Involving An Encoding Step Patents (Class 506/31)
  • Patent number: 10730906
    Abstract: Disclosed is a method for the manufacture of a library of complexes. The complexes comprise templated molecules attached to the template which directed the synthesis thereof. The templated molecules are produced in a step-by-step fashion which provides for a high local concentration of reactive groups involved in the formation of connections between the individual components of the template molecule.
    Type: Grant
    Filed: July 30, 2003
    Date of Patent: August 4, 2020
    Assignee: NUEVOLUTIONS A/S
    Inventor: Henrik Pedersen
  • Patent number: 10214761
    Abstract: There are provided amino acid derivatives of formula V and VI as defined herein which are pyrrolysine analogs for use in bioconjugation processes.
    Type: Grant
    Filed: June 1, 2017
    Date of Patent: February 26, 2019
    Assignee: MEDIMMUNE LIMITED
    Inventors: Kenneth H. Grabstein, Michael Van Brunt, Marcello Marelli
  • Patent number: 9994687
    Abstract: Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed.
    Type: Grant
    Filed: June 26, 2014
    Date of Patent: June 12, 2018
    Assignee: Illumina, Inc.
    Inventors: Lorenzo Berti, Andrew A. Brown, Wayne N. George
  • Publication number: 20150126381
    Abstract: The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of: a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c).
    Type: Application
    Filed: January 6, 2015
    Publication date: May 7, 2015
    Inventor: Peter Birk Rasmussen
  • Publication number: 20150105295
    Abstract: Analysis of a system and/or sample involves the use of absorption-encoded micro beads. Each type of micro bead is encoded with amounts of the k dyes in a proportional relationship that is different from proportional relationships of the k dyes of others of the n types of absorption-encoded micro beads. A system and/or a sample can be analyzed using information obtained from detecting the one or more types of absorption-encoded micro beads.
    Type: Application
    Filed: December 18, 2014
    Publication date: April 16, 2015
    Inventors: Peter Kiesel, Joerg Martini, Michael I. Recht
  • 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
  • Publication number: 20150051117
    Abstract: Methods and compositions for synthesizing nucleic acid sequences in an emulsion are provided.
    Type: Application
    Filed: August 15, 2014
    Publication date: February 19, 2015
    Inventors: George M. CHURCH, Richard C. TERRY, Sriram KOSURI, Di ZHANG
  • Publication number: 20150011430
    Abstract: Provided herein are methods, compositions, and kits for assays, many of which involve amplification reactions such as digital PCR or droplet digital PCR. The assays may be used for such applications as sequencing, copy number variation analysis, and others. In some cases, the assays involve subdividing a sample into multiple partitions (e.g., droplets) and merging the partitions with other partitions that comprise adaptors with barcodes.
    Type: Application
    Filed: September 22, 2014
    Publication date: January 8, 2015
    Inventor: Serge Saxonov
  • Patent number: 8927465
    Abstract: A process for making a micro-array. The process comprises the step of depositing a population of microbeads on a substrate having at least one fiducial. The population being comprised of at least two sub-populations, preferably multiple sub-populations, each comprising a known active agent capable of specific binding with at least one target analyte. The said subpopulations are deposited sequentially and at discrete periods of each other. The process also comprises the step of making images of the substrate after deposition of each subpopulation. The images are then compared using the fiducial as a reference to thereby determine the location of each microbead and to identify the subpopulation, and its known active agent, based on differences between each image. Also disclosed in a system for using the microarray.
    Type: Grant
    Filed: August 3, 2007
    Date of Patent: January 6, 2015
    Assignee: National University University of Singapore
    Inventors: Dieter Trau, Wen-Tso Liu, Kian Kok Johnson Ng
  • Publication number: 20150005200
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Application
    Filed: June 26, 2014
    Publication date: January 1, 2015
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • Publication number: 20150005198
    Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.
    Type: Application
    Filed: November 19, 2013
    Publication date: January 1, 2015
    Applicant: Firefly Bioworks, Inc.
    Inventors: Daniel C. Pregibon, Isaac Stoner, Andreas Windemuth, Timothy Erps
  • Publication number: 20140206569
    Abstract: Encoded microcarriers, and more specifically microcarriers having codes written on them. Methods for writing the codes on the microcarriers, methods of reading the codes, and methods of using the encoded microcarriers. A preferred method of encoding the microcarriers involves exposing microcarriers containing a bleachable substance to a high spatial resolution light source to bleach the codes on the microcarriers. The encoded microcarriers may be used, for example, as support materials in chemical and biological assays and syntheses.
    Type: Application
    Filed: March 25, 2014
    Publication date: July 24, 2014
    Applicant: Biocartis SA
    Inventors: Stefaan Cornelis De Smedt, Joseph Demeester, Christiaan Hubert Simon Roelant, Rudi Wilfried Jan Pauwels
  • Patent number: 8759007
    Abstract: The present invention provides a method for detecting modified LDL, abnormal cells or bacteria using an intermolecular interaction analysis method, in which a region involved in ligand recognition by a receptor is expressed, without modification or as a biotinylated protein, in cells or in a test tube, and thereafter, the expressed region or the expressed biotinylated protein is immobilized via avidin or streptavidin to a solid phase while the orientation thereof is maintained, and the immobilized protein is utilized; and a kit for detecting the modified LDL or the like.
    Type: Grant
    Filed: December 11, 2009
    Date of Patent: June 24, 2014
    Assignee: National Food Research Institute
    Inventors: Sachiko Machida, Kiyoshi Hayashi, Ken Tokuyasu, Yoshikiyo Sakakibara, Shigeru Matsunaga
  • Publication number: 20140100123
    Abstract: A plurality of isolated microvessels including a plurality of encoded microvessels each having a microbody and a reservoir core. The microbody is configured to separate a biological or chemical substance in the reservoir core from an ambient environment surrounding the microbody. The microbody includes a transparent material that at least partially surrounds the reservoir core and facilitates detection of an optical characteristic of the substance within the reservoir core. The microbody of each microvessel includes an identifiable code that distinguishes individual microvessels of the plurality of encoded microvessels from each other. The plurality of isolated microvessels also includes a plurality of compartments each configured to separate individual microvessels of the plurality of encoded microvessels from each other.
    Type: Application
    Filed: August 16, 2013
    Publication date: April 10, 2014
    Applicant: Illumina, Inc.
    Inventors: John A. Moon, M. Shane Bowen, Ryan C. Smith, Michel Perbost, Michal Lebl, Steven H. Modiano
  • Publication number: 20140066336
    Abstract: The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of: a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c).
    Type: Application
    Filed: October 30, 2013
    Publication date: March 6, 2014
    Applicant: ChemGene Holding ApS
    Inventor: Peter Birk Rasmussen
  • Publication number: 20130237459
    Abstract: The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of: a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c).
    Type: Application
    Filed: April 9, 2012
    Publication date: September 12, 2013
    Inventor: Peter Birk RASMUSSEN
  • Publication number: 20130109578
    Abstract: Techniques for differentiating isobaric species are described. An isobaric species may be substituted with a tagging species identified using mass spectrometry. The isobaric species may be a subunit of a first polymer having a defined sequence, e.g., the isobaric species may be an amino acid in a protein or a peptide sequence. A tagging species may be substituted for the isobaric species in a second polymer having an otherwise identical sequence as the first polymer. The second polymer may have the same number of sequences as the first polymer, and substantially the same sequence of subunits, with a few exceptions such as the tagging species for the isobaric species. The first polymer and the second polymer may be prepared in the same reaction vessel. A polymer/protein of defined subunit sequence containing an isobaric species or a tagging species may be analyzed by mass spectrometry to determine the sequence.
    Type: Application
    Filed: July 22, 2009
    Publication date: May 2, 2013
    Applicant: Agency for Science, technology and Research
    Inventors: James R. Heath, Su Seong Lee, Jaehong Lim, Junhoe Cha, Sylvia Tan, Shi Yun Yeo
  • Publication number: 20120309651
    Abstract: The present invention provides, among other things, methods and compositions for encoding a substrate for detecting and quantifying target nucleic acids.
    Type: Application
    Filed: August 7, 2012
    Publication date: December 6, 2012
    Applicant: FIREFLY BIOWORKS, INC.
    Inventors: Daniel C. Pregibon, Isaac Stoner, Andreas Windemuth, Timothy Erps
  • Patent number: 8298995
    Abstract: The invention relates to a method of producing a protein array (5) on one support surface (3) from a corresponding nucleic acid array on a separate surface (1), to protein arrays produced by the method, to uses of the protein arrays in the identification of interactions between arrayed proteins and other molecules, and to kits for producing said protein arrays.
    Type: Grant
    Filed: April 27, 2006
    Date of Patent: October 30, 2012
    Assignee: Babraham Institute
    Inventors: Michael John Taussig, Mingyue He
  • Patent number: 8206901
    Abstract: Disclosed is a method for obtaining a bifunctional complex comprising a display molecule part and a coding part, wherein a nascent bifunctional complex comprising a chemical reaction site and a priming site for enzymatic addition of a tag is reacted at the chemical reaction site with one or more reactants, and provided with respective tag(s) identifying the reactants(s) at the priming site using one or more enzymes.
    Type: Grant
    Filed: October 30, 2003
    Date of Patent: June 26, 2012
    Assignee: Nuevolution A/S
    Inventors: Per-Ola Freskgard, Thomas Franch, Alex Haahr Gouliaev, Mikkel Dybro Lundorf, Jakob Felding, Eva Kampmann Olsen, Anette Holtmann, Soeren Nyboe Jakobsen, Christian Klarner Sams, Sanne Schroeder Glad, Kim Birkebaek Jensen, Henrik Pedersen
  • Publication number: 20120053091
    Abstract: The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.
    Type: Application
    Filed: February 16, 2010
    Publication date: March 1, 2012
    Inventor: Richard W. Wagner
  • Patent number: 7989395
    Abstract: The present invention provides a method for identifying a compound of interest by screening libraries of molecules which include an encoding oligonucleotide tag.
    Type: Grant
    Filed: October 23, 2006
    Date of Patent: August 2, 2011
    Assignee: GlaxoSmithKline LLC
    Inventors: Barry Morgan, Stephen Hale, Christopher C. Arico-Muendel, Matthew Clark, Richard Wagner, David I. Israel, Malcolm L. Gefter, Dennis Benjamin, Nils Jakob Vest Hansen, Malcolm J. Kavarana, Steffen Phillip Creaser, George J. Franklin, Paolo A. Centrella, Raksha A. Acharya
  • Patent number: 7972994
    Abstract: The present invention provides methods of synthesizing libraries of molecules comprising a functional moiety which is operatively linked to an encoding oligonucleotide, wherein the encoding oligonucleotide comprises a capping sequence containing degenerate nucleotides.
    Type: Grant
    Filed: June 9, 2006
    Date of Patent: July 5, 2011
    Assignee: GlaxoSmithKline LLC
    Inventors: Barry Morgan, Stephen Hale, Christopher C. Arico-Muendel, Matthew Clark, Richard Wagner, David I. Israel, Malcolm L. Gefter, Dennis Benjamin, Nils Jakob Vest Hansen, Malcolm J. Kavarana, Steffen Phillip Creaser, George J. Franklin, Paulo A. Centrella, Raksha A. Acharya
  • Publication number: 20110143966
    Abstract: Novel processes are disclosed for forming an array of polymers by functionalizing the surface of particles by methods that include covalently attaching a functionalized silicon compound. Substrates such as microparticles having functionalized silicon compounds attached thereto are produced by introducing at least one carboxyl group directly by silanating a carboxylated silane compound to the surface of a microparticle. In a further aspect of the invention, the silane compound is a dipodal carboxylated silane.
    Type: Application
    Filed: August 2, 2010
    Publication date: June 16, 2011
    Applicant: Affymetrix, INC.
    Inventors: Glenn H. McGall, Anthony D. Barone
  • Patent number: 7935659
    Abstract: Combinations, called matrices with memories, of matrix materials with remotely addressable or remotely programmable recording devices that contain at least one data storage unit are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluophors or other luminescent moieties to produce luminescing matrices with memories. The data storage units are non-volatile antifuse memories or volatile memories, such as EEPROMS, DRAMS or flash memory. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided.
    Type: Grant
    Filed: December 14, 2004
    Date of Patent: May 3, 2011
    Assignee: Nexus Biosystems, Inc.
    Inventors: Michael P. Nova, Andrew E. Senyei, Zahra Parandoosh, Gary S. David, Xiao-Yi Xiao
  • Patent number: 7910523
    Abstract: The present invention includes composition and methods for making and using a combinatorial library to identify modified thioaptamers that bind to, and affect the immune response of a host animal, transcription factors such as IL-6, NF-?B, AP-1 and the like. Composition and methods are also provided for the treatment of viral infections, as well as, vaccines and vaccine adjuvants are provided that modify host immune responses.
    Type: Grant
    Filed: May 20, 2004
    Date of Patent: March 22, 2011
    Assignee: Board of Regents, The University of Texas System
    Inventors: David G. Gorenstein, Bruce A. Luxon, James Leary
  • Publication number: 20100130373
    Abstract: The present invention relates to genomic analysis. In particular, the present invention provides methods and compositions for mapping genomic interactions.
    Type: Application
    Filed: August 24, 2007
    Publication date: May 27, 2010
    Inventors: Job Dekker, Josee Dostie
  • Publication number: 20090233811
    Abstract: The present invention relates to a method of manufacturing an array chip, comprising the steps of: i) depositing at least one ligand onto the active surface of a wafer substrate, having at least one scribe line, the active surface being the reverse of the surface comprising the at least one scribe line; ii) detecting the ligand in relation to the at least one scribe line; and iii) breaking the wafer substrate along the at least one scribe line, to produce at least one array chip.
    Type: Application
    Filed: July 31, 2006
    Publication date: September 17, 2009
    Applicant: Randox Laboratories Ltd.
    Inventors: Sorin Bota, Ekaterina Arikainen, Robert Ivan McConnell, Stephen Peter Fitzgerald
  • Publication number: 20090181861
    Abstract: The present disclosure relates to methods and compositions for making paired tags and paired tag libraries.
    Type: Application
    Filed: January 8, 2009
    Publication date: July 16, 2009
    Inventors: Bin Li, Lei Xi, Swati S. Ranade, Yangzhou Wang
  • Publication number: 20080214410
    Abstract: Embodiments of a method for covalently immobilizing one or more discrete molecules on a substrate and embodiments of substrates having covalently-immobilized discrete molecules are disclosed. Embodiments of the method can include exposing a substrate to a functionalizing reagent to form a functionalized substrate and exposing the functionalized substrate to a solution comprising the molecule to be immobilized. A reaction-energy source then can be used to activate the functionalizing reagent and covalently bond one or more of the molecules to the substrate. All or a substantial portion of the unbonded molecules then can be removed. Controlling the concentration of the functionalizing reagent to which the substrate is exposed allows the density of the bonding sites on the substrate to be reduced so that, after removal of the unbonded molecules, at least one of the bonded molecules remains on the substrate spatially isolated from any other bonded molecules.
    Type: Application
    Filed: July 9, 2007
    Publication date: September 4, 2008
    Inventors: Mingdi Yan, Li Liu, John Gann
  • Publication number: 20080176765
    Abstract: Particles or other microdevices are disposed in an array having discreet regions (e.g. magnetic bars), oriented within a magnetic field, and then sorted through application of a removing force under conditions that remove a proper subset of the microdevices from the array as a function of differing orientations of the microdevices. Methods are also contemplated for using magnetic patterns to sort collections of microdevices by magnetic complementarity. Preferred methods use a capture and release process to sort microdevices (microdevices), and unlike conventional sorters, do not require high particle flow rates. Also contemplated are microdevice libraries in which microdevices have mutually distinct magnetic codes, and a region with a mutually distinct polymeric or other chemical moiety.
    Type: Application
    Filed: January 23, 2008
    Publication date: July 24, 2008
    Applicant: Arrayomics, Inc.
    Inventor: David Rothwarf