Labels Or Markers Utilized (e.g., Radiotracer, Affinity, Fluoroescent, Phosphorescent, Markers, Etc.) Patents (Class 536/25.32)
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Patent number: 8361727Abstract: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.Type: GrantFiled: May 24, 2011Date of Patent: January 29, 2013Assignee: Lasergen, Inc.Inventors: Weidong Wu, Vladislav A. Litosh, Brian P. Stupi, Michael L. Metzker
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Patent number: 8357789Abstract: Polynucleotides and polypeptides which participate in influenza virus infection of cells and nucleic acid molecules, which include a polynucleotide sequence capable of specifically binding the polypeptides of the present invention. Also provided are methods of using such nucleic acid molecules, polynucleotides and antibodies directed thereagainst for diagnosing, treating and preventing influenza virus infection.Type: GrantFiled: September 18, 2009Date of Patent: January 22, 2013Assignee: Yeda Research and Development Co. Ltd.Inventors: Ruth Arnon, Sung-Ho Jeon, Basak Kayhan, Tamar Ben-Yedidia
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Patent number: 8334370Abstract: Provided are nucleic acid compositions modified with intercalating aromatic compounds attached directly or indirectly through a linker arm thereto. Modifications to the nucleotides or to the oligo- or polynucleotides involve the pentosyl moieties, the abasic moieties (without a base) and the base moieties. Useful property changes are effected and can be measured or detected when such modified nucleic acids compositions have hybridized specifically to target nucleic acids.Type: GrantFiled: October 5, 1992Date of Patent: December 18, 2012Assignee: Enzo Biochem, Inc.Inventors: Jannis Stavrianopoulos, Elazar Rabbani
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Publication number: 20120294807Abstract: Compounds used as labels with properties comparable to known fluorescent compounds. The compounds can be conjugated to proteins and nucleic acids for biological imaging and analysis. Synthesis of the compounds, formation and use of the conjugated compounds, and specific non-limiting examples of each are provided.Type: ApplicationFiled: December 20, 2011Publication date: November 22, 2012Applicants: DYOMICS GMBH, PIERCE BIOTECHNOLOGY, INC.Inventors: Greg Hermanson, Peter T. Czerney, Surbhi Desai, Matthias S. Wenzel, Boguslawa Dworecki, Frank G. Lehmann
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Publication number: 20120288445Abstract: Compounds of the formula (I) are disclosed: 18F—(CHR)n(CH2)mCHO??(I) in which n and m are independently 0 and 1 with at least one of n and m being 1, and R (if present) is a hydrogen atom or a methyl group, subject to the proviso that if n is 1 and R is methyl then m is 0. Synthesis of the compounds is described together with their use in radiolabelling reactions, e.g. for the radiolabelling of peptides to facilitate detection by Positron Emission Tomography (PET) imaging. The preferred compound is [18F]Fluoroacetaldehyde.Type: ApplicationFiled: April 13, 2012Publication date: November 15, 2012Applicant: The University of ManchesterInventor: Christian PRENANT
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Patent number: 8293502Abstract: Compositions and methods of use are disclosed for clonally amplifying target polynucleotide sequences in solution and attaching the amplicons to a surface by activation of a masked binding moiety. In an embodiment, the amplicons comprise the masked binding moiety and the surface comprises a binding partner of the binding moiety. Upon activation of the binding moiety, the amplicons bind to the binding partner on the surface. In a non-limiting example, the masked binding moiety is caged biotin or caged fluorescein, while the corresponding binding partner is avidin or an anti-fluorescein antibody.Type: GrantFiled: April 14, 2011Date of Patent: October 23, 2012Assignee: Applied Biosystems, LLCInventor: Benjamin Schroeder
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Publication number: 20120252025Abstract: A method to link a light emitting reporter to biomolecules with nucleotide oligomers is described. The light reporter particles are silylated and functionalized to produce a coated light reporter particle, prior to covalently linking the biomolecules to the light reporter particle. The light reporter particle generated by the methods of the invention can be excited by a light excitation source such as UV or IR light, and when the biomolecule is DNA, the attached DNA molecule(s) are detectable by amplification techniques such as PCR.Type: ApplicationFiled: January 24, 2012Publication date: October 4, 2012Inventors: Thomas Kwok, Ming-Hwa Liang, Stephane Shu Kin So
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Patent number: 8278071Abstract: A method comprising subjecting one or more sample portion(s) to a single amplification step, thereby amplifying a single molecule in the sample portion to a detectable level, and, in some embodiments, then determining whether the sample portion contains at least one molecule of the target nucleic acid. In some embodiments, the sample portion is in a porous sample structure, or in a sample chamber which comprises means for minimizing diffusion of the sample portion, or in a sample chamber which is inside a microcapillary device, or in a sample retaining means.Type: GrantFiled: August 13, 2007Date of Patent: October 2, 2012Assignees: Applied Biosystems, LLC, The United States Department of Health and Human ServiceInventors: James F. Brown, Jonathan E. Silver
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Publication number: 20120225431Abstract: The present invention is generally related to composition, kits and methods for synthesizing nucleic acid molecules and particularly for synthesizing labeled nucleic acid molecules. Specifically, the invention relates to methods, kits and compositions for synthesizing indirectly labeled nucleic acid molecules. The labeled nucleic acid molecules produced in accordance with the invention are particularly suited as labeled probes for nucleic acid detection, diagnostics, and array analysis.Type: ApplicationFiled: February 6, 2012Publication date: September 6, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Jun E. Lee, Weidong Zheng
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Publication number: 20120219954Abstract: The object of the present invention is to provide a novel method that addresses the problem of differentiating large sets of genomic sequences. The invention relates to a method for genotyping N loci present in a sample in a target nucleic acid molecule, wherein each locus is located in a genotype marker region of the nucleic acid molecule, and corresponds to two or more genotypes. Furthermore the invention relates to a kit for performing said method for genotyping. Also the invention relates to a method for designing and producing selection primers, as well as a method for producing detection primers, all of said primers to be used in the method for genotyping or in the kit for performing the genotyping method. The invention further relates to selection primers adapted for genotyping of loci in a target nucleic acid molecule and a computer program product for designing selection primers.Type: ApplicationFiled: November 3, 2010Publication date: August 30, 2012Inventors: Mikael Leijon, Sándor Belák
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Publication number: 20120220468Abstract: The present invention relates to a target discriminative probe (TD probe) and its uses or applications. The TD probe is hybridized with a target nucleic acid sequence through both of the 5?-second hybridization portion and the 3?-first hybridization portion. When the TD probe is hybridized with a non-target nucleic acid sequence, both the 5?-second hybridization portion and the separation portion are not hybridized with the non-target nucleic acid sequence such that both portions form a single strand due to its low Tm value. As such, the TD probe exhibits distinctly different hybridization patterns for each of the target and the non-target nucleic acid sequence, discriminating the target nucleic acid sequence from the non-target nucleic acid sequence with much higher specificity.Type: ApplicationFiled: September 2, 2010Publication date: August 30, 2012Applicant: SEEGENE, INC.Inventors: Jong Yoon Chun, In Taek Hwang, Sang Kil Lee
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Patent number: 8212020Abstract: This invention relates to the field of nucleic acid chemistry, more specifically to the field of compositions of matter that comprise triphosphates of modified 2?-deoxynucleosides and oligonucleotides that are formed when these are appended to the 3?-end of a primer, wherein said modifications comprise NH2 moiety attached to their 3?-hydroxyl group and a fluorescent species in a form of a tag affixed to the nucleobase via a linker that can be cleaved. Such compositions and their associated processes enable and improve the sequencing of oligonucleotides using a strategy of cyclic reversible termination, as outlined in U.S. Pat. No. 6,664,079. Most specifically, the invention concerns compositions of matter that are 5?-triphosphates of ribo- and 2?-deoxyribonucleosides carrying detectable tags and oligonucleotides that might be derived from them.Type: GrantFiled: March 23, 2009Date of Patent: July 3, 2012Inventors: Steven Albert Benner, Daniel Hutter, Nicole Aurora Leal, Fei Chen
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Publication number: 20120156140Abstract: Compounds used as labels with properties comparable to known fluorescent compounds. The compounds can be conjugated to proteins and nucleic acids for biological imaging and analysis. Synthesis of the compounds, formation and use of the conjugated compounds, and specific non-limiting examples of each are provided.Type: ApplicationFiled: December 20, 2011Publication date: June 21, 2012Applicants: DYOMICS GMBH, PIERCE BIOTECHNOLOGY, INC.Inventors: Greg Hermanson, Peter T. Czerney, Surbhi Desai, Matthias S. Wenzel, Boguslawa Dworecki, Frank G. Lehmann
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Publication number: 20120157327Abstract: The present invention relates to methods and reagents for detecting analytes, e.g. nucleic acids. The new methods and reagents allow a simple and sensitive detection even in complex biological samples.Type: ApplicationFiled: March 2, 2012Publication date: June 21, 2012Applicant: BASECLICK GMBHInventors: Thomas CARELL, Anja SCHWÕEGLER, Glenn A. BURLEY, Johannes GIERLICH, Mohammad Reza MOFID
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Patent number: 8197759Abstract: The invention relates to compositions and methods useful in the labeling and identification of proteins. The invention provides for highly soluble zwitterionic dye molecules where the dyes and associated side groups are non-titratable and maintain their net zwitterionic character over a broad pH range, for example, between pH 3 and 12. These dye molecules find utility in a variety of applications, including use in the field of proteomics.Type: GrantFiled: August 31, 2009Date of Patent: June 12, 2012Assignee: Montana State UniversityInventors: Edward A. Dratz, Paul A. Grieco
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Patent number: 8197758Abstract: The invention relates to compositions and methods useful in the labeling and identification of proteins. The invention provides for highly soluble zwitterionic dye molecules where the dyes and associated side groups are non-titratable and maintain their net zwitterionic character over a broad pH range, for example, between pH 3 and 12. These dye molecules find utility in a variety of applications, including use in the field of proteomics.Type: GrantFiled: June 22, 2007Date of Patent: June 12, 2012Assignee: Montana State UniversityInventors: Edward A. Dratz, Paul A. Grieco
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Publication number: 20120123109Abstract: The quenching compounds of the invention are weakly luminescent cyanines that are substituted by one or more heteroaromatic quenching moieties. The quenching compounds of the invention exhibit little or no observable luminescence and efficiently quench a broad spectrum of luminescent compounds. The chemically reactive quenching compounds possess utility for labeling a wide variety of substances, including biomolecules. These labeled substances are highly useful for a variety of energy-transfer assays and applications.Type: ApplicationFiled: January 9, 2012Publication date: May 17, 2012Applicant: AnaSpec IncorporatedInventors: Zhenjun Diwu, Jianheng Zhang, Yi Tang
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Publication number: 20120115154Abstract: DNA oligomers comprising sequences that are absent from the genome of one or more organisms of interest are used as reference markers (RMs). The RMs are added to biological samples to “tag” and subsequently identify the samples as authentic and to distinguish tagged samples from samples obtained without said markers, for example, in forensic, medical, legal and other applications.Type: ApplicationFiled: October 17, 2011Publication date: May 10, 2012Inventor: Greg Hampikian
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Patent number: 8173445Abstract: The present invention provides compositions and methods for detecting incorporation of a labeled nucleotide triphosphate onto the growing end of a primer nucleic acid molecule. The method is used, for example, to genotype and sequence a nucleic acid. In a preferred embodiment, the method described herein detects individual NTP molecules.Type: GrantFiled: October 31, 2008Date of Patent: May 8, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: John G. K. Williams, Daniel R. Draney
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Publication number: 20120101268Abstract: Described herein are automated, integrated microfluidic device comprising a chemical reaction chip comprising for performing chemical reaction, a microscale column integrated with the chip and configured for liquid flow from the column to at least one flow channel, and wherein the fluid flow into the column is controlled by on-chip valves; and comprising at least two on-chip valves for controlling fluid flow in the microfluidic device.Type: ApplicationFiled: November 1, 2011Publication date: April 26, 2012Applicant: SIEMENS MEDICAL SOLUTIONS USA, INC.Inventors: Arkadij M. Elizarov, Hartmuth C. Kolb, R. Michael Van Dam, James R. Heath
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Publication number: 20120095201Abstract: Provided herein is a method for replacing the allyl group in a compound of formula R—O-allyl, R2N(allyl), RNH(allyl), RN(allyl)2 or R—S-allyl with a hydrogen, using a transition metal and one or more phosphine ligands.Type: ApplicationFiled: October 25, 2011Publication date: April 19, 2012Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: John MILTON, Xiaolin Wu, Mark Smith, Joseph Brennan, Colin Barnes, Xiaohai Liu, Silke Ruediger
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Patent number: 8148515Abstract: The present invention relates to dyes in general. The present invention provides a wide range of dyes and kits containing the same, which are applicable for labeling a variety of biomolecules such as nucleic acids, cells and microorganisms. The present invention also provides various methods of using the dyes for research and development, forensic identification, environmental studies, diagnosis, prognosis, and/or treatment of disease conditions.Type: GrantFiled: June 2, 2010Date of Patent: April 3, 2012Assignee: Biotium, Inc.Inventors: Fei Mao, Wai-Yee Leung, Hye Eun Hoover
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Publication number: 20120071644Abstract: The present application is directed to compounds of Formula I: wherein R1-R9, X, Y and Z are as defined in the application, and to the use of the compounds of Formula I, for example, for the fluorescent labeling of oligonucleotides.Type: ApplicationFiled: September 22, 2011Publication date: March 22, 2012Applicant: BROCK UNIVERSITYInventors: Hongbin Yan, Kha Tram
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Patent number: 8129509Abstract: Compounds and methods are provided for a single-step covalent attachment of a label to a molecule comprising forming a covalently attachable labeling reagent for alkylating the molecule. Then, combining the covalently attachable labeling reagent with a mixture containing the molecule, under conditions wherein the labeling reagent has reactivity with the molecule thereby forming a covalent bond.Type: GrantFiled: April 15, 2003Date of Patent: March 6, 2012Assignee: Mirus Bio LLCInventors: Paul M. Slattum, Jon A. Wolff, James E. Hagstrom, Vladimir G. Budker
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Publication number: 20120053336Abstract: Nucleic acid labeling compounds are disclosed. The compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.Type: ApplicationFiled: November 1, 2011Publication date: March 1, 2012Applicant: AFFYMETRIX, INC.Inventors: Glenn McGall, Anthony D. Barone
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Patent number: 8124756Abstract: A method for preparing amino linker oligonucleotides is provided. More specifically, a method of preparing 5?-amino-linker oligonucleotides comprising the steps of: introducing an amino linker having a protecting group into the 5? terminus of an oligonucleotide; and removing the protecting group from the amino linker oligonucleotide by contacting with acetic acid and 2,2,2-trifluoroethanol is provided. The amino protecting group is efficiently removed from the amino linker oligonucleotides, and thereby achieving a high yield of the amino linker oligonucleotides.Type: GrantFiled: September 15, 2009Date of Patent: February 28, 2012Assignees: Postech Academy-Industry Foundation, PoscoInventors: Jung-Hwan Lee, Hyun-Gu Kang, Sung-Ho Ryu, Jong-In Kim, Sun-Hak Lee, Hye-Jung Lee, Eun-Jung Jang
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Patent number: 8097409Abstract: Compositions, methods and kits for detecting Group B streptococci. Particularly described are oligonucleotides that are useful as amplification primers and hybridization probes for detecting very low levels of Group B streptococci nucleic acids.Type: GrantFiled: February 23, 2009Date of Patent: January 17, 2012Assignee: Gen-Probe IncorporatedInventors: Reinhold B. Pollner, Edgar J. Kamantigue
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Patent number: 8093003Abstract: A method is provided for detecting the presence of nucleotides or monitoring nucleotide amplification. It utilizes fluorescence energy transfer by competitive hybridization. Competitive hybridization is achieved by using unequal length complementary probes which have a fluorophore on one probe and a quencher on the other. The fluorophore and quencher are juxtaposed in a manner wherein the proximity of the quencher to the fluorophore produces quenching of the fluorescence of the fluorophore.Type: GrantFiled: August 27, 2010Date of Patent: January 10, 2012Assignee: Quest Diagnostics Investments IncorporatedInventors: Chih-Sheng Chiang, Jose F. Cuan
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Publication number: 20120003675Abstract: Engineered reaction containers that can be physically and chemically defined to control the flux of molecules of different sizes and charge are disclosed. Methods for constructing small volume reaction containers through a combination of etching and deposition are also disclosed. The methods allow for the fabrication of multiple devices that possess features on multiple length scales, specifically small volume containers with controlled porosity on the nanoscale.Type: ApplicationFiled: March 17, 2011Publication date: January 5, 2012Inventors: Scott T. Retterer, Mitchel J. Doktycz
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Patent number: 8076079Abstract: The present invention provides methods and compositions for highly sensitive nucleic acid detection, down to the single nucleic acid molecule level.Type: GrantFiled: December 17, 2004Date of Patent: December 13, 2011Assignee: Arizona Board of Regents, a body coporate acting for and on behalf of Arizona State UniversityInventors: Wayne Frasch, Lyian He
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Patent number: 8030460Abstract: A compound having the general formula shown below: where R1-6 are independently selected from the group consisting of an electron withdrawing group, an alkyl group, an aryl group, hydrogen, a heteroaryl group, and a five or six member ring structure formed from the R1 and R2 pair, the R3 and R4 pair, the R4 and R5 pair, or the R5 and R6 pair; R7 is a substituted or unsubstituted aryl group; and Y is a nucleophile.Type: GrantFiled: August 10, 2010Date of Patent: October 4, 2011Assignee: Integrated DNA Technologies, Inc.Inventors: Andrei Laikhter, Joseph A. Walder, Mark Behlke, Mikhail Podyminogin, Yawfui Yong
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Publication number: 20110217791Abstract: The present invention relates to a method for quantifying or detecting DNA having a target DNA region, and so on.Type: ApplicationFiled: August 18, 2009Publication date: September 8, 2011Applicant: Sumitomo Chemical Company, LimitedInventors: Yoshitaka Tomigahara, Hideo Satoh, Hirokazu Tarui
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Publication number: 20110212442Abstract: A nucleic acid probe set includes (A) a fluorescent probe and (B) a binding probe. The fluorescent probe (A) is formed of an oligonucleotide, which includes (a) a nucleotide unit labeled with (d) a fluorescent substance. The binding probe (B) is formed of an oligonucleotide having (b1) a fluorescent probe binding region, which can hybridize to the fluorescent probe (A), and (b2) a target nucleic acid binding region, which can hybridize to a target nucleic acid sequence (C). The fluorescent substance (d) is a fluorescent substance which changes in fluorescent character upon interaction with guanine. At least one of nucleotide units which constitute the fluorescent probe (A) is an artificial nucleotide unit having a function to raise a dissociation temperature between the probe (A) and the fluorescent probe binding region (b1). The nucleic acid probe is provided with an improved fluorescence quenching efficiency.Type: ApplicationFiled: July 30, 2009Publication date: September 1, 2011Applicant: Nippon Steel Kankyo Engineering Co., Ltd.Inventors: Yuji Sekiguchi, Naohiro Noda, Ryo Miyata, Kazunori Nakamura, Shinya Kurata, Satoshi Tsuneda, Hidenori Tani
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Publication number: 20110207125Abstract: A method for labeling a product includes a step of adding on or in the product a plurality of single-stranded polynucleotides, which plurality of polynucleotides includes at least one target polynucleotide constituted of a single-stranded polynucleotide of predetermined length and sequence, and decoy polynucleotides which have identical or different predetermined lengths and identical or different predetermined sequence, which decoy polynucleotides have a length or lengths identical to or different from and sequences different from the sequence of the at least one target polynucleotide, wherein each of the target and decoy polynucleotides does not hybridize with any of the other polynucleotides of the plurality of polynucleotides and wherein the polynucleotides of the plurality of polynucleotides are deoxyribonucleic or ribonucleic acid sequences, respectively having the same proportion of the four, natural or modified, bases A, C, G, and T, or A, C, G and U.Type: ApplicationFiled: April 10, 2009Publication date: August 25, 2011Applicants: BIOQUANTA, BIOQUANTA CORP.Inventors: Alexandre Jacob, Carlosse Keumeugni Kwemo, Sylvain Loric, Stephane Moutereaux, Nicolas Delacotte
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Publication number: 20110201515Abstract: The invention provides compositions and methods for the detection of small RNA molecules in a multiplexed reaction. The assays and kits described herein are applicable for the identification, diagnosing, and monitoring of disorders including, but not limited to cancer, developmental and degenerative disease, neurological disorders, and stem cell disorders.Type: ApplicationFiled: February 11, 2011Publication date: August 18, 2011Inventors: Philippa J. Webster, Lucas M. Dennis, Richard K. Boykin
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Patent number: 7998706Abstract: Disclosed, among other things, are compounds having the structure wherein X comprises a bond or a linker, LABEL comprises at least one detectable label, W1 taken alone is —H or —OH, W2 is —OH or a non-extendable moiety, W3 when taken alone is —H or when taken together with W1 is —CH2—O—, and W4 is OH, monophosphate, diphosphate, or triphosphate. Also disclosed are labeled polynucleotide compounds and methods of use thereof.Type: GrantFiled: December 17, 2004Date of Patent: August 16, 2011Assignee: Applied Biosystems, LLCInventors: Barnett B. Rosenblum, Geun-sook Jeon, Shaheer H. Khan
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Patent number: 7993841Abstract: A polynucleotide consisting of the base sequence of SEQ ID NO: 2, or a complementary strand thereto, wherein the X is one of the group being defined by the bases A, C or T. A primer and a probe specific for that polynucleotide, wherein the primer and/or probe contains at the least 10 consecutive nucleotides, and finally use of the probe for proving parkinsonism inheritance.Type: GrantFiled: April 30, 2009Date of Patent: August 9, 2011Assignee: Mayo Foundation for Medical Education and ResearchInventors: Jan O Aasly, Zbigniew K Wszolek, Matthew J Farrer
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Patent number: 7994304Abstract: The invention provides a family of tethered nucleotide analogs useful in sequencing nucleic acids containing a homopolymer region comprising, for example, two or more base repeats, and to sequencing methods using such tethered nucleotide analogs.Type: GrantFiled: October 30, 2007Date of Patent: August 9, 2011Assignee: Helicos Biosciences CorporationInventors: Suhaib Siddiqi, Hernan Orgueira, Edyta Olejnik, Subramanian Marappan, Philip R. Buzby, Atanu Roy
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Patent number: 7981603Abstract: The present invention provides methods and kits for identifying an increased risk of developing cancer in a subject. The methods include analyzing a first biological sample, such as a blood sample, from the subject for loss of imprinting of the IGF2 gene. According to the methods a loss of imprinting is indicative of an increased risk of developing cancer. The method can include analyzing genomic DNA from the sample for altered methylation of the IGF2 or the H19 gene. The altered methylation for example includes hypomethylation of a differentially methylated region of IGF2, corresponding to SEQ ID NO:1 and/or a polymorphism or fragment thereof, or hypomethylation of a differentially methylated region of H19 corresponding to SEQ ID NO:6, or a polymorphism, or fragment thereof. In certain aspects, hypomethylation of the H19 DMR or the IGF2 DMR indicates an increased risk of developing colorectal cancer.Type: GrantFiled: July 28, 2003Date of Patent: July 19, 2011Assignee: The Johns Hopkins University School of MedicineInventor: Andrew P. Feinberg
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Publication number: 20110171634Abstract: Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g., determining structural variations and copy number variations between individuals.Type: ApplicationFiled: June 30, 2009Publication date: July 14, 2011Applicant: Bionanomatrix, Inc.Inventors: Ming Xiao, Parikshit A. Deshpande, Han Cao, Michael Austin, Kandaswamy Vijayan, Alexey Y. Sharonov, Michael Boyce-Jacino
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Patent number: 7977108Abstract: The present invention provides methods and probe nucleic acids for detecting mutant forms of target nucleic acids that comprise repetitive nucleotide sequences. In certain embodiments, for example, these approaches and reagents can be used to detect instability in regions of genomic DNA that include microsatellite markers. The invention also provides related reaction mixtures, systems, and kits.Type: GrantFiled: July 13, 2006Date of Patent: July 12, 2011Assignee: Roche Molecular Systems, Inc.Inventors: Christopher D. Newhouse, Stephen Gordon Will, Amar P. Gupta
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Publication number: 20110165564Abstract: A method for detecting sequence specific methylation in a biomolecule, comprising: (a) contacting the biomolecule with an S-adenosyl-L-methionine-dependent methyltransferase in the presence of a detectable cofactor of said methyltransferase; and (b) detecting whether the recognition sequence of said methyltransferase has been modified with the cofactor or a derivative thereof, wherein modification of the recognition sequence of said methyltransferase is indicative of an absence of methylation at said recognition sequence. Also disclosed is a cofactor specific for S-adenosyl-L-methionine-dependent methyltransferases, wherein said cofactor is an N-adenosylaziridine derivative with a reporter group attached to the 6 or 7 position of the adenine ring or attached to the aziridine ring. A complex of the cofactor and a methyltransferase a composition comprising the cofactor or the complex and the use of the cofactor or the complex for detecting sequence-specific methylation in DNA molecules are also disclosed.Type: ApplicationFiled: June 14, 2005Publication date: July 7, 2011Applicant: MAX-PLANCK-GESELLSCHAFT ZUR FÖRDERUNG DER WISSENSCHAFTEN E.V.Inventors: Elmar Weinhold, Thomas Meier, Hartmut Düfel, Christine Markert-Hahn, Rainer Schmuck
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Patent number: 7964352Abstract: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.Type: GrantFiled: November 11, 2008Date of Patent: June 21, 2011Assignee: LaserGen, Inc.Inventors: Weidong Wu, Vladislav A. Litosh, Brian P. Stupi, Michael L. Metzker
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Patent number: 7964345Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.Type: GrantFiled: April 5, 2005Date of Patent: June 21, 2011Assignee: Cancer Genetics, Inc.Inventors: Nallasivam Palanisamy, Raju S. Chaganti
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Patent number: 7947477Abstract: Compositions and methods of use are disclosed for clonally amplifying target polynucleotide sequences in solution and attaching the amplicons to a surface by activation of a masked binding moiety. In an embodiment, the amplicons comprise the masked binding moiety and the surface comprises a binding partner of the binding moiety. Upon activation of the binding moiety, the amplicons bind to the binding partner on the surface. In a non-limiting example, the masked binding moiety is caged biotin or caged fluorescein, while the corresponding binding partner is avidin or an anti-fluorescein antibody.Type: GrantFiled: January 25, 2010Date of Patent: May 24, 2011Assignee: Applied Biosystems, LLCInventor: Benjamin Schroeder
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Publication number: 20110111514Abstract: A process for synthesis of a labelling reagent, a process for the labelling of a biological molecule, a labelled biological molecule obtained by the process, a process for labelling and fragmentation of a single or double strand nucleic acid, a labelled nucleic acid capable of being obtained by the process, a kit for detection of a target nucleic acid containing a labelled nucleic acid, a solid support onto which is attached a reagent and a process for capture of nucleic acids.Type: ApplicationFiled: July 28, 2009Publication date: May 12, 2011Applicants: BIOMERIEUX, UNIVERSITE DE STRASBOURG, CNRSInventors: Alain Laurent, Ali Laayoun, Mitsuhara Kotera
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Patent number: 7932025Abstract: This invention generally relates to nucleic acid synthesis, in particular DNA synthesis. More particularly, the invention relates to the production of long nucleic acid molecules with precise user control over sequence content. This invention also relates to the prevention and/or removal of errors within nucleic acid molecules.Type: GrantFiled: December 10, 2003Date of Patent: April 26, 2011Assignee: Massachusetts Institute of TechnologyInventors: Peter A. Carr, Brian Y. Chow, Joseph M. Jacobson, David W. Mosley, Christopher Emig
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Patent number: 7928210Abstract: Disclosed herein are novel radiolabeled nucleosides and methods for detecting cellular proliferation in a mammal, the method comprising administrating an effective amount of a radiolabeled nucleoside; the method comprising: a) administering to the mammal a diagnostically effective amount of the nucleoside to the mammal; b) allowing the nucleoside to distribute into the effective tissue; and c) imaging the tissue, wherein an increase in binding of the compound to tissue compared to a normal control level of binding indicates that the mammal is suffering from a disease involving cellular proliferation.Type: GrantFiled: March 3, 2008Date of Patent: April 19, 2011Assignee: Siemens Medical Solutions USA, Inc.Inventors: Hartmuth C. Kolb, Joseph C. Walsh, Robert M Yeh, Kai Chen, Umesh Gangadharmath, Brian Duclos, Vani P. Mocharla, Farhad Karimi, Henry C. Padgett, Qianwa Liang, Tieming Zhao
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Patent number: RE42325Abstract: The invention provides methods and devices for analyzing sequence variations in nucleic acid samples comprising multiple loci, each having two, three or more possible allelic sequences. The method involves combining at least a first and second pair of oligonucleotide probes with the nucleic acid sample. The first pair of probes is capable of hybridizing in proximity to each other within a segment of the nucleic acid sample comprising the first locus and the second pair is capable of hybridizing in proximity to each other within a segment of the nucleic acid sample comprising the second locus. The first member of each probe pair comprises a FRET donor and the second member comprises a FRET acceptor, the FRET acceptor of the first probe pair member having a different emission spectrum from the FRET acceptor of the second probe pair.Type: GrantFiled: June 20, 2007Date of Patent: May 3, 2011Assignee: University of Utah Research FoundationInventors: Carl T. Wittwer, Mark G. Herrman
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Patent number: RE43096Abstract: This invention provides a duplex comprising an oligonucleotide primer and a template, wherein the primer is coupled chemically to a chromophore or fluorophore so as to allow chain extension by a polymerase. In one embodiment, the primer is extended by a polymerase to generate the complement of the template. In a further embodiment, the extended primer is separated from the template for use in a number of methods, including sequencing reactions. Methods of generating these compositions of matter are further provided.Type: GrantFiled: March 13, 2003Date of Patent: January 10, 2012Assignee: California Institute of TechnologyInventors: Lloyd M. Smith, Leroy E. Hood, Michael W. Hunkapiller, Timothy Hunkapiller, Charles R. Connell