Acellular Preparation Of Polynucleotide Patents (Class 435/91.5)
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Publication number: 20110189736Abstract: Methods and compositions for performing nucleic acid duplication and amplification reactions are provided. A single-stranded nucleic acid binding protein is selected and provided in the reaction mixture which is assembled at a low, nonstringent temperature to include all of the necessary reagents for successful nucleic acid duplication or amplification reactions. By incorporating a single-stranded nucleic acid binding protein into the reaction mixture at low temperature, the generation of nonspecific products such as amplification products is improved despite the reaction mixture having been fully assembled at a nonstringent temperature.Type: ApplicationFiled: March 29, 2011Publication date: August 4, 2011Applicant: AFFYMETRIX, INC.Inventors: Christopher J. Kubu, Jeannine C. Muller-Greven, Robert B. Moffett
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Publication number: 20110189659Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions and/or heterologous or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include reduced reaction rates at one or more steps of the polymerase kinetic cycle, increased closed polymerase/DNA complex stability, enhanced metal ion coordination, reduced exonuclease activity, decreased branching fractions, and the like. Polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog, are also provided. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: ApplicationFiled: September 30, 2010Publication date: August 4, 2011Applicant: Pacific Biosciences of California, Inc.Inventors: Sonya Clark, Arek Bibillo, Paul Peluso, Fred Christians, Molly He, Insil Park, Harold Lee, Keith Bjornson, Lei Jia, Robin Emig
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Publication number: 20110177508Abstract: This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns. This invention also provides neobases and methods of sequencing for methylation patterns using neobases.Type: ApplicationFiled: July 22, 2009Publication date: July 21, 2011Inventors: Timothy H. Bestor, John R. Edwards, Jingyue Ju, Xiaoxu Li
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Publication number: 20110172105Abstract: Provided are compositions, libraries, and methods for the synthesis of transcripts that can be processed to produce nucleic acid capture probes. Also provided methods for using such nucleic acid capture probes in a variety of downstream applications, including, e.g., determining the sequence of an exon-exon junction.Type: ApplicationFiled: June 4, 2009Publication date: July 14, 2011Applicant: Salk Institute for Biological StudiesInventors: Fred H. Gage, Jonathan Scolnick, Gene Wei Ming Yeo
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Publication number: 20110160076Abstract: Disclosed herein are uniquely specific nucleic acid probes and methods for their use and production. The disclosed probes have reduced or eliminated background signal while reducing or eliminating the use of blocking DNA during hybridization. In one example, probes are produced by a method that includes joining at least a first binding region and a second binding region in a pre-determined order and orientation, wherein the first binding region and second binding region are complementary to uniquely specific nucleic acid sequences, wherein the uniquely specific nucleic acid sequences are represented only once in a genome of an organism and wherein the first binding region and the second binding region include about 20% or less of a genomic target nucleic acid molecule. In particular examples, the binding regions (“uniquely specific binding regions”) are complementary to non-contiguous portions of the genomic target nucleic acid.Type: ApplicationFiled: December 30, 2010Publication date: June 30, 2011Inventors: Nelson Alexander, Stacey Stanislaw, James Grille, Mark B. Leick
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Publication number: 20110160289Abstract: The present invention relates to nucleic acid inhibitors, compositions and method for enhancing synthesis of nucleic acid molecules. In a preferred aspect, the invention relates to inhibition or control of nucleic acid synthesis, sequencing or amplification. Specifically, the present invention discloses nucleic acids having affinity for polypeptides with polymerase activity for use in such synthesis, amplification or sequencing reactions. The nucleic acid inhibitors are capable of inhibiting nonspecific nucleic acid synthesis under certain conditions (e.g., at ambient temperatures). Thus, in a preferred aspect, the invention relates to “hot start” synthesis of nucleic acid molecules. Accordingly, the invention prevents, reduces or substantially reduces nonspecific nucleic acid synthesis. The invention also relates to kits for synthesizing, amplifying, reverse transcribing or sequencing nucleic acid molecules comprising one or more of the nucleic acid inhibitors or compositions of the invention.Type: ApplicationFiled: May 3, 2010Publication date: June 30, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Mekbib ASTATKE, Deb K. Chatterjee, Gary F. Gerard
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Publication number: 20110159551Abstract: The present invention provides compositions and methods for a reverse transcription reaction using a reversibly inactivated reverse transcriptase enzyme. The reversibly inactivated reverse transcriptase enzyme results from a chemical modification which inactivates the reverse transcriptase enzyme. The activity of the reverse transcriptase enzyme is recovered by an incubation of the reaction mixture at elevated temperature prior to, or as part of the reverse transcription reaction. The reverse transcriptase enzyme of the present invention provides for a signficant reduction in non-specific reverse transcription from template nucleic acid molecules because the formulation of the reaction mixture does not support the formation of reverse transcription products prior to activation of the reverse transcriptase.Type: ApplicationFiled: October 8, 2010Publication date: June 30, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Lei (a.k.a Larry) Xi, Roland Nagel, Stephen Hendricks, Jennifer Berkman, Marian Peris, Yulei Wang
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Publication number: 20110151520Abstract: Methods for making cDNA molecules, for amplification of RNA by PCR and for preparation of cDNA libraries are provided. Kits for making cDNA molecules also are provided. Compositions are also provided comprising mixtures of reagents, including reverse transcriptases, buffers, cofactors and other components, suitable for immediate use in conversion of RNA into cDNA and RT PCR without dilution or addition of further components. These compositions are useful, alone or in the form of kits, for cDNA synthesis or nucleic acid amplification (e.g., by the Polymerase Chain Reaction) or for any procedure utilizing reverse transcriptases in a variety of research, medical, diagnostic, forensic and agricultural applications.Type: ApplicationFiled: December 8, 2009Publication date: June 23, 2011Applicant: QUANTA BIOSCIENCESInventors: Ayoub Rashtchian, David Schuster
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Publication number: 20110143399Abstract: The present invention provides a method to directionally clone any linear template DNA molecule into any linearized vector. The vector ends may be generated from any restriction enzyme cleavage. The method does not require a ligation step nor the use of carefully controlled conditions as is required with methods involving specific exonucleases alone. It has been determined that specific DNA polymerases are able to efficiently join one or more linear DNA molecules sharing ends with appropriate complementation.Type: ApplicationFiled: July 15, 2009Publication date: June 16, 2011Applicant: University of GuelphInventors: David Evans, David O. Willer, Xiao-Dan Yao
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Publication number: 20110143401Abstract: A polynucleotide device is provided that add one or more bases to a single stranded polynucleotide. Methods of using the device and kits comprising the device are also provide.Type: ApplicationFiled: November 23, 2010Publication date: June 16, 2011Applicant: SWIFT BIOSCIENCES, INC.Inventor: Vladimir Makarov
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Publication number: 20110129878Abstract: This invention relates to agents and conjugates that can be used to detect and isolate target components from complex mixtures such as nucleic acids from biological samples, cells from bodily fluids, and nascent proteins from translation reactions. Agents comprise a detectable moiety bound to a photoreactive moiety. Conjugates comprise agents coupled to substrates by covalent bounds which can be selectively cleaved with the administration of electromagnetic radiation. Targets substances labeled with detectable molecules can be easily identified and separated from a heterologous mixture of substances. Exposure of the conjugate to radiation releases the target in a functional form and completely unaltered. Using photocleavable molecular precursors as the conjugates, label can be incorporated into macromolecules, the nascent macromolecules isolated and the label completely removed.Type: ApplicationFiled: November 11, 2010Publication date: June 2, 2011Inventors: Kenneth J. Rothschild, Sanjay M. Sonar, Jerzy Olejnik
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Publication number: 20110124054Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.Type: ApplicationFiled: March 17, 2009Publication date: May 26, 2011Inventors: Jerzy Olejnik, Evan Goggenheim, Visalakshi Visalakshi
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Publication number: 20110124055Abstract: In a method for synthesizing a long nucleic acid molecule, a first immobilized nucleic acid has a first 5? region and a first 3? region and a second immobilized nucleic acid has a second 5? region and a second 3? region, wherein the second 3? region and the first 5? region have identical nucleic acid sequences. The first immobilized nucleic acid is hybridized with an oligonucleotide under conditions promoting hybridization of the oligonucleotide to the first 3? region, extending the hybridized oligonucleotide and producing a first extension product having a 3? region that is complementary to the first 5? region.Type: ApplicationFiled: February 1, 2011Publication date: May 26, 2011Applicant: MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Peter A. Carr, Brian Y. Chow, Joseph M. Jacobson, David W. Mosley, Christopher Emig
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Publication number: 20110111409Abstract: The invention relates to methods of depleting RNA from a nucleic acid sample. The RNA may be any RNA, including, but not limited to, rRNA, tRNA, and mRNA. The method is useful for depleting RNA from a nucleic acid sample obtained from a fixed paraffin-embedded tissue (FPET) sample. The method may also be used to prepare cDNA, in particular, a cDNA library for further analysis or manipulation.Type: ApplicationFiled: November 5, 2010Publication date: May 12, 2011Inventors: Dominick Sinicropi, John Morlan
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Publication number: 20110111514Abstract: A process for synthesis of a labelling reagent, a process for the labelling of a biological molecule, a labelled biological molecule obtained by the process, a process for labelling and fragmentation of a single or double strand nucleic acid, a labelled nucleic acid capable of being obtained by the process, a kit for detection of a target nucleic acid containing a labelled nucleic acid, a solid support onto which is attached a reagent and a process for capture of nucleic acids.Type: ApplicationFiled: July 28, 2009Publication date: May 12, 2011Applicants: BIOMERIEUX, UNIVERSITE DE STRASBOURG, CNRSInventors: Alain Laurent, Ali Laayoun, Mitsuhara Kotera
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Publication number: 20110098200Abstract: The present invention provides methods of producing dsDNA molecules that can be used to mediate RNA interference (RNAi). These methods include the production of hairpin DNAs including random sequences, and the use of convergent promoters to co-express sense and antisense RNAs. As such, the invention allows the production of random short hairpin RNA (shRNA) and a small interfering RNA (siRNA) expression libraries for forward genetic screening.Type: ApplicationFiled: September 4, 2003Publication date: April 28, 2011Inventors: Gregory Martin Arndt, Murray Cairns, Nham Tran, Angela Lai
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Publication number: 20110097722Abstract: The present invention provides cold shock protein-containing compositions for improved DNA synthesis reactions with improved reactivity, methods for synthesizing DNA using such compositions, kits for use in such methods, and DNA compositions yielded by such methods. The present invention further provides cold shock protein-containing compositions for the identification of endoribonuclease cleavage sites, methods for identifying endoribonuclease cleavage sites using such compositions, and kits for use in such methods.Type: ApplicationFiled: March 2, 2009Publication date: April 28, 2011Applicant: UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEYInventors: Masayori Inouye, Sangita Phadtare, Ikunoshin Kato, Ling Zhu, Hiroyuki Mukai, Takashi Uemori, Kazue Nishiwaki
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Publication number: 20110091939Abstract: The present invention provides methods, compositions and kits for removing specific target nucleic acid(s) from a nucleic acid sample. In particular, present invention provides a blocker oligonucleotide to prevent the target nucleic acid from binding to captor oligonucleotides, thus removing the target nucleic acid from a captor-binding nucleic acid pool. The present invention can be applied, for example, to remove high abundance mRNAs/cDNAs in high throughput nucleic acid sequencing.Type: ApplicationFiled: October 19, 2010Publication date: April 21, 2011Inventor: Longze Cui
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Publication number: 20110081688Abstract: The present invention provides novel, water-soluble, red-emitting fluorescent rhodamine dyes and red-emitting fluorescent energy-transfer dye pairs, as well as labeled conjugates comprising the same and methods for their use. The dyes, energy-transfer dye pairs and labeled conjugates are useful in a variety of aqueous-based applications, particularly in assays involving staining of cells, protein binding, and/or analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing.Type: ApplicationFiled: August 12, 2010Publication date: April 7, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Linda G. Lee, Ronald J. Graham, William E. Werner, Elana Swartzman, Lily Lu
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Publication number: 20110076728Abstract: The current inventors have discovered that the incorporation of a triplex forming monomer unit into oligonucleotides surprisingly gives the oligonucleotide a number of favorable characteristics. The oligonucleotides are advantageous because they allow modulation of the melting temperature of an oligonucleotide, they have improved sequence specificity and they can form triplexes by Hoogsteen or reverse Hoogsteen base pairing with double stranded nucleic acids. Moreover, some of the oligonucleotides of the invention have useful fluorescent characteristics, and the oligonucleotides comprising a triplex forming monomer can be used as substrates for enzymatic manipulations such as primer extension.Type: ApplicationFiled: March 10, 2009Publication date: March 31, 2011Inventor: Gorm Lisby
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Patent number: 7914982Abstract: The invention is based upon the discovery that small nucleic acids from non-viral pathogens are able to cross the kidney and are present in urine of a subject when the subject is infected with the non-viral pathogen. These transrenal DNAs are especially prevalent at smaller sizes under about 300 bp. Thus the invention provides compositions and methods for the diagnosis of infection of a subject with non-viral pathogens through the detection of transrenal nucleic acids from those pathogens in the urine of the subject.Type: GrantFiled: February 10, 2006Date of Patent: March 29, 2011Assignee: Trovagene, Inc.Inventors: Hovsep Melkonyan, Angela Cannas, Louis David Tomei, Samuil R. Umansky
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Patent number: 7910304Abstract: The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.Type: GrantFiled: October 31, 2007Date of Patent: March 22, 2011Assignee: Callida Genomics, Inc.Inventor: Radoje T. Drmanac
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Publication number: 20110059432Abstract: Aspects of the present invention relate to compositions and methods for providing DNA fragments from a remote sample. In particular aspects a remote sample comprising DNA is provided, DNA is isolated from the remote sample, and the isolated DNA is treated in a way which allows differentiation of methylated and unmethylated cytosine. Additional, particular embodiments provide compositions and methods for methylation analysis of DNA derived from a remote sample. Other aspects provide for compositions and methods of whole genome amplification of bisulfite treated DNA.Type: ApplicationFiled: April 17, 2006Publication date: March 10, 2011Applicant: EPIGENOMICS AGInventors: Matthias Ballhause, Kurt Berlin, Theo De Vos, Dimo Dietrich, Volker Liebenberg, Catherine Lofton-Day, Joe Lograsso, Jennifer Maas, Fabian Model, Matthias Schuster, Andrew Z. Sledziewski, Reimo Tetzner
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Publication number: 20110053153Abstract: A new class of nucleic acid substrates for AP endonucleases and members of the glycosylase/lyase family of enzymes is described. Representatives of each family, the enzymes Nfo and fpg, respectively, cleave nucleic acid backbones at positions in which a base has been replaced by a linker to which a variety of label moieties may be attached. The use of these synthetic substrates embedded within oligonucleotides is of utility in a number of applications.Type: ApplicationFiled: May 18, 2010Publication date: March 3, 2011Applicant: Alere San Diego, Inc.Inventors: Olaf Piepenburg, Niall A. Armes
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Publication number: 20110053245Abstract: This invention relates generally to enzymes, polynucleotides encoding the enzymes, the use of such polynucleotides and polypeptides and more specifically to enzymes having isomerase activity, e.g., racemase activity, e.g., amino acid racemase activity, alanine racemase activity, and/or epimerase activity, and/or catalyze the re-, arrangement of atoms within a molecule, catalyze the conversion of one isomer into another, catalyze the conversion of an optically active substrate into a raceme, which is optically inactive, catalyze the interconversion of substrate enantiomers, catalyze the stereochemical inversion around the asymmetric carbon atom in a substrate having only one center of asymmetry, catalyze the stereochemical inversion of the configuration around an asymmetric carbon atom in a substrate having more than one asymmetric center, and/or catalyze the racemization of amino acids.Type: ApplicationFiled: December 22, 2008Publication date: March 3, 2011Applicant: VERENIUM CORPORATIONInventors: David P. Weiner, Peter Luginbuhl, Analia Bueno, Joslin M. Cuenca, Mervyn L. De Souza, Sherry Kollmann
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Publication number: 20110053782Abstract: The present invention relates to unnatural base pairs of Ds (a 5-amino-7-(2-thienyl)-3H-imidazo[4,5-b]pyridine-3-yl group) and a Pa derivative (a 2-nitro-1H-pyrrole-1-yl group bearing a substituent having a ?-electron system attached at position 4) that can be replicated with high selectivity/high efficiency, and methods for replicating nucleic acids containing the unnatural base pairs. The present invention also relates to methods for incorporating an unnatural base bearing a functional substituent attached thereto into DNA by a nucleic acid replication reaction. The present invention also relates to methods for replicating and selectively collecting a nucleic acid containing an unnatural base pair from a nucleic acid pool. The present invention also relates to methods for determining a sequence of natural bases in the proximity of an unnatural base in DNA for achieving highly efficient and highly selective replication of a nucleic acid containing the unnatural base.Type: ApplicationFiled: March 31, 2009Publication date: March 3, 2011Applicant: RIKENInventors: Ichiro Hirao, Michiko Hirao, Shigeyuki Yokoyama
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Publication number: 20110045489Abstract: Compositions and methods are provided that relate to a recombinant protein with DNA polymerase activity in which one or more amino acids are mutated compared with the corresponding wild type protein. The recombinant protein is capable of incorporating one or more modified nucleotides into a nucleic acid substrate with a specific activity greater than 200.Type: ApplicationFiled: April 20, 2009Publication date: February 24, 2011Applicant: NEW ENGLAND BIOLABS, INC.Inventors: Andrew Gardner, Lucia Greenough, William E. Jack
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Publication number: 20110045990Abstract: Disclosed is a composition comprising a nucleic acid and a chemical compound, said composition forming a star structure defining 3 or more stems extending from a reaction center. The stems are formed by a nucleic acid duplex and the chemical compound has been formed in the reaction center as the reaction product of 3 or more chemical groups. The advantage of the composition is that a close proximity is provided between the chemical groups in the reaction center, thereby promoting a reaction. The invention also relates to a method for preparation of the composition. The advantage of the method is that it does not require the pre-synthesis of a large number of templates and that it is not dependent upon codon/anti-codon recognition for an encoded molecule to be formed.Type: ApplicationFiled: November 8, 2005Publication date: February 24, 2011Applicant: Vipergen Parmaceiticals APSInventors: Nils Jakob Vest Hansen, Peter Blaksjaer, Margit Haahr Hansen, Lars Kolster Petersen, Tara Renee Heitner
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Publication number: 20110045541Abstract: A nucleic acid molecule can be annealed to an appropriate immobilised primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilised primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilised nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.Type: ApplicationFiled: April 30, 2010Publication date: February 24, 2011Applicants: ILLUMINA CAMBRIDGE, LTD., ILLUMINA, INC.Inventors: Eric H. Kawashima, Laurent Farinelli, Pascal Mayer
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Publication number: 20110045542Abstract: The present invention relates to a reaction mixture for the amplification of nucleic acids, the non-methylated cytosine bases of which have been converted to uracil bases by means of a bisulfition reaction. The invention also discloses methods for amplifying bisulfited nucleic acid and for determining the nucleic acid methylation state, and also kits based on the reaction mixture according to the invention.Type: ApplicationFiled: February 6, 2009Publication date: February 24, 2011Inventors: Christian Korfhage, Dirk Loeffert, Ralf Peist, Nicolas Rudinger
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Publication number: 20110039722Abstract: The present disclosure relates to methods and materials for enhancing the binding affinity of an antibody by means of generating a library or an array of targeted amino acid changes (e.g., mutations) at one or more positions in an antibody variable domain. The present disclosure relates to libraries or arrays and their uses for enhancing antibody affinity. The present disclosure relates to methods and materials for mutagenesis, including for the generation of novel or improved antibody variable domains and libraries or arrays of mutant antibody variable domains or nucleic acids encoding such mutant or modified variable domains.Type: ApplicationFiled: December 31, 2008Publication date: February 17, 2011Applicant: XOMA TECHNOLOGY LTD.Inventors: Toshihiko Takeuchi, Gary Studnicka
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Patent number: 7888017Abstract: The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital PCR is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.Type: GrantFiled: February 2, 2007Date of Patent: February 15, 2011Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Stephen Quake, Hei-Mun Christina Fan
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Publication number: 20110033862Abstract: Methods for cell genotyping are disclosed herein. A method for determining the genomic data of one or a small number of cells, or from fragmentary DNA, where a limited quantity of genetic data is available may include adding one or more targeted primers to a whole genome amplification of a cell, increasing the accuracy with which key alleles are measured in the context of a whole genome amplification. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, allowing the reconstruction of the cells haplotype. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, and the distribution of the various alleles in the different fractions may be used to determine the ploidy state of one or a plurality of chromosomes in the cell.Type: ApplicationFiled: February 19, 2009Publication date: February 10, 2011Inventors: Matthew Rabinowitz, David S. Johnson, Johan Baner, Zachary Demko, Cengiz Cinnioglu
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Publication number: 20110033845Abstract: The teachings relate to methods and kits for detecting whether target nucleic acid sequences are present and/or quantitating target nucleic acid sequences.Type: ApplicationFiled: January 9, 2009Publication date: February 10, 2011Applicant: LIFE TECHNOLOGIES CORPORATION, a Delaware CorporationInventor: Eugene G. SPIER
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Publication number: 20110027794Abstract: The invention relates to a method for synthesizing a nucleic acid containing modified nucleotides. The method encompasses the following steps: a matrix strand is provided; —a primer which at least partially hybridizes on the matrix strand is provided; —nucleoside triphosphates, at least some of which are modified nucleoside triphosphates, are provided; —a polymerase activity is supplied; and—the matrix strand, the primer, and the nucleoside triphosphates are incubated so as to synthesize a nucleic acid that is substantially complementary to the matrix strand. The polymerase activity can be a reverse transcriptase activity.Type: ApplicationFiled: October 15, 2010Publication date: February 3, 2011Applicant: NOXXON PHARMA AGInventors: Sven Klussmann, Florian Jarosch, Axel Vater
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Publication number: 20110027789Abstract: The present invention relates to methods and kits for preserving genomic DNA sequence complexity within chemically and/or enzymatically converted DNA by an enzyme or series of enzymes that adds a methyl group to a cytosine outside of CpG dinucleotide sequences of genomic DNA. Further, the present invention relates to methylation analysis of the genomic DNA.Type: ApplicationFiled: August 2, 2010Publication date: February 3, 2011Applicant: EPIGENOMICS AGInventor: Joern Lewin
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Publication number: 20110027834Abstract: The invention refers to a method for providing a decontaminated template nucleic acid for enzymatic amplification reactions suitable for DNA methylation analysis.Type: ApplicationFiled: June 8, 2007Publication date: February 3, 2011Inventors: Reimo Tetzner, Dimo Dietrich
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Publication number: 20110027835Abstract: A method of double crossover homologous recombination in a host cell comprising: a first homologous recombination event between a donor DNA molecule comprising a first element of a selectable allele and an acceptor DNA molecule comprising a second element of the selectable allele in the host cell, thereby to form a product of the first homologous recombination event in the host cell; and a second homologous recombination event within the product of the first homologous recombination event, thereby to form a product of the second homologous recombination event in the host cell which confers a selectable phenotype on the host cell, wherein the selectable phenotype arises following and in dependency on the formation of a selectable allele from the first and second elements of the selectable allele.Type: ApplicationFiled: February 13, 2009Publication date: February 3, 2011Applicant: THE UNIVERSITY OF NOTTINGHAMInventors: John Timothy Heap, Nigel Peter Minton
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Publication number: 20110027786Abstract: Disclosed are methods and compositions for use in nucleic acid amplification or extension reactions.Type: ApplicationFiled: July 2, 2010Publication date: February 3, 2011Inventor: Brent C. Satterfield
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Patent number: 7879582Abstract: A method for the recombination of a gene is disclosed. The method involves the design of unpaired forward and reverse primers having homology to the 5? end of one template and to the 3? end of another template. Short primer extension periods results in a recombined template having paired 5? and 3? ends that can then be amplified. The amplified sample is devoid of any parental template.Type: GrantFiled: February 26, 2003Date of Patent: February 1, 2011Assignee: E. I. du Pont de Nemours and CompanyInventors: Joseph Milano, Xiao-Song Tang
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Patent number: 7871767Abstract: The present invention relates to a polymorphic CYP2C8-polynucleotide. Moreover, the invention relates to genes or vectors comprising the polynucleotides of the invention and to a host cell genetically engineered with the polynucleotide or gene of the invention. Further, the invention relates to methods for producing molecular variant polypeptides or fragments thereof, methods for producing cells capable of expressing a molecular variant polypeptide and to a polypeptide or fragment thereof encoded by the polynucleotide or the gene of the invention or which is obtainable by the method or from the cells produced by the method of the invention. Furthermore, the invention relates to an antibody which binds specifically the polypeptide of the invention. Moreover, the invention relates to a transgenic non-human animal. The invention also relates to a solid support comprising one or a plurality of the above mentioned polynucleotides, genes, vectors, polypeptides, antibodies or host cells.Type: GrantFiled: May 31, 2002Date of Patent: January 18, 2011Assignee: PGxHealth, LLCInventors: Anja Penger, Reimund Sprenger, Ulrich Brinkmann
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Publication number: 20110009281Abstract: The invention relates to the control of gene expression. Specifically, the invention provides compositions and methods for the production and use of recombinant nucleic acid molecules that have the ability to specifically downregulate an expressed target gene in vivo. In some aspects, the invention provides methods for producing a hairpin DNA molecule where part of the molecule is derived from an mRNA that is a target for a small interfering RNA (siRNA) derived from the hairpin. In other aspects, the invention provides synthetic hairpin adapter oligonucleotides that are used in the construction of siRNA-producing cassettes. In other aspects, the invention provides methods for testing for the presence or absence of specific inhibitory activity of an RNAi trigger molecule, and in still other aspects, the invention provides methods for identifying an active RNAi trigger molecule from a library of RNAi trigger molecules.Type: ApplicationFiled: December 23, 2008Publication date: January 13, 2011Inventors: David Micklem, James Lorens
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Publication number: 20110008775Abstract: The present invention relates to the field of analysis of nucleic acid sequences. More specifically, the present invention relates to the method and instrument for high throughput parallel DNA sequencing. The present invention also provides method for selection of sequences from analyte samples for enrichment of the target sequences or depletion of the selected molecules and in particular undesirable sequence templates from sequencing samples.Type: ApplicationFiled: December 10, 2008Publication date: January 13, 2011Inventors: Xiaolian Gao, Xiaochuan Zhou
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Publication number: 20110008781Abstract: Methods for isothermal amplification of nucleic acid by means of a solid support are disclosed. These methods are useful for applications needing high throughput, in particular nucleic acid sequencing.Type: ApplicationFiled: May 5, 2010Publication date: January 13, 2011Applicants: ILLUMINA CAMBRIDGE, LTD., ILLUMINA, INC.Inventor: Pascal Mayer
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Publication number: 20110003305Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.Type: ApplicationFiled: July 1, 2010Publication date: January 6, 2011Applicant: GEN-PROBE INCORPORATEDInventors: Steven T. BRENTANO, Dmitry LYAKHOV, Norman C. NELSON, James D. CARLSON, Michael M. BECKER, Lyle J. ARNOLD, JR.
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Publication number: 20110003881Abstract: The invention provides compositions and methods for reducing expression of a target gene in a cell, involving contacting a cell with an isolated double stranded nucleic acid (dsNA) in an amount effective to reduce expression of a target gene in a cell. The dsNAs of the invention possess a single stranded extension (in most embodiments, the single stranded extension comprises at least one modified nucleotide and/or phosphate back bone modification). Such single stranded extended Dicer-substrate siRNAs (DsiRNAs) were demonstrated to be effective RNA inhibitory agents compared to corresponding double stranded DsiRNAs.Type: ApplicationFiled: June 25, 2010Publication date: January 6, 2011Inventor: BOB D. BROWN
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Publication number: 20110003343Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are polymerase-nanoparticle conjugates including a polymerase linked to a nanoparticle, wherein the conjugate has polymerase activity. Such conjugates can exhibit reduced aggregation and improved stochiometries wherein the average biomolecule:nanoparticle ratio approaches or equals 1:1. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.Type: ApplicationFiled: March 26, 2010Publication date: January 6, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Theo Nikiforov, Daniel Mazur, Xinzhan Peng, Tommie Lloyd Lincecum, JR., Yuri Belosludtsev, Howard Reese, Dmitriy Gremyachinskiy, Roman Rozhkov, John M. Mauro, Joseph Beechem, Eric Tulsky, Imad Naasani, Kari Haley, Joseph A. Treadway
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Publication number: 20110003309Abstract: Provided are non-competitive internal controls for use in nucleic acid tests (NATs), which are obtained from the organisms Methanobacterium thermoautrophicum (MET) and Zea mays (Corn). The non-competitive internal controls have utility in DNA and RNA NATs selected from Influenza A, Influenza B, parainfluenza viruses 1 to 4 (PIV-1 to PIV-4), respiratory syncytial virus type A (RSV A), RSV B, human metapneumovirus (hMPV), Chlamydia trachomatis (CT), and Neisseria gonorrhea (GC), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Human Immunodeficiency Virus I (HIV-1), and Severe Acute Respiratory Syndrome (SARS).Type: ApplicationFiled: March 19, 2009Publication date: January 6, 2011Applicant: SIEMENS HEALTHCARE DIAGNOSTICS INC.Inventors: Jill Detmer, Xiaoqiao Jiang, Minh Le, David Sherman
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Publication number: 20110003308Abstract: There is described a new class or type of initiators for polymerization as a means of signal enhancement, nanoparticle initiators, and methods for amplifying signal resulting from recognition events, thereby enhancing the detection of those recognition events. Methods include amplification achieved through polymerization using a nanoparticle initiator conjugated recognition element that is not consumed during the reaction. The polymer formed as a result of the absorption of light by the nanoparticle initiator and introduction of reactive species into a surrounding polymerizable monomer solution occurs in a spatially-limited region directly surrounding the nanoparticle initiator and is indicative of the recognition event(s). In one embodiment, a semiconductor quantum dot nanoparticle initiator is utilized. In another embodiment, a metal nanoparticle is utilized. In another embodiment, the signal is detected without instrumentation.Type: ApplicationFiled: March 18, 2009Publication date: January 6, 2011Applicant: INDEVR, INC.Inventors: Kathy L. Rowlen, Amber W. Taylor
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Publication number: 20100323405Abstract: A method of amplifying a nucleic acid, the method comprising cycling an amplification-ready droplet through a temperature gradient to locations within the temperature gradient suitable for effecting steps in an amplification reaction.Type: ApplicationFiled: June 23, 2008Publication date: December 23, 2010Applicant: ADVANCED LIQUID LOGIC, INC.Inventors: Michael G. Pollack, Vamsee K. Pamula, Philip Paik, Allen Eckhardt