Synthesis Of Polynucleotides Or Oligonucleotides Patents (Class 536/25.3)
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Publication number: 20090208564Abstract: The present invention provides asymmetrical duplex RNA molecules that are capable of effecting sequence-specific gene silencing. The RNA molecule comprises a first strand and a second strand. The first strand is longer than the second strand. The RNA molecule comprises a double-stranded region formed by the first strand and the second strand, and two ends independently selected from the group consisting of 5?-overhang, 3?-overhang, and blunt end. The RNA molecules of the present invention can be used as research tools and/or therapeutics.Type: ApplicationFiled: August 27, 2008Publication date: August 20, 2009Inventors: Chiang Jia Li, Xiangao Sun, Harry Rogoff, Youzhi Li
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Publication number: 20090209479Abstract: Aspects of the invention include 2? protected nucleoside monomers that are protected at the 2? site with thiocarbon protecting groups. Thiocarbon protecting groups of interest include thiocarbonate, thionocarbonate, dithiocarbonate groups, as well as thionocarbamate protecting groups. Aspects of the invention further include nucleic acids that include the protecting groups of the invention, as well as methods of synthesizing nucleic acids using the protecting groups of the invention.Type: ApplicationFiled: May 9, 2008Publication date: August 20, 2009Inventors: Douglas J. Dellinger, Agnieszka Sierzchala, John Turner, Joel Myerson, Zoltan Kupihar, Fernando Ferreira, Marvin H. Caruthers
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Publication number: 20090209751Abstract: Methods and materials are disclosed for use in recovering a biopolymer from a solution. In particular, the invention provides methods for extraction and isolation of nucleic acids from biological materials. The nucleic acids can be separated by forming a stable complex with soluble polysaccharide polymers and magnetic particles, in the presence of detergents and solvent. When the particles are magnetically separated out of the solution, the nucleic acids are separated with them. The nucleic acids can subsequently be released and separated from the particles. The nucleic acid preparation is useful for achieving efficient and accurate results in downstream molecular techniques such as quantification, identification of the source of the nucleic acids, and genotyping.Type: ApplicationFiled: February 13, 2009Publication date: August 20, 2009Applicant: LEFE TECHNOLOGIES CORPORATION, a Delaware CorporationInventors: Maxim G. Brevnov, Hemant S. Pawar, Manohar R. Furtado, Jaiprakash Shewale
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Publication number: 20090202584Abstract: The present invention relates to a vaccine for the treatment or prevention of an EBV-associated disease in a subject, wherein said vaccine comprises a synthetic polypeptide comprising a plurality of different segments of at least one parent EBV polypeptide, and wherein the segments are linked together in a different relationship relative to their linkage in the at least one parent EBV polypeptide.Type: ApplicationFiled: December 6, 2006Publication date: August 13, 2009Applicant: Savine Therapeutics PtyInventors: Scott Anthony Thomson, Jai Kumar Duraiswamy, Denis James Moss
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Publication number: 20090203135Abstract: The present invention relates to agents, compositions and methods for inhibiting the expression of a target gene, comprising an RNAi agent bearing at least one galactosyl moiety. These are useful for delivering the gene expression inhibiting activity to cells, particularly hepatocytes, and more particularly in therapeutic applications.Type: ApplicationFiled: April 23, 2008Publication date: August 13, 2009Applicant: Alnylam Pharmaceuticals, Inc.Inventors: Andrea Forst, Philipp Hadwiger, Hans-Peter Vornlocher
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Publication number: 20090203897Abstract: A method of synthesizing oligonucleotides is claimed. The method utilizes a synthesis column incorporating a filter-like porous polymer cartridge which contains derivatized Controlled Pore Glass (CPG) or cross-linked Polystyrene (PS) directly embedded into the polymer cartridge. Small-scale synthesis of oligonucleotides of a predetermined sequence may be accomplished by introducing reagents of the phosphoramidite method into the synthesis column. These reagents flow through the cartridge allowing the reaction sequence to take place on the derivatized CPG or PS incorporated within the polymer cartridge.Type: ApplicationFiled: February 8, 2008Publication date: August 13, 2009Applicant: Operon Biotechnologies, Inc.Inventors: Lance Larka, Philipp Wenter, Patrick A. Weiss
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Patent number: 7572908Abstract: In various embodiments of the invention, novel compositions having a polynucleotide bound to a substrate via a cleavable linker are provided, and methods of cleaving a polynucleotide from a substrate are provided.Type: GrantFiled: March 23, 2006Date of Patent: August 11, 2009Assignees: Agilent Technologies, Inc., The Regents of the University of ColoradoInventors: Douglas J Dellinger, Zoltan Timar, Joel Myerson, Geraldine Dellinger, Marvin Caruthers
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Patent number: 7572907Abstract: Methods of forming polynucleotides are disclosed.Type: GrantFiled: April 29, 2005Date of Patent: August 11, 2009Assignees: Agilent Technologies, Inc., The Regents of the University of ColoradoInventors: Douglas J. Dellinger, Geraldine Dellinger, Marvin H. Caruthers, Zoltan Kupihar
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Patent number: 7572582Abstract: The present invention relates to novel bicyclic and tricyclic nucleoside and nucleotide analogues as well as to oligonucleotides comprising such elements. The nucleotide analogues, LNAs (Locked Nucleoside Analogues), are able to provide valuable improvements to oligonucleotides with respect to affinity and specificity towards complementary RNA and DNA oligomers. The novel type of LNA modified oligonucleotides, as well as the LNAs as such, are useful in a wide range of diagnostic applications as well as therapeutic applications. Among these can be mentioned antisense applications, PCR applications, strand displacement oligomers, as substrates for nucleic acid polymerases, as nucleotide based drugs, etc. The present invention also relates to such applications.Type: GrantFiled: May 18, 2005Date of Patent: August 11, 2009Assignee: Exiqon A/SInventors: Jesper Wengel, Poul Nielsen
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Patent number: 7569686Abstract: The present invention provides compounds and methods of using them for preparing bicyclic nucleosides. The bicyclic nucleosides are useful for preparing chemically modified oligomeric compounds. Oligomeric compounds comprising these bicyclic nucleosides have enhanced properties such as increased nuclease resistance.Type: GrantFiled: May 10, 2007Date of Patent: August 4, 2009Assignee: Isis Pharmaceuticals, Inc.Inventors: Balkrishen Bhat, Jie Xia, Punit P. Seth, Guillermo Vasquez, Michael T. Migawa, Charles Allerson, Thazha P. Prakash, Eric E. Swayze
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Patent number: 7569659Abstract: The invention concerns compositions comprising a nucleic acid mimic. The compositions may be used in the diagnosis and treatment of diseases amenable through modulation of nucleic acids which encode proteins that are implicated in disease states. In accordance with preferred embodiments, mimics are comprised of non-naturally occurring backbones to which are appended modified heterocyclic bases. Such bases preferably have sterically bulky substituents 1, 2, or 3 atoms removed from the sites of attachment to the backbone.Type: GrantFiled: March 7, 1997Date of Patent: August 4, 2009Inventors: Leif Christensen, Henrik Frydenlund Hansen, Peter E. Nielsen
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Patent number: 7569685Abstract: The purpose of the present invention is to develop a system for efficiently constituting cyanoethyl ethers under mild conditions and probability of the ethers as functional groups for imparting specific functions and to make a contribution to the production of novel functional nucleic acids. The present invention relates to a nucleoside that is represented by the general formula (I) or a nucleotide derived therefrom: wherein X and Y may be the same as or different from each other, and are hydrogen, optionally substituted silyl group, 4-methoxytrityl group, 4,4?-dimethoxytrityl group or a group represented by the general formula (II): wherein R1 and R2 may be the same as or different from each other, representing an alkyl group having 1-7 carbon atoms such as diisopropyl, or they are united with each other to form a ring structure, R3 represents a protective group for a phosphoric acid such as 2-cyanoethyl; and B1 represents an optionally substituted pyrimidine or purine base.Type: GrantFiled: March 2, 2005Date of Patent: August 4, 2009Assignee: Japan Sciencce and Technology AgencyInventors: Mitsuo Sekine, Kohji Seio, Hisao Saneyoshi
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Publication number: 20090191622Abstract: A synthetic nucleic acid molecule is provided that includes nucleotides of a coding region for a fluorescent polypeptide having a codon composition differing at more than 25% of the codons from a parent nucleic acid sequence encoding a fluorescent polypeptide. The synthetic nucleic acid molecule has at least 3-fold fewer transcription regulatory sequences relative to the average number of such sequences in the parent nucleic acid sequence. The polypeptide encoded by the synthetic nucleic acid molecule preferably has at least 85% sequence identity to the polypeptide encoded by the parent nucleic acid sequence.Type: ApplicationFiled: November 25, 2008Publication date: July 30, 2009Applicant: Promega CorporationInventors: Brian D. Almond, Monika G. Wood, Keith V. Wood
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Patent number: 7566775Abstract: The present invention is directed to a nucleic acid binding compound comprising N8- or C8-linked purine bases or structurally related heterocycles, a compound useful for the preparation of such compound, a binding product of this nucleic acid binding compound with a nucleic acid, a method for the determination of a nucleic acid using said compound, and several uses of 8-linked purine bases and structurally related heterocycles. Compounds according to the present invention have advantageous properties when used in hybridization methods.Type: GrantFiled: January 23, 2006Date of Patent: July 28, 2009Assignee: Roche Molecular Systems, Inc.Inventors: Frank Seela, Frank Bergmann, Dieter Heindl, Herbert Von der Eltz
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Patent number: 7566703Abstract: The invention relates to specific C-Class semi-soft CpG immunostimulatory oligonucleotides that are useful for stimulating an immune response. In particular the oligonucleotides are useful for treating allergy, such as allergic rhinitis and asthma, cancer and infectious disease, such as hepatitis B and hepatitis C.Type: GrantFiled: October 20, 2005Date of Patent: July 28, 2009Assignees: Coley Pharmaceutical Group, Inc., Coley Pharmaceutical GmbHInventors: Arthur M. Krieg, Ulrike Samulowitz, Jörg Vollmer, Eugen Uhlmann
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Patent number: 7566420Abstract: This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions.Type: GrantFiled: December 26, 2006Date of Patent: July 28, 2009Assignee: Boston Probes, Inc.Inventors: James M. Coull, Mark J. Fiandaca, Mark D. Kristjanson, Jens J. Hyldig-Nielsen, Theresa S. Creasey
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Publication number: 20090183281Abstract: The present invention provides a technology for modifying the gene expression of a plant body in combination with using histone-chaperon-activity of protein 6b. According to the invention, gene expression is changed or modified globally.Type: ApplicationFiled: May 25, 2006Publication date: July 16, 2009Applicant: NATIONAL UNIVERSITY CORPORATION NAGOYA UNIVERSITYInventors: Yasunori Machida, Kenzo Nakamura
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Publication number: 20090182135Abstract: The present invention provides a compound of formula (1): wherein: X is an electron-donating group, amino modifiers formed by reacting an amino alcohol with compounds of formula (1), amino-modified biomolecules formed by reacting said amino modifiers with a biomolecule and methods for producing the same.Type: ApplicationFiled: April 30, 2008Publication date: July 16, 2009Inventors: Mikhail S. Shchepinov, Pablo Bernad
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Patent number: 7560254Abstract: A method of characterizing a nucleic acid sample is provided that includes the steps of: (a) conducting a DNA polymerase reaction that includes the reaction of a template, an allele specific primer, at least one terminal phosphate-labeled nucleotide, DNA polymerase, and optionally an enzyme having 3??5? exonuclease activity when the primer is non-hydrolyzable, which reaction results in the production of labeled polyphosphate; (b) permitting the labeled polyphosphate to react with a phosphatase to produce a detectable species; (c) detecting the detectable species; and (d) characterizing the nucleic acid sample based on such detection.Type: GrantFiled: August 29, 2003Date of Patent: July 14, 2009Assignee: GE Healthcare Bio-Sciences Corp.Inventors: Anup Sood, Shiv Kumar, Carl Fuller, John Nelson, John Macklin
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Patent number: 7560231Abstract: The present invention is related to compounds comprising mannitol or glucitol derivatives which may be used to build up oligomeric compounds. The invention is further related to uses of these oligomeric compounds for hybridization and as probes. In addition, methods for the detection of nucleic acids are disclosed wherein the oligomeric compounds are used.Type: GrantFiled: December 5, 2003Date of Patent: July 14, 2009Assignee: Roche Molecular Systems, Inc.Inventors: Frank Bergmann, Herbert Von Der Eltz, Christoph Seidel, Kurt Weindel
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Publication number: 20090175867Abstract: Multivalent binding peptides, including bi-specific binding peptides, having immunoglobulin effector function are provided, along with encoding nucleic acids, vectors and host cells as well as methods for making such peptides and methods for using such peptides to treat or prevent a variety of diseases, disorders or conditions, as well as to ameliorate at least one symptom associated with such a disease, disorder or condition.Type: ApplicationFiled: March 3, 2008Publication date: July 9, 2009Applicant: TRUBION PHARMACEUTICALS, INC.Inventors: Peter A. Thompson, Jeffrey A. Ledbetter, Martha S. Hayden-Ledbetter, William Brady
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Patent number: 7557069Abstract: The present invention provides methods for synthesizing arrays of polymers. A barrier to a reaction is applied to select features of the array thereby limiting the reaction to the remaining features.Type: GrantFiled: May 6, 2006Date of Patent: July 7, 2009Inventor: Michael Paul Strathmann
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Publication number: 20090170802Abstract: The invention relates to a method for producing polymers, in particular synthetic nucleic acid double strands of optional sequence, comprising the steps: (a) provision of a support having a surface area which contains a plurality of individual reaction areas, (b) location-resolved synthesis of nucleic acid fragments having in each case different base sequences in several of the individual reaction areas, and (c) detachment of the nucleic acid fragments from individual reaction areas.Type: ApplicationFiled: March 9, 2009Publication date: July 2, 2009Applicant: Febit Holding GmbHInventors: Peer F. Stahler, Cord F. Stahler, Manfred Muller
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Publication number: 20090171076Abstract: Methods of nucleic acid preparation are described, including preparation of MnRNA, using FMOC derivatives to synthesize oligonucleotides in addition to applying FMOC protocols to various therapeutic and diagnostic methods. In some embodiments a single stranded oligonucleotide is synthesized bound to a polymer support (such as optic fiber glass filters) using said FMOC derivatives.Type: ApplicationFiled: March 19, 2008Publication date: July 2, 2009Inventor: Gabriel Alvarado
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Publication number: 20090171077Abstract: A process for preparing a microparticulate complex is provided. The process comprises (a) combining a particle-forming component (“PFC”) and a nucleic acid-like component (“NAC”) in a monophasic composition comprising water and a water-miscible, organic solvent to form a mixture wherein the PFC and the NAC are independently molecularly or micellarly soluble in the aqueous/organic solvent system, and (b) reducing the amount of the organic solvent in the mixture. This effects formation of the microparticulate complex of the NAC and the PFC. Also provided is a microparticulate complex that comprises a particle-forming component complexed to a nucleic acid-like component forming an approximately spherical particle, wherein the particle-forming component encloses an interior of the particle containing the nucleic acid-like component and the so-enclosed interior volume has less than about 50% (preferably less than 20%) of the volume containing free water.Type: ApplicationFiled: March 10, 2009Publication date: July 2, 2009Inventors: Keelung Hong, Wei-Wen Zheng, Daryl C. Drummond, Dmitri B. Kirpotin, Mark Eamon Hayes
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Patent number: 7553943Abstract: The invention provides a hairpin polynucleotide, having a loop and a stem region, characterised in that a sulfur-based nucleophile is attached to an internal nucleotide in the hairpin through a linker to enable binding to a solid support.Type: GrantFiled: November 8, 2004Date of Patent: June 30, 2009Assignee: Illumina Cambridge LimitedInventors: Darren James Ellis, Colin Lloyd Barnes, Harold Philip Swerdlow, Tom Brown
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Patent number: 7553958Abstract: A method of modulation of synthesis capacity on and cleavage properties of synthetic oligomers from solid support is described. The method utilizes linker molecules attached to a solid surface and co-coupling agents that have similar reactivities to the coupling compounds with the surface functional groups. The preferred linker molecules provide an increased density of polymers and more resistance to cleavage from the support surface. The method is particularly useful for synthesis of oligonucleotides, oligonucleotides microarrays, peptides, and peptide microarrays. The stable linkers are also coupled to anchor molecules for synthesis of DNA oligonucleotides using on support purification, eliminating time-consuming chromatography and metal cation presence. Oligonucleotides thus obtained can be directly used for mass analysis, DNA amplification and ligation, hybridization, and many other applications.Type: GrantFiled: March 21, 2007Date of Patent: June 30, 2009Assignee: The Regents of the University of MichiganInventors: Xiaolian Gao, Hua Zhang, Peilin Yu, Eric Leproust, Jean Philippe Pellois, Qin Xiang, Xiaochuan Zhou
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Publication number: 20090163372Abstract: The invention relates to a method for isolating and/or identifying known or unknown, nucleic acid sequences (target sequences) which are marked, optionally, with reporter groups, by base specific hybridisation with, essentially, complementary sequences, which belong to a library or sequences. The sample sequences are characterised in that they support, on one of the termini thereof (5?-ends or 3?-ends, preferably on 5?-ends), a single double or multi-chained lipid part, which spreads in a monomolecular layer on a liquid gas or liquid-liquid phase boundary layer. The invention also relates to a system for detecting or isolating nucleic acids.Type: ApplicationFiled: June 22, 2006Publication date: June 25, 2009Inventor: Helmut Rosemeyer
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Publication number: 20090162836Abstract: The present invention relates to prognostic and diagnostic markers for cell proliferative disorders of the breast tissues. The present invention therefore provides methods and nucleic acids for the analysis of biological samples for features associated with the development of breast cell proliferative disorders. Furthermore, the invention provides for prognosis of treatment effects relating to drug therapy, in particular hormonal/antihormonal therapy, chemotherapy and/or adjuvant therapy.Type: ApplicationFiled: October 14, 2004Publication date: June 25, 2009Applicant: Epigenomics AGInventor: Martin Widschwendter
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Patent number: 7550410Abstract: A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.Type: GrantFiled: November 14, 2006Date of Patent: June 23, 2009Inventor: Robert S. Foote
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Patent number: 7550582Abstract: The present invention relates to PNA derivatives which carry, at the C terminus, or at both the C and N termini of the PNA backbone, one or more phosphoryl radicals. The phosphoryl radicals carry, where appropriate, one or more labeling groups, groups for crosslinking, groups which promote intracellular uptake, or groups which increase the binding affinity of the PNA derivative for nucleic acids. The invention furthermore relates to a process for preparing the above-mentioned PNA derivatives and to their use as pharmaceuticals or diagnostic agents.Type: GrantFiled: September 14, 2007Date of Patent: June 23, 2009Assignee: sanofi-aventis Deutschland GmbHInventors: Eugen Uhlmann, Gerhard Breipohl, David William Will
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Patent number: 7550581Abstract: It is intended to provide a novel monomer unit by which Z type DNA can be more effectively stabilized, a reagent for integrating this monomer unit into an oligonucleotide, and a method of stabilizing Z type DNA by using the reagent. Namely, a guanosine derivative represented by the following general formula [1]: wherein R1 represents acyl; R2 represents lower alkyl; R3 represents tri-substituted silyloxy or tetrahedropyranyloxy; and R4 represents cyanoethyl or allyl; a reagent for stabilizing Z type DNA which contains the guanosine derivative; and a method of stabilizing Z type DNA by using the guanosine derivative. It is also intended to provide a method of transferring guanosine having lower alkyl at the 8-position into an oligonucleotide by using the guanosine derivative; and an oligonucleotide carrying guanosine having lower alkyl at the 8-position transferred thereinto.Type: GrantFiled: February 23, 2004Date of Patent: June 23, 2009Assignee: Japan Science and Technology AgencyInventors: Hiroshi Sugiyama, Yan Xu, Reiko Ikeda
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Publication number: 20090155174Abstract: Double-stranded RNA (dsRNA) induces sequence-specific post-transcriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 19-23 nt short RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III-like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3? ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the produced siRNP complex.Type: ApplicationFiled: October 29, 2008Publication date: June 18, 2009Applicant: Max-Planck-Gesellschaft zur Foerderung Der Wissenschaften e.V.Inventors: Thomas Tuschl, Sayda Mahgoub Elbashir, Winfried Lendeckel
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Patent number: 7547775Abstract: The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).Type: GrantFiled: January 3, 2006Date of Patent: June 16, 2009Assignee: Affymetrix, Inc.Inventors: Robert G. Kuimelis, Glenn H. McGall
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Patent number: 7544793Abstract: The present invention relates generally to the fields of genomics, synthetic biology and genetic engineering. More particularly, the present invention concerns the methods that enable parallel multiplex ligation and amplification on surface for making assemblies of nucleic acids of various biological applications and for analysis of biological samples such as DNA, RNA, and proteins.Type: GrantFiled: March 1, 2006Date of Patent: June 9, 2009Inventors: Xialoian Gao, Xiaochuan Zhou, Xiaolin Zhang, Nuing Sheng, Qi Zhu
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Publication number: 20090143232Abstract: 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: ApplicationFiled: July 24, 2008Publication date: June 4, 2009Applicant: Nuevolution A/SInventors: Henrik Pedersen, Anette Holtmann, Thomas Franch, Alex Haahr Gouliaev, Jakob Felding
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Patent number: 7541448Abstract: The invention is directed to an oligonucleotide comprising a molecular rod, wherein preferentially the molecular rod covalently connects the 3? end of a first nucleotide residue with the 5? end of a second nucleotide residue. Such oligonucleotides are highly advantageous for real time PCR melting curve analysis.Type: GrantFiled: December 2, 2004Date of Patent: June 2, 2009Assignee: Roche Diagnostis Operations, Inc.Inventors: Dieter Heindl, Astrid Reiser, Karim Tabiti, Martina Junius, Alexander Hauber
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Patent number: 7541314Abstract: The present invention provides a microarray having base cleavable, sulfonyl-containing linkers and a process to make the microarray. Oligonucleotides of any sequence may be synthesized on the microarray having the cleavable linker. The oligonucleotides may be cleaved and recovered as a pool of oligonucleotides having a three prime phosphate moiety. Specifically, the microarray is an electrode containing microarray, and the oligonucleotides are electrochemically synthesized.Type: GrantFiled: February 24, 2006Date of Patent: June 2, 2009Assignee: CombiMatrix CorporationInventors: Dominic Suciu, Hetian Gao
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Patent number: 7541444Abstract: The invention provides modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3?-OH blocking group covalently attached thereto, such that the 3? carbon atom has attached a group of the structure —O-Z wherein Z is any of —C(R?)2-O—R?, —C(R?)2-N(R?)2, —C(R?)2-N(H)R?, —C(R?)2-S—R? and —C(R?)2-F, wherein each R? is or is part of a removable protecting group; each R? is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group; or (R?)2 represents an alkylidene group of formula ?C(R??)2 wherein each R?? may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups; and wherein said molecule may be reacted to yield an intermediate in which each R? is exchanged for H or, where Z is —C(R?)2-F, the F is exType: GrantFiled: August 22, 2003Date of Patent: June 2, 2009Assignee: Illumina Cambridge LimitedInventors: John Milton, Xiaolin Wu, Mark Smith, Joseph Brennan, Colin Barnes, Xiaohai Liu, Silke Ruediger
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Publication number: 20090136940Abstract: Described are phosphoramidite nucleoside analog monomers, precursors thereof, and oligonucleotides including one or more of the monomers. The monomers can be used during automated synthesis of oligonucleotide derivatives, and allow for incorporation of one or several reporter groups, organic molecules, bio-molecules, small molecules or other chemical groups at the internucleoside phosphotriesters. Oligonucleotides including the monomers have a number of uses in therapeutic, diagnostic, and research applications.Type: ApplicationFiled: August 29, 2008Publication date: May 28, 2009Applicants: University of Massachusetts, Massachusetts General HospitalInventors: Alexei Bogdanov, Valeriy Metelev, David Tabatadze, Paul Zamecnik
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Publication number: 20090131635Abstract: For synthesizing a polymer, a substrate is placed within a reaction chamber, and a polymer synthesis sample is fed into the reaction chamber for forming the polymer on the substrate. In addition, the reaction chamber is shaken during formation of the polymer on the substrate within the reaction chamber for increased reaction yield. In addition, forming bubbles of the inactive gas in the polymer synthesis sample during formation of the polymer on the substrate further increases reaction yield.Type: ApplicationFiled: July 30, 2008Publication date: May 21, 2009Inventors: Sung-Min Chi, Man-Hyoung Ryoo, Jung-Hwan Hah, Kyoung-Seon Kim, Won-Sun Kim, Sun-Ok Jung
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Publication number: 20090131648Abstract: The present invention provides novel dendrimers having a multimeric structure obtainable by reaction of a core molecule having an adamantoid structure with branching synthons and terminating synthons, said dendrimers immobilised on a support and a method of hybridisation which uses said dendrimers immobilised on a support.Type: ApplicationFiled: April 30, 2008Publication date: May 21, 2009Inventor: Mikhail S. Shchepinov
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Patent number: 7534854Abstract: An apparatus for treating polymeric materials comprises a treatment chamber adapted to maintain a selected atmosphere; a means for supporting the polymeric material within the chamber; and, a source of plasma-derived gas containing at least one reactive oxidative species whereby the polymer is stabilized and cross linked through exposure to the oxidative species in the chamber at a selected temperature. The polymer may be directly exposed to the plasma, or alternatively, the plasma may be established in a separate volume from which the reactive species may be extracted and introduced into the vicinity of the polymer. The apparatus may be configured for either batch-type or continuous-type processing. The apparatus and method are especially useful for preparing polymer fibers, particularly PAN fibers, for later carbonization treatments.Type: GrantFiled: January 31, 2006Date of Patent: May 19, 2009Assignee: UT-Battelle, LLCInventors: Felix L. Paulauskas, Terry L. White, Daniel M. Sherman
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Patent number: 7534872Abstract: Methods of nucleic acid preparation are described, including preparation of mRNA, using FMOC derivatives to synthesize oligonucleotides in addition to applying FMOC protocols to various therapeutic and diagnostic methods. In some embodiments a single stranded oligonucleotide is synthesized bound to a polymer support (such as optic fiber glass filters) using said FMOC derivatives.Type: GrantFiled: September 24, 2003Date of Patent: May 19, 2009Assignee: Syngen, Inc.Inventor: Gabriel Alvarado
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Patent number: 7534561Abstract: Methods and devices for producing a nucleic acid arrays using in situ nucleic acid array synthesis protocols are provided. A feature of certain embodiments of the invention is that control probes are produced in collections of features, e.g., columns, of the arrays that have been selected according to a particular efficient control probe feature/column selection protocol. A feature of certain other embodiments of the invention is that an “all-bases-all-layers” probe set is produced in at least one of column of the arrays. Also provided are devices configured for use in the subject methods, as well as arrays produced using the subject methods and devices as well as methods for using such arrays.Type: GrantFiled: April 2, 2003Date of Patent: May 19, 2009Assignee: Agilent Technologies, Inc.Inventors: Theodore R. Sana, Eric M. Leproust, Michel G. M. Perbost, Paul K. Wolber
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Publication number: 20090124571Abstract: Method for the synthesis of nucleotide derivatives wherein molecules of interest are grafted on the oligonucleotide with the help of a “click chemistry” reaction between an azide function on the molecule of interest and an alkyne function on the oligonucleotide, or between an alkyne function on the molecule of interest and an azide function on the oligonucleotide. Intermediate molecules, notably alkyne functionalized oligonucleotides, grafted oligonucleotides, azide functionalized oligonucleotides, oligonucleotide micro arrays containing them and the use of those grafted oligonucleotides for biological investigation and for cell targeting.Type: ApplicationFiled: April 26, 2007Publication date: May 14, 2009Inventors: Francois Morvan, Albert Meyer, Jean-Jacques Vasseur, Sebastien Vidal, Jean-Pierre Cloarec, Yann Chevolot, Eliane Souteyrand
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Publication number: 20090118128Abstract: The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5? end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction.Type: ApplicationFiled: July 20, 2006Publication date: May 7, 2009Inventors: Xiaohai Liu, John Milton, Geoffrey Paul Smith, Colin Barnes, Isabelle Marie Julia Rasolonjatovo, Roberto Rigatti, Xiaolin Wu, Tobias William Barr Ost, Graham John Worsley, David James Earnshaw, Gerardo Turcatti, Anthony Romieu
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Publication number: 20090111100Abstract: The incorporation of a minor groove binder spaced close to one member of a matched FRET set in a minor groove binder-oligonucleotide conjugate significantly reduces background fluorescence of a FRET probe or pair of probes and, consequently, increases the S/B ratios. Fluorescent-labeled probes are useful in carrying out hybridization, multiplex nucleic acid detection, and other procedures.Type: ApplicationFiled: October 30, 2007Publication date: April 30, 2009Inventors: Eugene Lukhtanov, Noah Scarr
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Patent number: 7524942Abstract: Embodiments of labeled nucleotide compositions are described. Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled nucleotide composition to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.Type: GrantFiled: July 31, 2006Date of Patent: April 28, 2009Assignee: Agilent Technologies, Inc.Inventors: Hui Wang, Jeffrey R. Sampson
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Patent number: 7524950Abstract: Inkjet printhead solvents and methods of forming an addressable nucleotide array are disclosed.Type: GrantFiled: April 29, 2005Date of Patent: April 28, 2009Assignee: Agilent Technologies, Inc.Inventors: Douglas J. Dellinger, Eric LeProust, Bill Peck, Marvin H. Caruthers, Peter Cogan