Involving A Hydrolase (3.) Patents (Class 435/91.53)
  • Patent number: 9677067
    Abstract: Methods and compositions are provided for assembly of large nucleic acids where the assembled large nucleic acids lack internal sequence modifications made during the assembly process.
    Type: Grant
    Filed: May 13, 2016
    Date of Patent: June 13, 2017
    Assignee: TWIST BIOSCIENCE CORPORATION
    Inventors: Esteban Toro, Sebastian Treusch, Siyuan Chen, Cheng-Hsien Wu
  • Patent number: 9150879
    Abstract: Disclosed herein are engineered cleavage half-domains; fusion polypeptides comprising these engineered cleavage half-domains; polynucleotides encoding the engineered cleavage half-domains and fusion proteins; and cells comprising said polynucleotides and/or fusion proteins. Also described are methods of using these polypeptides and polynucleotides, for example for targeted cleavage of a genomic sequence.
    Type: Grant
    Filed: January 2, 2014
    Date of Patent: October 6, 2015
    Assignee: Sangamo BioSciences, Inc.
    Inventors: Yannick Doyon, Jeffrey C. Miller
  • Publication number: 20150147785
    Abstract: The present invention relates to methods for generating a labelled nucleic acid from an RNA comprising a 5? protecting group, said method comprises the steps of obtaining a mixture of template strands of nucleic acids, said mixture comprising said RNA and further potentially other nucleic acids without a 5? protecting group, annealing at least one oligonucleotide primer to the template strand of said RNA and potentially other nucleic acids, and template sequence dependent extending said primer, thereby obtaining a complementary nucleic acid strand annealed to its template strand, or providing the RNA in duplex with a complementary nucleic acid strand annealed to its template strand, and optionally modifying the extension product of said nucleic acids without 5? protecting group either on the 5? end of the template strand or on the 3? end of the complementary strand, or both, and labelling a complementary nucleic acid of a double stranded nucleic acid not modified, wherein therefore the labelled nucleic acid d
    Type: Application
    Filed: July 10, 2013
    Publication date: May 28, 2015
    Inventors: Alexander Seitz, Irmlind Gabler, Lukas Paul
  • Patent number: 8962281
    Abstract: Disclosed herein are engineered cleavage half-domains; fusion polypeptides comprising these engineered cleavage half-domains; polynucleotides encoding the engineered cleavage half-domains and fusion proteins; and cells comprising said polynucleotides and/or fusion proteins. Also described are methods of using these polypeptides and polynucleotides, for example for targeted cleavage of a genomic sequence.
    Type: Grant
    Filed: February 7, 2011
    Date of Patent: February 24, 2015
    Assignee: Sangamo BioSciences, Inc.
    Inventors: Yannick Doyon, Jeffrey C. Miller
  • Publication number: 20150037843
    Abstract: A mixed polynucleotide includes a first double stranded (ds) portion, a second portion including at least one single stranded (ss) portion, and a third ds portion. The second portion connects the first ds portion and the third ds portion to provide a modified polynucleotide.
    Type: Application
    Filed: August 28, 2013
    Publication date: February 5, 2015
    Applicant: INTERNATIONAL BUSINESS MACHINES CORPORATION
    Inventors: Binquan Luan, Ajay K. Royyuru, Gustavo A. Stolovitzky, Chao Wang, Deqiang Wang
  • Publication number: 20150031090
    Abstract: Disclosed herein are compositions and methods for generating chromosomal translocations and targeted deletions of specific lengths and at specific locations the genome of cell.
    Type: Application
    Filed: September 30, 2014
    Publication date: January 29, 2015
    Inventors: Fyodor Urnov, Jianbin Wang
  • Publication number: 20150024972
    Abstract: Provided herein are nucleic acids and methods for selectively amplifying in parallel tens of thousands of high quality oligonucleotides without common sequences. The resultant oligonucleotides can be used for a variety of purposes and applications including but not limited to DNA nano structure synthesis.
    Type: Application
    Filed: February 8, 2013
    Publication date: January 22, 2015
    Applicant: President and Fellows of Harvard College
    Inventors: Thorsten Lars Schmidt, Mark Theilmann, William M. Shih
  • Patent number: 8911948
    Abstract: The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3? end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.
    Type: Grant
    Filed: July 22, 2009
    Date of Patent: December 16, 2014
    Assignee: Integrated DNA Technologies, Inc.
    Inventors: Joseph Alan Walder, Mark Aaron Behlke, Scott Rose, Joseph Dobosy
  • Publication number: 20140295503
    Abstract: Various aspects and embodiments of the present disclosure relate to methods of obtaining and manipulating nucleic acids from samples. In some embodiments, the samples are known to comprise or are suspected of comprising microorganisms such as bacteria and the methods of the invention are used to identify such microorganisms.
    Type: Application
    Filed: March 13, 2014
    Publication date: October 2, 2014
    Applicant: PathoGenetix, Inc.
    Inventors: Ekaterina Protozanova, Mohan Nair Manoj Kumar, Dirk Peter Ten Broeck, Jimmy Symonds
  • Publication number: 20140287468
    Abstract: Methods and compositions are provided for enriching for target sequences from a population of nucleic acids, that includes combining in solution, a population of nucleic acids and a target isolation probe wherein the target isolation probe includes an affinity binding domain; permitting a single stranded region of the target isolation probe to hybridize to all or a portion of a target sequence in the population of nucleic acids; selectively immobilizing the hybridized nucleic acids from the population containing the target sequences by associating the target isolation probe with a capture domain and removing unbound material; and removing from the 3? end of the target sequence, a non-target sequence by means of one or more 3? single strand specific exonucleases. Target enrichment may be used to detect variations in nucleotide sequence for detecting phenotypic changes related to health or disease.
    Type: Application
    Filed: March 19, 2014
    Publication date: September 25, 2014
    Applicant: DIRECTED GENOMICS, LLC
    Inventor: Cynthia L. Richard
  • Publication number: 20140255925
    Abstract: The invention provides a provides improvements to assays that employ RNase H cleavage for biological applications related to nucleic acid amplification and detection, where the RNase H has been reversibly inactivated.
    Type: Application
    Filed: March 15, 2013
    Publication date: September 11, 2014
    Applicant: Integrated DNA Technologies
    Inventors: Joseph Alan WALDER, Mark Aaron BEHLKE, Scott D. ROSE, Joseph DOBOSY, Susan Marie RUPP
  • Publication number: 20140248254
    Abstract: This invention provides the use of AChE as nuclease. The use of AChE in regulating the stability of nucleic acid and cell apoptosis, as well as a series of agents based on the use, including the agents for promoting or inhibiting cell apoptosis, the agents for inhibiting tumors, and the agents for protecting nucleic acid from impairing, are provided.
    Type: Application
    Filed: August 8, 2012
    Publication date: September 4, 2014
    Applicant: SHANGHAI INSTITUTES FOR BIOLOGICAL SCIENCES, CHINESE ACADEMY OF SCIENCES
    Inventors: Xuejun Zhang, Jing Xie, Aiying Du, Kaijie Guo, Jun Wu
  • Patent number: 8809023
    Abstract: The present invention relates to combinatorial variants of a parent glucoamylase that have altered properties for reducing the synthesis of condensation products during hydrolysis of starch. Accordingly the variants of a parent glucoamylase are suitable such as for use within brewing and glucose syrup production. Also disclosed are DNA constructs encoding the variants and methods of producing the glucoamylase variants in host cells.
    Type: Grant
    Filed: August 18, 2010
    Date of Patent: August 19, 2014
    Assignee: Danisco US Inc.
    Inventors: Peter Edvard Degn, Richard Bott, Casper Willem Vroemen, Martijn Silvan Scheffers, Wolfgang Aehle
  • Publication number: 20140220586
    Abstract: Filtering small nucleic acids using permeabilized cells and methods for using the filtering to detect genomic DNA accessibility are described.
    Type: Application
    Filed: April 18, 2014
    Publication date: August 7, 2014
    Applicant: Bio-Rad Laboratories, Inc.
    Inventors: Yanhong Kong, Steven T. Okino, Xiangdong Meng
  • Patent number: 8785157
    Abstract: Kits and a method for cleaving double-stranded DNA using Ref and RecA protein and variants thereof at a site having a DNA sequence homologous to the sequence on a single-stranded DNA targeting fragment are disclosed.
    Type: Grant
    Filed: August 12, 2011
    Date of Patent: July 22, 2014
    Assignee: Wisconsin Alumni Research Foundation
    Inventors: Michael M. Cox, Marielle C. Eichhorn-Gruenig, James L. Keck
  • Publication number: 20140178942
    Abstract: Meganuclease variants which cleave at least one target in the provirus of a retrovirus and in particular which cleave the genomic insertion of the provirus. The present invention particular relates to meganuclease variants which cleave the provirus of the Human Immunodeficiency Virus genome following genomic insertion. Vector encoding such variants, as well as to a cell or multi-cellular organism modified by such a vector and use of said meganuclease variants and derived products for genome engineering and for in vivo and ex vivo (gene cell therapy) genome therapy.
    Type: Application
    Filed: October 28, 2013
    Publication date: June 26, 2014
    Applicant: CELLECTIS
    Inventors: ANDRE CHOULIKA, ROMAN GALETTO
  • Patent number: 8759023
    Abstract: The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.
    Type: Grant
    Filed: January 26, 2012
    Date of Patent: June 24, 2014
    Assignee: Novozymes Inc.
    Inventor: Nikolaj Spodsberg
  • Patent number: 8753847
    Abstract: Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer.
    Type: Grant
    Filed: August 13, 2013
    Date of Patent: June 17, 2014
    Assignee: New England Biolabs, Inc.
    Inventors: Yu Zheng, Richard J. Roberts
  • Publication number: 20140127752
    Abstract: A composition and method of cleaving a target DNA and isolating a DNA sequence of interest, directed by a targeting oligonucleotide (“ON”) including a DNA binding agent (stable or unstable), is disclosed. The targeting ON binds to the target DNA before or during DNA cleavage. After cleavage, the isolation of the DNA fragment of interest is facilitated by the affinity tag on the targeting ON or an affinity tag attached using either ligation or polymerase extension method.
    Type: Application
    Filed: November 7, 2013
    Publication date: May 8, 2014
    Inventors: Zhaohui Zhou, Yue Xu, Qun Shan
  • Publication number: 20140090112
    Abstract: A method of gene editing or gene stacking within a FAD2 loci by cleaving, in a site directed manner, a location in a FAD2 gene in a cell, to generate a break in the FAD2 gene and then ligating into the break a nucleic acid molecule associated with one or more traits of interest is disclosed.
    Type: Application
    Filed: September 5, 2013
    Publication date: March 27, 2014
    Inventors: Noel Cogan, John Forster, Matthew Hayden, Tim Sawbridge, German Spangenberg, Steven R. Webb, Manju Gupta, William Michael Ainley, Matthew J. Henry, Jeffrey C. Miller, Dmitry Y. Guschin
  • Publication number: 20140068797
    Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.
    Type: Application
    Filed: March 15, 2013
    Publication date: March 6, 2014
    Applicants: UNIVERSITY OF VIENNA, THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Jennifer A. Doudna, Martin Jinek, Emmanuelle Charpentier, Krzysztof Chylinski, James Harrison Doudna Cate, Wendell Lim, Lei Qi
  • Publication number: 20140038240
    Abstract: The present invention consists of methods for joining DNA molecules (parts) together to form larger DNA molecules (assemblies) of specified sequence and organization. The invention exhibits three necessary characteristics. Firstly, the invention enables 2 or more parts to be joined in a single reaction. Secondly, the seam between joined parts is scarless, producing no residual sequence dependencies like restriction enzyme recognition sites. Thirdly, parts are modular and can easily be reused in novel assemblies without modification. Prior technologies have exhibited no more than two of the three necessary characteristics, limiting their utility in synthesizing and editing DNA molecules of arbitrary sequence.
    Type: Application
    Filed: July 10, 2013
    Publication date: February 6, 2014
    Applicant: PIVOT BIO, INC.
    Inventors: Karsten Temme, Alvin Tamsir
  • Publication number: 20140038239
    Abstract: An I-CreI variant, wherein one of the two I-CreI monomers has at least two substitutions, one in each of the two functional subdomains of the LAGLIDADG core domain situated respectively from positions 26 to 40 and 44 to 77 of I-CreI, said variant being able to cleave a DNA target sequence from the human beta globin gene. Use of said variant and derived products for the prevention and the treatment of pathological conditions caused by a mutation in the human beta globin gene (sickle cell disease, beta-thalassemia).
    Type: Application
    Filed: June 4, 2013
    Publication date: February 6, 2014
    Applicant: Cellectis
    Inventor: Christophe PEREZ-MICHAUT
  • Publication number: 20140038241
    Abstract: By using engineered sequence specific DNA nuclease (“SSDN”), the composition, reagent kit and method of the present invention can cut and release a DNA sequence of interest 1×104-1×107-base pairs long from a source DNA as large as the whole genome. The SSDN further includes an affinity tag or is bound to a solid support that facilitates the isolation of the DNA sequence of interest. The SSDN can include a RecA and Ref combination, a transcription activator like effector nuclease, or a sequence specific chemical nuclease. When applied to genomic sequencing, specific region(s) of interest in the genome can be cut and isolated. Because the irrelevant part of the genome is removed from the sequencing reaction, the speed, cost, and accuracy of genomic sequencing can be improved.
    Type: Application
    Filed: August 3, 2013
    Publication date: February 6, 2014
    Inventors: Zhaohui Zhou, Qun Shan
  • Publication number: 20140017731
    Abstract: An I-CreI variant, wherein at least one of the two I-CreI monomers has at least two substitutions, one in each of the two functional subdomains of the LAGLIDADG core domain situated respectively from positions 26 to 40 and 44 to 77 of I-CreI, said variant being able to cleave a DNA target sequence from the human IL2RG gene. Use of said variant and derived products for the prevention and the treatment of X-linked severe combined immunodeficiency.
    Type: Application
    Filed: May 29, 2013
    Publication date: January 16, 2014
    Applicant: CELLECTIS
    Inventors: Agnes GOUBLE, Sylvestre Grizot
  • Patent number: 8623618
    Abstract: Disclosed herein are engineered cleavage half-domains; fusion polypeptides comprising these engineered cleavage half-domains; polynucleotides encoding the engineered cleavage half-domains and fusion proteins; and cells comprising said polynucleotides and/or fusion proteins. Also described are methods of using these polypeptides and polynucleotides, for example for targeted cleavage of a genomic sequence.
    Type: Grant
    Filed: December 30, 2011
    Date of Patent: January 7, 2014
    Assignee: Sangamo BioSciences, Inc.
    Inventors: Yannick Doyon, Jeffrey C. Miller
  • Patent number: 8592185
    Abstract: 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: Grant
    Filed: August 3, 2012
    Date of Patent: November 26, 2013
    Assignee: Brookhaven Science Associates, LLC
    Inventor: John J. Dunn
  • Publication number: 20130309675
    Abstract: A microparticle having a probe molecule able to capture a specific nucleic acid group to be analyzed is used to extract only the specific nucleic acid group to be analyzed from a nucleic acid sample and the microparticle is thereafter directly immobilized on a smooth plate, whereby a device for nucleic acid analysis is rapidly prepared. Immobilizing a single capture probe molecule onto an individual microparticle in advance and forming, at regular positions on the smooth substrate, an adhesion pad on which a functional group that binds to the microparticle has been introduced makes it possible to readily and rapidly prepare the device for nucleic analysis, where the nucleic acid sample to be analyzed is arranged molecule by molecule in a lattice shape on the smooth substrate.
    Type: Application
    Filed: January 26, 2012
    Publication date: November 21, 2013
    Applicant: HITACHI HIGH-TECHNOLOGIES CORPORATION
    Inventors: Toshiro Saito, Kazumichi Imai, Takayuki Obara, Eri Tarasawa
  • Publication number: 20130288245
    Abstract: The invention provides a provides improvements to assays that employ RNase H cleavage for biological applications related to nucleic acid amplification and detection, where the RNase H has been reversibly inactivated.
    Type: Application
    Filed: March 15, 2013
    Publication date: October 31, 2013
    Applicant: Integrated DNA Technologies
    Inventors: Joseph Alan WALDER, Mark Aaron BEHLKE, Scott D. ROSE, Joseph DOBOSY, Susan Marie RUPP
  • Patent number: 8557545
    Abstract: The invention relates to phosphatases and more in specific to (genetically) modified phosphatases, pharmaceutical compositions comprising (genetically) modified phosphatases and the use of (genetically) modified phosphatases for treating or curing for example sepsis, inflammatory bowel disease or other inflammatory diseases, or renal failure. The invention further relates to a method for producing phosphatases.
    Type: Grant
    Filed: April 25, 2008
    Date of Patent: October 15, 2013
    Assignee: Am-Pharma B.V.
    Inventors: Markwin Paul Velders, Luigi Johannes Cornelius Jonk, Willem Raaben, Marty Bernardus Fransiscus Wulferink
  • Patent number: 8551753
    Abstract: The invention provides methods of removing nucleic acid contamination from reverse transcription reactions and hot-start PCR, wherein said hot-start PCR is a barrier hot-start PCR set up and/or involves a hot-start DNA polymerase, which methods comprise use of a DNase that is substantially irreversibly inactivated by heating at a temperature of about 50° C. for 5 minutes, and that is substantially specific for double stranded DNA. The invention further provides a DNase that is substantially irreversibly inactivated by heating at a temperature of about 50° C. for 5 minutes, and that is substantially specific for double stranded DNA, nucleic acids encoding said DNase and kits or compositions comprising said DNase or said nucleic acid.
    Type: Grant
    Filed: July 21, 2010
    Date of Patent: October 8, 2013
    Assignee: Biotec Pharmacon ASA
    Inventors: Olav Lanes, Morten Elde, Dag Rune Gjellesvik
  • Publication number: 20130210681
    Abstract: A method for performing homologous recombination between at least a first nucleic acid molecule and a second nucleic acid molecule which share at least one region of sequence homology. A method for improving the efficiency of homologous recombination.
    Type: Application
    Filed: June 10, 2011
    Publication date: August 15, 2013
    Inventors: Youming Zhang, Jun Fu, Adrian Francis Stewart
  • Publication number: 20130196864
    Abstract: Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.
    Type: Application
    Filed: February 8, 2013
    Publication date: August 1, 2013
    Applicant: DNA TWOPOINTO, INC.
    Inventors: Sridhar Govindarajan, Jeremy S. Minshull, Jon E. Ness
  • Publication number: 20130196926
    Abstract: Described herein are bioresponsive protein polymers for therapeutic applications, including delivery to physiologically demanding environments, such as the eye surface. Bioresponsive protein polymers can be fused with biopharmaceuticals using genetic engineering techniques for enhanced therapeutic activity. In certain embodiments, the unique temperature-sensitive phase separation properties of bioresponsive protein polymers, allows generation of therapeutics resistant to ocular clearance. Such fusion proteins containing bioresponsive protein polymers and biopharmaceuticals allow retention of drugs in the eye for much longer periods of time.
    Type: Application
    Filed: July 26, 2012
    Publication date: August 1, 2013
    Applicant: UNIVERSITY OF SOUTHERN CALIFORNIA
    Inventors: John Andrew MacKay, Wan Wang
  • Publication number: 20130196373
    Abstract: Disclosed herein are enhanced polypeptides, polynucleotides encoding these polypeptides, cells and organisms comprising novel DNA-binding domains, including TALE DNA-binding domains. Also disclosed are methods of using these novel DNA-binding domains for modulation of gene expression and/or genomic editing of endogenous cellular sequences.
    Type: Application
    Filed: November 16, 2012
    Publication date: August 1, 2013
    Applicant: SANGAMO BIOSCIENCES, INC.
    Inventor: Sangamo BioSciences, Inc.
  • Patent number: 8497110
    Abstract: Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.
    Type: Grant
    Filed: November 15, 2010
    Date of Patent: July 30, 2013
    Assignee: Battelle Energy Alliance, LLC
    Inventors: David N. Thompson, William A. Apel, Vicki S. Thompson, David W. Reed, Jeffrey A. Lacey, Emily D. Henriksen
  • Publication number: 20130183718
    Abstract: The present invention relates to a method of RNA synthesis by RNA-dependent RNA polymerases (RdRp) displaying an RNA polymerase activity on single-stranded DNA templates and to a kit for carrying out the method. The RdRp showing DNA-dependent RNA polymerase activity has a “right hand conformation” and the amino acid sequence of said RdRp comprises a conserved arrangement of the following sequence motifs: a. XXDYS, b. GXPSG, c. YGDD, d. XXYGL, e. XXXXFLXRXX (with the following meanings: D: aspartate, Y: tyrosine, S: serine, G: glycine, P: proline, L: leucine, F: phenylalanine, R: arginine, X: any amino acid). This class of RdRp is exemplified by the RdRp enzymes of viruses of the Caliciviridae family. The present invention also relates to a method for transferring at least one ribonucleotide (rC, rA, rU or rG) to the 3?-end of a single-stranded DNA by using the RdRp of the invention.
    Type: Application
    Filed: September 20, 2011
    Publication date: July 18, 2013
    Applicant: RibpxX GmbH
    Inventor: Jacques Rohayem
  • Patent number: 8486666
    Abstract: Methods and compositions are provided for efficiently removing a guanine cap from the 5? end of an RNA using enzymes. Decapped RNA can be used for cloning, sequencing or other RNA manipulations.
    Type: Grant
    Filed: September 26, 2011
    Date of Patent: July 16, 2013
    Assignee: New England Biolabs, Inc.
    Inventor: Ira Schildkraut
  • Publication number: 20130157870
    Abstract: The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.
    Type: Application
    Filed: September 10, 2012
    Publication date: June 20, 2013
    Applicant: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Dmitry Pushkarev, Stephen R. Quake, Ayelet Voskoboynik, Michael Kertesz
  • Publication number: 20130145490
    Abstract: Methods and means are provided to modify in a targeted manner the plant genome of transgenic plants comprising chimeric genes wherein the chimeric genes have a DNA element commonly used in plant molecular biology. Re-designed meganucleases to cleave such an element commonly used in plant molecular biology are provided.
    Type: Application
    Filed: June 7, 2011
    Publication date: June 6, 2013
    Applicant: BAYER CROPSCIENCE NV
    Inventor: Kathleen D'Halluin
  • Publication number: 20130130248
    Abstract: The present disclosure provides variant Csy4 endoribonucleases, nucleic acids encoding the variant Csy4 endoribonucleases, and host cells genetically modified with the nucleic acids. The variant Csy4 endoribonucleases find use in a variety of applications, which are also provided. The present disclosure also provides methods of detecting a specific sequence in a target polyribonucleotide; and methods of regulating production of a target RNA in a eukaryotic cell.
    Type: Application
    Filed: November 7, 2012
    Publication date: May 23, 2013
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventor: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
  • Publication number: 20130117869
    Abstract: The present invention relates to a method for the generation of compact Transcription Activator-Like Effector Nucleases (TALENs) that can efficiently target and process double-stranded DNA. More specifically, the present invention concerns a method for the creation of TALENs that consist of a single TALE DNA binding domain fused to at least one catalytic domain such that the active entity is composed of a single polypeptide chain for simple and efficient vectorization and does not require dimerization to target a specific single double-stranded DNA target sequence of interest and process DNA nearby said DNA target sequence. The present invention also relates to compact TALENs, vectors, compositions and kits used to implement the method.
    Type: Application
    Filed: April 5, 2012
    Publication date: May 9, 2013
    Applicant: Cellectis S.A.
    Inventors: PHILIPPE DUCHATEAU, Julien Valton, Claudia Bertonati, Jean-Charles Epinat, George H. Silva, Alexandre Juillerat
  • Publication number: 20130085073
    Abstract: A reaction mixture including (a) a nucleic acid having a primer hybridized to a template, (b) nucleotide analogs, wherein the nucleotide analogs have a blocking moiety; (c) a polymerase that is capable of forming an extended primer by adding the nucleotide analogs to the primer, and (d) a deblocking agent that is capable of removing the blocking moiety from the extended primer. Also provided is a method of synthesizing a polynucleotide including sequentially adding a plurality of the different nucleotides analogs to the nucleic acid via several reaction cycles in the reaction mixture, wherein each reaction cycle includes (i) the polymerase adding a nucleotide analog to the nucleic acid to form a transient nucleic acid species comprising a blocking moiety, and (ii) the deblocking agent modifying the transient nucleic acid species to remove the blocking moiety.
    Type: Application
    Filed: September 26, 2012
    Publication date: April 4, 2013
    Applicant: ILLUMINA CAMBRIDGE LIMITED
    Inventor: Illumina Cambridge Limited
  • Publication number: 20130040861
    Abstract: Methods useful in constructing libraries that collectively display and/or express members of diverse families of peptides, polypeptides or proteins and the libraries produced using those methods are disclose. Methods of screening those libraries and the peptides, polypeptides or proteins identified by such screens are also disclosed.
    Type: Application
    Filed: May 4, 2012
    Publication date: February 14, 2013
    Applicant: DYAX CORP.
    Inventors: Robert C. Ladner, Edward H. Cohen, Horacio G. Nastri, Kristin L. Rookey, Rene Hoet, Hendricus Renerus Jacobus Mattheus Hoogenboom
  • Publication number: 20130005612
    Abstract: A method for synthesizing a nucleic acid having a desired sequence and length comprises providing a solid support having an immobilized nucleic acid, performing a nucleic acid addition reaction to elongate the immobilized nucleic acid by adding a nucleotide or an oligonucleotide attached to a protecting group to the nucleic acid, determining whether the nucleotide or the oligonucleotide is added to the nucleic acid, removing the protecting group, and continuing until the immobilized nucleic acid has a desired sequence and length.
    Type: Application
    Filed: September 11, 2012
    Publication date: January 3, 2013
    Applicant: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Peter A. Carr, Brian Y. Chow, Joseph M. Jacobson, David W. Mosley, Christopher Emig
  • Publication number: 20120329067
    Abstract: Provided herein are zinc linger nucleases having altered, arid in particular, improved catalytic activity and methods of generating such nucleases. Accordingly, there are provided methods for identifying improved catalytic activity of a ZFN by expressing a mutated zinc finger nuclease in a cell containing a reporter construct with a toxic gene, and a zinc finger nuclease cleavage site that is recognized by the ZFN. Survival of the cell is positively correlated with catalytic activity of the ZFN; thus, libraries of mutated ZFKs may be selected for altered catalytic activity based on relative survival rates, Methods of using identified ZFNs are also provided.
    Type: Application
    Filed: January 21, 2011
    Publication date: December 27, 2012
    Inventors: Carlos F. Barbas III, Jing Guo
  • Publication number: 20120316075
    Abstract: The present invention relates to a method for conversion of a target nucleic acid molecule according to a predetermined nucleotide code into a converted nucleic acid molecule. The converted nucleic acid molecule has utility for determining the nucleotide sequence of the target nucleic acid molecule, for example, using a nanopore.
    Type: Application
    Filed: March 30, 2012
    Publication date: December 13, 2012
    Applicant: NOBLEGEN BIOSCIENCES, INC.
    Inventors: Philip R. BUZBY, Amit MELLER, Benjamin MCNALLY, Andy FAN, Edyta OLEJNIK-KRZYNMANSKA
  • Publication number: 20120301499
    Abstract: The invention relates to the finding that virus like particles (VLPs) can be loaded with immunostimulatory substances, in particular with DNA oligonucleotides containing non-methylated C and G (CpGs). Such CpG-VLPs are dramatically more immunogenic than their CpG-free counterparts and induce enhanced B and T cell responses. The immune response against antigens optionally coupled, fused or attached otherwise to the VLPs is similarly enhanced as the immune response against the VLP itself. In addition, the T cell responses against both the VLPs and antigens are especially directed to the Th1 type. Antigens attached to CpG-loaded VLPs may therefore be ideal vaccines for prophylactic or therapeutic vaccination against allergies, tumors and other self-molecules and chronic viral diseases.
    Type: Application
    Filed: November 10, 2011
    Publication date: November 29, 2012
    Applicant: CYTOS BIOTECNOLOGY AG
    Inventors: MARTIN BACHMANN, TAZIO STORNI, PATRIK MAURER, ALAIN TISSOT, KATRIN SCHWARZ, EDWIN MEIJERINK, GERD LIPOWSKY, PAUL PUMPENS, INDULIS CIELENS, REGINA RENHOFA
  • Patent number: 8298767
    Abstract: Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.
    Type: Grant
    Filed: August 13, 2010
    Date of Patent: October 30, 2012
    Assignee: Population Genetics Technologies Ltd
    Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
  • Patent number: 8293502
    Abstract: Compositions and methods of use are disclosed for clonally amplifying target polynucleotide sequences in solution and attaching the amplicons to a surface by activation of a masked binding moiety. In an embodiment, the amplicons comprise the masked binding moiety and the surface comprises a binding partner of the binding moiety. Upon activation of the binding moiety, the amplicons bind to the binding partner on the surface. In a non-limiting example, the masked binding moiety is caged biotin or caged fluorescein, while the corresponding binding partner is avidin or an anti-fluorescein antibody.
    Type: Grant
    Filed: April 14, 2011
    Date of Patent: October 23, 2012
    Assignee: Applied Biosystems, LLC
    Inventor: Benjamin Schroeder