in a biological sample are provided. Depending on the sequence to be detected, the processes can be used, for example, to diagnose a genetic disease or chromosomal abnormality; a predisposition to a disease or condition, infection by a pathogenic organism, or for determining identity or heredity.Type: ApplicationFiled: October 26, 1998Publication date: April 11, 2002Inventors: HUBERT KOSTER, DANIEL P. LITTLE, ANDREAS BRAUN, DAVID M. LOUGH, GUOBING XIANG, DIRK VAN DEN BOOM, CHRISTIAN JURINKE, ANDREAS RUPPERT
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Patent number: 6368803Abstract: A method is disclosed for modifying an oligonucleotide, which method has application to the detection of a polynucleotide analyte. An oligonucleotide is reversibly hybridized with a polynucleotide, for example, a polynucleotide analyte, in the presence of a 5′-nuclease under isothermal conditions. The polynucleotide analyte serves as a recognition element to enable a 5′-nuclease to cleave the oligonucleotide to provide (i) a first fragment that is substantially non-hybridizable to the polynucleotide analyte and (ii) a second fragment that lies 3′ of the first fragment (in the intact oligonucleotide) and is substantially hybridizable to the polynucleotide analyte. At least a 100-fold molar excess of the first fragment and/or the second fragment are obtained relative to the molar amount of the polynucleotide analyte. The presence of the first fragment and/or the second fragment is detected, the presence thereof indicating the presence of the polynucleotide analyte.Type: GrantFiled: June 30, 2000Date of Patent: April 9, 2002Assignee: Dade Behring Inc.Inventors: Linda M. Western, Samuel J. Rose, Edwin F. Ullman
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Patent number: 6326166Abstract: Chineric proteins containing composite DNA-binding regions are disclosed together with DNA constructs encoding them, compositions containing them and applications in which they are useful.Type: GrantFiled: March 16, 1998Date of Patent: December 4, 2001Assignee: Massachusetts Institute of TechnologyInventors: Joel L. Pomerantz, Phillip A. Sharp, Carl O. Pabo