Method Of Creating A Library (e.g., Combinatorial Synthesis, Etc.) Patents (Class 506/23)
  • Patent number: 9981264
    Abstract: Methods and systems are provided for a lateral flow test device. In one example a lateral flow test device may include a housing comprising an upper first portion and a lower second portion, the lower second portion further including a planar surface, a nitrocellulose matrix strip, the strip disposed on the planar surface, and one or more ligand regions included in the strip, the ligand regions comprising one or more ligands. The strip may be formed from a liquid polymer mixture dispensed onto the planar surface via a dispensing device positioned vertically above the planar surface.
    Type: Grant
    Filed: November 3, 2015
    Date of Patent: May 29, 2018
    Assignee: Grace Bio-Labs, Inc.
    Inventors: Charles Greef, Joshua Snider, Steven Weaver, Jennipher Grudzien
  • Patent number: 9938572
    Abstract: Systems and methods are provided for forming emulsions from an aqueous fluid and oil. The aqueous fluid-in-oil emulsions are useful for numerous molecular biology techniques. The system is configured to cyclically translate a chamber containing the emulsion components, along a cycle path, while maintaining the axial orientation of the chamber with respect to a horizontal plane, and without rotating the chamber.
    Type: Grant
    Filed: September 8, 2016
    Date of Patent: April 10, 2018
    Assignee: RainDance Technologies, Inc.
    Inventors: Darren R. Link, Patrick Odoy, Akim Lennhoff, John Luckey, Xinyu Li
  • Patent number: 9328378
    Abstract: The invention relates to a method of preparing a library of template polynucleotides which reduces and/or prevents the formation of adaptor-dimers. The invention also relates to the use of a library of templates prepared using the method of the invention for solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends which is substantially free of adaptor-dimers.
    Type: Grant
    Filed: July 30, 2007
    Date of Patent: May 3, 2016
    Assignee: Illumina Cambridge Limited
    Inventors: David James Earnshaw, Niall Anthony Gormley, Helen Rachel Bignell, Melanie Anne Smith
  • Patent number: 9309566
    Abstract: In some embodiments, the present teachings provide methods for paired end sequencing. In some embodiment, a polynucleotide template to be subjected to paired end sequencing comprises at least one cross linking moiety and at least one scissile moiety. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cleavage step, and (c) a reverse sequencing step. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cross-linking step, (c) a cleavage step, and (d) a reverse sequencing step.
    Type: Grant
    Filed: March 14, 2013
    Date of Patent: April 12, 2016
    Inventors: Bin Li, Kai Qin Lao, Jennifer O'Neil, Jennifer Kunkel, Kellie Haley, Rachel Kasinskas, Zhaochun Ma, Pius Brzoska
  • Patent number: 9255348
    Abstract: Exposure to ionizing radiation can produce a well-defined dose dependent signature in terms of changes in gene expression. In approaches and devices described herein, such a signature can be used to generate and use a self-contained radiation biodosimeter device, based on, for example, a blood finger stick. Various aspects of the invention are directed to biodosimetry with a fully integrated biochip using gene expression signatures.
    Type: Grant
    Filed: August 24, 2007
    Date of Patent: February 9, 2016
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Frederic Zenhausern, Christine Orozco, Mark Richards, Carl Yamashiro, Sally A. Amundson, Ralf Lenigk, Michael L. Bittner, Yoganand Balagurunathan
  • Patent number: 9040465
    Abstract: A combination of deposition processes can be used to evaluate layer properties using a combinatorial workflow. The processes can include a base ALD process and another process, such as a PVD process. The high productivity combinatorial technique can provide an evaluation of the material properties for given ALD base layer and PVD additional elements. An ALD process can then be developed to provide the desired layers, replacing the ALD and PVD combination.
    Type: Grant
    Filed: November 19, 2012
    Date of Patent: May 26, 2015
    Assignee: Intermolecular, Inc.
    Inventors: Prashant B Phatak, Venkat Ananthan, Wayne R French
  • Patent number: 9034798
    Abstract: Capture compounds and collections thereof and methods using the compounds for the analysis of biomolecules are provided. In particular, collections, compounds and methods are provided for analyzing complex protein mixtures, such as the proteome. The compounds are multifunctional reagents that provide for the separation and isolation of complex protein mixtures. Automated systems for performing the methods also are provided.
    Type: Grant
    Filed: February 26, 2010
    Date of Patent: May 19, 2015
    Inventors: Hubert Köster, Daniel Paul Little, Suhaib Mahmood Siddiqi, Matthew Peter Grealish, Subramanian Marappan, Chester Frederick Hassman, III, Ping Yip
  • Publication number: 20150133319
    Abstract: Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins.
    Type: Application
    Filed: February 27, 2013
    Publication date: May 14, 2015
    Inventors: Glenn K. Fu, Stephen P.A. Fodor, Julie Wilhelmy
  • Publication number: 20150133317
    Abstract: Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest.
    Type: Application
    Filed: April 27, 2012
    Publication date: May 14, 2015
    Applicants: Department of Veterans Affairs, The Board of Trustees of the Leland Stanford Junior University
    Inventors: William H. Robinson, Yann Chong Tan, Jeremy Sokolove
  • Publication number: 20150105298
    Abstract: The disclosure relates to in situ hybridization probes for the detection of target nucleic acid sequences within a sample and methods of making and using the same. The in situ hybridization probes of the current disclosure include a plurality of nucleic acid elements capable of selectively hybridizing to at least a portion of a nucleic acid of interest and/or other nucleic acid elements of the in situ hybridization probe, which enable the detection of a target nucleic acid. The current disclosure also relates to kits which incorporate the in situ hybridization probe compositions of the instant disclosure.
    Type: Application
    Filed: October 10, 2014
    Publication date: April 16, 2015
    Applicant: The Research Foundation for The State University of New York
    Inventor: Kevin Czaplinski
  • Publication number: 20150105285
    Abstract: The present invention relates to a method for the production of a library comprising recombinant derivatives of the SH3 domain of the Fyn kinase of SEQ ID NO: 1 as well as a method for selecting from a library comprising recombinant derivatives of the SH3 domain of the Fyn kinase of SEQ ID NO: 1 one or more of said derivatives having a specific binding affinity to a protein or peptide.
    Type: Application
    Filed: September 19, 2014
    Publication date: April 16, 2015
    Inventors: Dragan GRABULOVSKI, Dario NERI
  • Patent number: 9006150
    Abstract: Disclosed is a composition comprising the 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: Grant
    Filed: May 17, 2012
    Date of Patent: April 14, 2015
    Assignee: Vipergen ApS
    Inventors: Nils Jokob Vest Hansen, Peter Blakskjaer, Margit Haahr Hansen, Lars Kolster Petersen, Tara Renee Heitner
  • Patent number: 8999897
    Abstract: The use of a tag moiety comprising a biotinylation domain, such as biotin carboxyl carrier protein (BCCP), as a protein folding marker and protein solubility enhancer in the orientated surface capture of products of heterologously expressed genes is described. Methods for increasing the solubility of proteins and determining the folded state of a protein are also disclosed. The uses and methods of the invention can be carried out in a multiplexed manner on more than one protein in the formation of libraries. In addition the nucleic acid molecule encoding the biotinylation domain of the tag moiety can be used to increase the proportion of clones in a library that express the protein of interest.
    Type: Grant
    Filed: January 29, 2003
    Date of Patent: April 7, 2015
    Assignee: Sense Proteomic Limited
    Inventors: Mitali Samaddar, Jonathan Michael Blackburn, Darren James Hart, Michael Richard Dyson
  • Publication number: 20150094238
    Abstract: A system for inserting reagent or macrobeads into bores of a sample plate is disclosed comprising an insertion device arranged to retain one or more reagent or macrobeads by means of a vacuum whilst inserting the reagent or macrobeads into bores of the sample plate.
    Type: Application
    Filed: March 6, 2013
    Publication date: April 2, 2015
    Applicant: Dynex Technologies, Inc.
    Inventors: Adrian Bunce, Andrew Fusellier
  • Publication number: 20150080266
    Abstract: The present disclosure provides methods for optimizing barcode design for multiplex DNA sequencing. Also disclosed are DNA barcodes optimized for use with particular sequencing technologies.
    Type: Application
    Filed: September 4, 2012
    Publication date: March 19, 2015
    Applicant: Atreca, Inc.
    Inventors: Wayne Volkmuth, Yann Chong Tan
  • Publication number: 20150072897
    Abstract: A sample loader for loading a liquid sample into a plurality of reaction sites within a substrate is provided. The sample loader includes a first blade, and a second blade coupled to the first blade. The sample loader further comprises a flow path between the first blade and second blade configured to dispense a liquid sample to a substrate including a plurality of reaction sites. Further, in various embodiments the liquid sample has an advancing contact angle of 85+/?15 degrees with the first and second blade. Furthermore, loading of the liquid sample dispensed from the flow path to the plurality of reaction sites may be based on capillary action.
    Type: Application
    Filed: March 15, 2013
    Publication date: March 12, 2015
    Inventors: Michael C. Pallas, James C. Nurse, Gary Lim, Theodore E. Straub, Evan W. Foster
  • Publication number: 20150057191
    Abstract: Compositions are provided, which can be used as frameworks for the creation of very stable and soluble single-chain Fv antibody fragments. These frameworks have been selected for intracellular performance and are thus ideally suited for the creation of scFv antibody fragments or scFv antibody libraries for applications where stability and solubility are limiting factors for the performance of antibody fragments, such as in the reducing environment of a cell. Such frameworks can also be used to identify highly conserved residues and consensus sequences which demonstrate enhanced solubility and stability.
    Type: Application
    Filed: August 26, 2014
    Publication date: February 26, 2015
    Inventors: Kathrin Tissot, Stefan Ewert, Adrian Auf Der Maur, Alcide Barberis, Dominik Escher
  • Publication number: 20150038373
    Abstract: De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.
    Type: Application
    Filed: August 5, 2014
    Publication date: February 5, 2015
    Inventors: William Banyai, Bill James Peck, Andres Fernandez, Siyuan Chen, Pierre Indermuhle
  • Publication number: 20150018253
    Abstract: Disclosed are compositions and methods for the labeling of two or more targets with different labels. Specifically, disclosed are compositions for biotin and the protection of biotin within multilabel assays which employ the biotin-biotin binding protein binding relationship for each distinct label in relation to targets such as nucleic acids, polypeptides, antibodies or cells. These multilabel assays are enabled through the use of biotin with desthiobiotin, orthogonal protecting schemes for biotin, or a combination of the approaches.
    Type: Application
    Filed: July 29, 2014
    Publication date: January 15, 2015
    Inventors: Robert G. KUIMELIS, Glenn H. MCGALL, Stephen P. A. FODOR
  • Publication number: 20150018252
    Abstract: The invention provides methods relating methods for environmentally sealing, protecting, and providing analysis chips for processing and analysis. The analysis chips are bonded directly or indirectly to chip carriers which are held within the chambers of an environmental packaging strip. The chambers are sealed with a sealing film such that the chip carriers are extracted using a piercing tool and an extraction tool.
    Type: Application
    Filed: May 22, 2014
    Publication date: January 15, 2015
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Paul Newby, William R. Hanson
  • Patent number: 8932994
    Abstract: The invention relates to a method of preparing a library of template polynucleotides with uniform sequence representation and to use of a library of templates prepared using this method for solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends, which contains even representation of all the fragments present in a starting sample of nucleic acid before fragmentation. The invention is especially applicable to the preparation of short insert libraries, where the sample fragments are less than 150 base pairs in length.
    Type: Grant
    Filed: August 23, 2007
    Date of Patent: January 13, 2015
    Assignee: Illumina, Inc.
    Inventors: Niall Anthony Gormley, Melanie Anne Smith
  • Patent number: 8932879
    Abstract: Methods are described for phototransferring a compound from a first surface to a second surface. Compounds are described with photocleavable linkers. Compounds attached to a first surface through a photocleavable linker are put in proximity (or contact) with a second surface, and then phototransferred to the second surface upon exposure to electromagnetic radiation. Illuminating the compound with radiation photocleaves the compound from the first surface and transfers the compound to the second surface.
    Type: Grant
    Filed: October 30, 2008
    Date of Patent: January 13, 2015
    Assignee: Ambergen, Inc.
    Inventors: Mark J. Lim, Kenneth J. Rothschild
  • Patent number: 8932995
    Abstract: A combinatorial processing chamber is provided. The combinatorial processing chamber is configured to isolate a radial portion of a rotatable substrate support, which in turn is configured to support a substrate. The chamber includes a plurality of clusters process heads in one embodiment. An insert having a base plate disposed between the substrate support and the process heads defines a confinement region for a deposition process in one embodiment. The base plate has an opening to enable access of the deposition material to the substrate. Through rotation of the substrate and movement of the opening, multiple regions of the substrate are accessible for performing combinatorial processing on a single substrate.
    Type: Grant
    Filed: December 21, 2011
    Date of Patent: January 13, 2015
    Assignee: Intermolecular, Inc.
    Inventors: Rick Endo, Kurt Weiner, Indranil De, James Tsung, Maosheng Zhao, Jeremy Cheng
  • Publication number: 20150011513
    Abstract: A triazole bridged flavonoid dimer compound library was efficiently constructed via the cycloaddition reaction of a series of flavonoid-containing azides (Az 1-15) and alkynes (Ac 1-17). These triazole bridged flavonoid dimers and their precursor alkyne- and azide-containing flavonoids were screened for their ability to modulate multidrug resistance (MDR) in P-gp-overexpressed cell line (LCC6MDR), MRP1-overexpressed cell line (2008/MRP1) and BCRP-overexpressed cell line (HEK293/R2 and MCF7-MX100). Generally, they displayed very promising MDR reversal activity against P-gp-, MRP1- and BCRP-mediated drug resistance. Moreover, they showed different levels of selectivity for various transporters. Overall, they can be divided into mono-selective, dual-selective and multi-selective modulators for the P-gp, MRP1 and BCRP transporters.
    Type: Application
    Filed: March 1, 2013
    Publication date: January 8, 2015
    Inventors: Larry Ming Cheung Chow, Tak Hang Chan, Kin Fai Chan, Iris Lai King Wong, Man Chun Law
  • Publication number: 20150005197
    Abstract: A photonic crystal-immunoassay platform wherein the periodicity of wells in an array are designed based on the leaky wave-guided modes of high refractive index material and a wavelength of excitation and/or emission of electromagnetic radiation associated with a signal used in the assay.
    Type: Application
    Filed: January 7, 2013
    Publication date: January 1, 2015
    Applicant: The Regents of the University of California
    Inventors: Ian M. Kennedy, Jin-Hee Han, Sudheendra Lakshmana
  • Publication number: 20140378330
    Abstract: Disclosed is a multi-primer amplification assay, method and kits for detecting Mycoplasma species and closely related species utilizing a plurality of oligonucleotide primers in contact with a sample in a single vessel and detecting the amplification product, wherein the presence of an amplification product indicates Mycoplasma in the sample.
    Type: Application
    Filed: June 25, 2014
    Publication date: December 25, 2014
    Inventors: Olga PETRAUSKENE, Pius Brzoska, Somaya Bit, Jen-Kuei Liu, Robert Tebbs, Manohar Furtado
  • Publication number: 20140378348
    Abstract: Microfluidic system, including methods and apparatus, for processing fluid, such as by droplet generation. In some embodiments, the system may include a well and a channel component attached to the well. The channel component may include (a) a body, (b) an input tube (a “fluid pickup”) projecting from a bottom surface of the body and having an open bottom end disposed in the input well, (c) a microchannel, and (d) a passage extending through the input tube and the body and connecting the well to the microchannel. The system may be configured to receive a sample-containing fluid in the well and retain the sample-containing fluid below a top end of the passage, until a pressure differential is created that drives at least a portion of the sample-containing fluid from the well via the passage and through the microchannel.
    Type: Application
    Filed: June 23, 2014
    Publication date: December 25, 2014
    Inventors: Anthony J. Makarewicz, JR., Luc Bousse, Stefano Schiaffino
  • Patent number: 8912130
    Abstract: Disclosed herein are methods of method of making a substrate for performing a chemical synthesis reaction.
    Type: Grant
    Filed: September 16, 2011
    Date of Patent: December 16, 2014
    Assignee: Illumina, Inc.
    Inventors: Brett Ellman, Michal Lebl, Aaron Jones, Steve Fambro, David Heiner
  • Publication number: 20140350088
    Abstract: The present invention is related to a method for generating a nucleic acid molecule capable of binding to a target molecule comprising the following steps: a) providing a reference nucleic acid molecule, wherein the reference nucleic acid molecule is capable of binding to the target molecule and wherein the reference nucleic acid molecule comprises a sequence of nucleotides, wherein the sequence of nucleotides comprises n nucleotides; b) preparing a first level derivative of the reference nucleic acid molecule, wherein the first level derivative of the reference nucleic acid molecule differs from the reference nucleic acid molecule at one nucleotide position, wherein the first level derivative is prepared by replacing the ribonucleotide at the one nucleotide position by a 2?-deoxyribonucleotide in case the reference nucleic acid has a ribonucleotide at the nucleotide position and wherein the first level derivative is prepared by replacing the 2?-deoxyribonucleotide at the one nucleotide position by a ribonucl
    Type: Application
    Filed: January 10, 2012
    Publication date: November 27, 2014
    Inventors: Florian Jarosch, Sven Klussmann, Simone Sell, Werner Purschke, Christian Maasch, Axel Vater, Kai Hohlig
  • Publication number: 20140349889
    Abstract: The present disclosure discloses a method to prepare a supra-monolayer nanopattern and its uses.
    Type: Application
    Filed: December 11, 2012
    Publication date: November 27, 2014
    Inventors: Guangzhao Mao, Daniel J. Sobczynski, Sunxi Wang, Juxhin Xhahysa, Pedram Jahanian
  • Publication number: 20140323357
    Abstract: The present technology provides for a microfluidic substrate configured to carry out PCR on a number of polynucleotide-containing samples in parallel. The substrate can be a single-layer substrate in a microfluidic cartridge. Also provided are a method of making a microfluidic cartridge comprising such a substrate. Still further disclosed are a microfluidic valve suitable for use in isolating a PCR chamber in a microfluidic substrate, and a method of making such a valve.
    Type: Application
    Filed: April 28, 2014
    Publication date: October 30, 2014
    Applicant: HANDYLAB, INC.
    Inventor: Kalyan Handique
  • Patent number: 8871688
    Abstract: The present invention relates to a method for absolute quantification of polypeptides.
    Type: Grant
    Filed: June 2, 2008
    Date of Patent: October 28, 2014
    Assignees: INSERM (Institut National de la Sante et de la Recherche Medicale), Commissariat a l'Energie Atomique
    Inventors: Virginie Brun, Alain Dupuis, Jerome Garin
  • Publication number: 20140315755
    Abstract: The present invention relates to the generation and construction of libraries for genome-wide antisense oligonucleotide and siRNA.
    Type: Application
    Filed: December 26, 2013
    Publication date: October 23, 2014
    Inventors: Tao Chen, Jinghan Li, Lei Xi, Shangan Zhang
  • Publication number: 20140315762
    Abstract: The present invention relates to oligonucleotide-encoded libraries and methods of tagging such libraries. In particular, the methods and oligonucleotides can include one or more 2?-substituted nucleotides, such as 2?-O-methyl or 2?-fluoro nucleotides, and other conditions or reagents to enhance enzyme ligation or one or more chemical functionalities to support chemical ligation.
    Type: Application
    Filed: September 7, 2012
    Publication date: October 23, 2014
    Applicant: X-Chem, Inc.
    Inventors: Anthony D. Keefe, Richard W. Wagner, Alexander Litovchick, Matthew Clark, John W. Cuozzo, Ying Zhang, Paolo A. Centrella, Christopher D. Hupp
  • Publication number: 20140309136
    Abstract: The invention relates to the detection of three different bacterial species which are responsible for sexually-transmitted diseases, i.e., Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Mycoplasma genitalium (MG). The invention more particularly relates to the detection of these three species in real-time PCR, in multiplex PCR and in real-time multiplex PCR. The invention provides reference templates sequences, which are especially adapted to the design of primers and probes, which can be used together in the same tube to detect CT and/or MG and/or NG by real-time multiplex amplification.
    Type: Application
    Filed: May 22, 2014
    Publication date: October 16, 2014
    Inventor: Gervais CLAREBOUT
  • Publication number: 20140303040
    Abstract: Multiplexed microarrays, multiplexed microarray cassettes, and methods for fabricating multiplexed microarrays are disclosed. In some embodiments, the multiplexed microarrays include a substrate, a chamber layer, and at least one channel layer. The topmost channel layer forms a port layer and may be compressible. The multiplexed microarrays may also include a compressible or non-compressible cover or sealing film. The multiplexed microarray cassette includes a base and may also include a cover. The base of the multiplexed microarray cassette includes a plurality of tracks to receive corresponding multiplexed microarrays.
    Type: Application
    Filed: May 7, 2014
    Publication date: October 9, 2014
    Inventor: John A. Luckey
  • Patent number: 8846576
    Abstract: A method of evaluating the effect of a xenobiotic on biomarkers, such as drug transporters and drug-metabolizing enzymes in hepatocytes is provided. The method comprises the formation of a xenobiotic-stimulated biological sample, such as whole blood, which contains a plurality of cytokines. A portion of xenobiotic-stimulated biological sample is cultured with hepatocytes. The hepatocytes are then analyzed to evaluate the activity of drug transporters and/or drug-metabolizing enzymes, or other biomarkers to determine the effect of the xenobiotic on drug metabolism in the hepatocytes.
    Type: Grant
    Filed: May 25, 2012
    Date of Patent: September 30, 2014
    Assignee: Xenotech LLC
    Inventors: Maciej Czerwinski, David Benjamin Buckley, Faraz Kazmi
  • Publication number: 20140271617
    Abstract: Disclosed is a library consisting essentially of a plurality of antigen-binding molecules differing in sequence from each other, wherein an antigen-binding domain in each of the antigen-binding molecules comprises at least one amino acid residue that changes the antigen-binding activity of the antigen-binding molecule depending on ion concentration conditions. Also disclosed are a composition comprising a plurality of polynucleotide molecules each encoding the antigen-binding molecules, a composition comprising a plurality of vectors each comprising the polynucleotide molecules, a method for selecting the antigen-binding molecules, a method for isolating the polynucleotide molecules, a method for producing the antigen-binding molecules, and a pharmaceutical composition comprising any of the antigen-binding molecules.
    Type: Application
    Filed: September 28, 2012
    Publication date: September 18, 2014
    Inventors: Tomoyuki Igawa, Shinya Ishii, Miho Funaki, Naoka Hironiwa, Shun Shimizu
  • Patent number: 8825411
    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: Grant
    Filed: May 4, 2005
    Date of Patent: September 2, 2014
    Assignee: DNA Twopointo, Inc.
    Inventors: Sridhar Govindarajan, Jeremy S. Minshull, Jon E. Ness
  • Patent number: 8815781
    Abstract: The present patent application introduces methods for generating mixture compound libraries from a drug lead. The mixture compound libraries are then screened for the discovery of modified drug lead compounds which possess desired improved drug properties. The process utilizes a non-selective reaction to modify the drug lead compound structure. Compared to existing methods of modifying a drug lead compound, this new method can modify more structural positions of a drug lead compound. As a consequence, there will be greater probability of finding a product with improved drug properties.
    Type: Grant
    Filed: November 15, 2010
    Date of Patent: August 26, 2014
    Inventor: Xueheng Cheng
  • Patent number: 8809239
    Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PTOCE (PTO Cleavage and Extension) assay. The present invention detects a target nucleic acid sequence in which the PTO (Probing and Tagging Oligonucleotide) hybridized with the target nucleic acid sequence is cleaved to release a fragment and the fragment is hybridized with the CTO (Capturing and Templating Oligonucleotide) to form an extended duplex, followed by detecting the presence of the extended duplex. The extended duplex provides signals (generation, increase, extinguishment or decrease of signals) from labels indicating the presence of the extended duplex and has adjustable Tm value, which are well adoptable for detection of the presence of the target nucleic acid sequence.
    Type: Grant
    Filed: January 11, 2012
    Date of Patent: August 19, 2014
    Assignee: Seegene, Inc.
    Inventors: Jong Yoon Chun, Young Jo Lee
  • Patent number: 8808984
    Abstract: The invention relates to a method for synthesizing templated molecules attached to the templated which directed the synthesis thereof. The method involves a template, a scaffold functional entity and a functional entity attached to a building block, which, in turn, is attached the template. The scaffold functional entity and the functional entity of the building block are both provided with complementary dimerization domains allowing the functional entities to come into close proximity when the complementary domains interact with to each other. The method may be used for generating libraries of templated molecules which may be selected for biological activity.
    Type: Grant
    Filed: July 24, 2008
    Date of Patent: August 19, 2014
    Assignee: Neuvolution A/S
    Inventors: Henrik Pedersen, Anette Holtmann, Thomas Franch, Alex Haahr Gouliaev, Jakob Felding
  • Patent number: 8802024
    Abstract: A method for manufacturing a biochip is provided. First, a first self-assembled monolayer is coated on a substrate. Next, a plurality of first biomedical molecular dots are formed on the first self-assembled monolayer by micro-titration technique. After the bonding reaction between the first biomedical molecular point and the first self-assembled monolayer, a second self-assembled monolayer is deposited on the surface of the first self-assembled monolayer by evaporation. The second self-assembled monolayer attached on the plurality of first biomedical molecular dots and the first self-assembled monolayer not bonded to the substrate are removed, so that the first biomedical molecular dots immobilized on the first self-assembled monolayer are exposed. Finally, a second biomedical molecular layer is immobilized on the exposed portions of the first biomedical molecular dots.
    Type: Grant
    Filed: September 28, 2007
    Date of Patent: August 12, 2014
    Assignee: National Tsing Hua University
    Inventors: Fan Gang Tseng, Hsin Yi Hsieh, Chun Lung Wu
  • Publication number: 20140221250
    Abstract: The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity. The libraries are designed to reflect the preimmune repertoire naturally created by the human immune system, with or without DH segments derived from other species, and are based on rational design informed by examination of publicly available databases of antibody sequences.
    Type: Application
    Filed: April 18, 2014
    Publication date: August 7, 2014
    Applicant: Adimab, LLC
    Inventors: Maximiliano Vasquez, Michael Feldhaus, Tillman U. Gerngross, K. Dane Wittrup
  • Patent number: 8778848
    Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.
    Type: Grant
    Filed: June 8, 2012
    Date of Patent: July 15, 2014
    Assignee: Illumina, Inc.
    Inventors: Shengrong Lin, Yir-Shyuan Wu, Kevin Gunderson, John A. Moon
  • Patent number: 8778849
    Abstract: A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.
    Type: Grant
    Filed: October 26, 2012
    Date of Patent: July 15, 2014
    Assignee: Illumina, Inc.
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Patent number: 8728986
    Abstract: A metering device, a metering element, and a method for operating same, the metering element having a storage container open on one side for receiving the substances to be metered and a plunger which is axially movable and reversibly seals the opening of the storage container and which preferably has at least one centrally located metering opening for metering the substances provided in the storage container, the plunger including a separation device for particles.
    Type: Grant
    Filed: June 14, 2012
    Date of Patent: May 20, 2014
    Assignee: Robert Bosch GmbH
    Inventors: Thomas Brinz, Jane Lewis, Markus Tiefenbacher, Thomas Geiger
  • Publication number: 20140135235
    Abstract: Highly specific and novel methods for reversible hydrazone solid-phase extraction (rHSPE) are provided for glycan or glycopeptide isolation from proteins, peptides, and other contaminants for glycan and glycopeptide analysis. Glycans or glycopeptides in complex mixtures can be conjugated onto solid support or affinity or chemical tags via reversible hydrazone bond. The conjugation methods of the present invention are chemically specific and provide unique means for the removal of other non-glycan containing molecules in the complex sample before the glycans or glycopeptides are hydrolyzed and recovered for analysis. The hydrazone formation and hydrolysis of the novel methods allows for the analysis of glycans and glycopeptides. The hydrazide coating on the solid-phase surfaces are useful for surface glycan capture and on target glycan analysis. Uses of the information generated by the inventive methods for diagnosis and treatment are also disclosed.
    Type: Application
    Filed: June 6, 2012
    Publication date: May 15, 2014
    Inventors: Hui Zhang, Shuang Yang
  • Publication number: 20140135236
    Abstract: A custom-made matrix suitable for receiving a tissue sample is described as well as the use thereof to obtain a multiplex histological preparation. The invention also relates to a multiplex biopsy array comprising tissue and/or cell samples arranged in a matrix material and to a method for the preparation of a multiplex biopsy array. Methods for preparing blocks of matrix material to be used in multiplex biopsy arrays are also described, as well as methods for loading biopsy samples in said blocks, and methods for treating and processing said blocks to form biopsy arrays. The biopsy arrays made using the block of matrix material can be used to prepare sections and slides for histological procedures, including quantitative analyses and parallel processing.
    Type: Application
    Filed: June 28, 2012
    Publication date: May 15, 2014
    Inventor: Sorin Musat
  • Patent number: 8722585
    Abstract: Disclosed are methods, compositions and kits related to making double-tagged DNA libraries from RNA/DNA samples. A double-tagged oligonucleotide (DTO) is employed to efficiently add two different tags to ends of DNAs to make a double-tagged DNA libraries. Also disclosed are methods to make mate pair libraries using the double-tagged oligonucleotide, and methods to make double-tagged single stranded DNA. The double-tagged DNA libraries of the invention are ready to be used on next generation sequencing machines.
    Type: Grant
    Filed: June 7, 2012
    Date of Patent: May 13, 2014
    Inventor: Yan Wang