Trivalent Phosphorus Compound Utilized Patents (Class 536/25.34)
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Publication number: 20080207551Abstract: The synthesis and biochemical utility of modified oligonucleotides containing diphosphodiester internucleotide linkages. The synthesis of these compounds was carried out using diphosphitylating reagents. Oligonucleotides containing diphosphate diester bridges wherein said oligonucleotides are synthesized via a solid-phase synthesis strategy to form modified oligonucleotides. Diphosphitylating, triphosphitylating, tetraphosphitylating, ?-triphosphitylating, bifunctional diphosphitylating, bifunctional triphosphitylating, and bifunctional tetraphosphitylating reagents wherein, the phosphorus atoms are linked together through oxygen, sulfur, amino, or methylene groups and/or are substituted with chlorine, diisopropylamine and cyanoethoxy groups.Type: ApplicationFiled: January 10, 2008Publication date: August 28, 2008Applicant: BOARD OF GOVERNORS FOR HIGHER EDUCATION, STATE OF RHODE ISLAND AND PROVIDENCEInventors: Keykavous Parang, Yousef Ahamdibeni
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Patent number: 7417139Abstract: Methods of forming an internucleotide bond are disclosed. Such methods find use in synthesis of polynucleotides. The method involves contacting a functionalized support with a precursor having an exocyclic amine triaryl methyl protecting group under conditions and for a time sufficient to result in internucleotide bond formation. The functionalized support includes a solid support, a triaryl methyl linker group, and a nucleoside moiety having a reactive site hydroxyl, the nucleoside moiety attached to the solid support via the triaryl methyl linker group.Type: GrantFiled: August 30, 2003Date of Patent: August 26, 2008Assignee: Agilent Technologies, Inc.Inventors: Douglas J Dellinger, Agnieszka B. Sierzchala, Marvin H Caruthers, Geraldine F Dellinger
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Patent number: 7411061Abstract: A method of synthesizing polynucleotides is disclosed. The method involves contacting a first nucleotide with a selected reactive group in the presence of an ionic liquid. The selected reactive group may be on a second nucleotide, a polynucleotide, or on a moiety on an insoluble substrate, for example in an oligonucleotide synthesizer.Type: GrantFiled: December 22, 2004Date of Patent: August 12, 2008Assignee: Agilent Technologies, Inc.Inventors: Joel Myerson, Michel G. M. Perbost, Douglas J. Dellinger, Geraldine F Dellinger
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Patent number: 7385050Abstract: Functionalized supports for polynucleotide synthesis are disclosed. The supports have linker moieties that are stable to conditions used in polynucleotide synthesis, but may be cleaved to release synthesized polynucleotides from the support. Methods of making the functionalized supports and methods of using are also disclosed.Type: GrantFiled: August 30, 2003Date of Patent: June 10, 2008Assignee: Agilent Technologies, Inc.Inventors: Douglas J Dellinger, Geraldine F Dellinger, Marvin H Caruthers
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Patent number: 7381820Abstract: A method for producing 2?-deoxy-2?-fluoro-?-D-arabinonucleoside represented by formula (II): (wherein B represents a base), in particular, 2?-deoxy-2?-fluoro-?-D-arabinopurinenucleoside, which method comprises causing a nucleoside phosphorylase to act on ?-1-phosphorylated-2-deoxy-2-fluoroarabinoside represented by formula (I): or a mixture of ?- and ?-isomers of 1-phosphorylated-2-deoxy-2-fluoroarabinoside represented by formula (V?): and on a base. The compound can be produced at high yield and in a convenient and highly stereoselective manner.Type: GrantFiled: October 22, 2004Date of Patent: June 3, 2008Assignee: Yamasa CorporationInventors: Kohei Yamada, Noritake Matsumoto, Hiroyuki Hayakawa
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Patent number: 7378516Abstract: Methods for the formation of sulfurized oligonucleotides are provided. The methods allow for the formation of phosphorothioate linkages in the oligonucleotides or derivatives, without the need for complex solvent mixtures and repeated washing or solvent changes. Oligonucleotides having from about 8, and up to about 50, nucleotides can be sulfurized according to the methods of the invention with higher yields than have been previously reported.Type: GrantFiled: May 17, 2004Date of Patent: May 27, 2008Assignee: ISIS Pharmaceuticals, Inc.Inventors: Douglas L. Cole, Vasulinga T. Ravikumar, Zacharia S. Cheruvallath
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Publication number: 20080096193Abstract: Methods of determining the presence or amount of a target polynucleotide in a sample are provided. A sample that contains a target polynucleotide, a nucleic acid analog that is complementary to a target nucleic acid sequence of the target polynucleotide, and a dye for which the rate of change in an optical property is different in the presence and absence of a target polynucleotide/nucleic acid analog hybrid are combined to produce a reaction mixture. The rate of change in an optical property of the dye in the reaction mixture is compared to a reference value characteristic of the rate of change in the optical property of the dye in a similar reaction mixture containing a known amount of a polynucleotide/nucleic acid analog hybrid to determine a relative rate of change in the optical property. The relative rate of change in the optical property of dye in the reaction mixture is correlated with the presence or amount of the specified target polynucleotide in the sample.Type: ApplicationFiled: October 24, 2006Publication date: April 24, 2008Inventors: Charles Robert Bupp, K. Yeon Choi, Heather Koshinsky, Christopher Nulf, Mickey Urdea, Miaomiao Wang, Michael Zwick
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Patent number: 7355037Abstract: Provided is a hydroxyl-protected alcohol of the formula R—O—Pg, wherein Pg is a protecting group of the formula: wherein Y, Z, W, R1, R1a, R2, R2a, R3, R3a, R4, R4a, a, b, c, d, e and f are defined herein and R is a nucleosidyl group, an oligonucleotidyl group with 2 to about 300 nucleosides, or an oligomer with 2 to about 300 nucleosides. Also provided is a deprotection method, which includes heating the hydroxyl-protected alcohol at a temperature effective to cleave thermally the hydroxyl-protecting group therefrom.Type: GrantFiled: December 3, 2002Date of Patent: April 8, 2008Assignee: The United States of America as represented by the Department of Health and Human ServicesInventors: Serge L. Beaucage, Andrzej Grajkowski, Andrzej Wilk
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Patent number: 7348391Abstract: The present invention provides solid support media for use in oligomer synthesis, methods of producing the media, and methods of using the media. In some embodiments, the processes of the invention comprise (a) providing an organic phase comprising an olefin monomer, a cross-linker, a functionalizing reagent and an initiator; and (b) contacting the organic phase with an aqueous phase under conditions of time and temperature effective to form the polymeric bead.Type: GrantFiled: September 2, 2005Date of Patent: March 25, 2008Assignees: Isis Pharmaceuticals, Inc., Nitto Denko CorporationInventors: Vasulinga Ravikumar, Raju K. Kumar, Kenjirou Mori, Tatsuya Konishi, Ayako Matsunawa, Takeo Matsumura, Cheiko Kitaura, Gang Zhao
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Patent number: 7339052Abstract: The present invention provides an improved phosphoramidite activator comprising a solution of 5-benzylmercaptotetrazole in acetonitrile and N-alkyimidazole. Further provided are improved methods of oligonucleotide synthesis wherein a phosphoramidite activator comprising a solution of 5-benzylmercaptotetrazole in acetonitrile and N-alkyimidazole is used to prepare internucleoside linkages.Type: GrantFiled: February 8, 2005Date of Patent: March 4, 2008Assignee: Honeywell International Inc.Inventor: Kalakota S. Reddy
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Patent number: 7276599Abstract: The invention provides for methods of manufacturing an oligonucleotide comprising a pentavalent phosphate triester. In particular, the method comprises providing a 5? blocked-nucleoside, deblocking the 5? blocked-nucleoside to form a 5? OH-nucleoside, coupling the 5? OH-nucleoside with a phosphoramidite to form and oligonucleotide comprising a trivalent phosphite triester; and oxidizing the oligonucleotide comprising a trivalent phosphite triester to the oligonucleotide comprising a pentavalent phosphate triester. In some embodiments, the wash between any of the steps above is with at least one solvent wash comprising a toluene.Type: GrantFiled: June 2, 2004Date of Patent: October 2, 2007Assignee: Isis Pharmaceuticals, Inc.Inventors: Max N. Moore, Mark Andrade, Recaldo Carty, Anthony Scozzari, Achim Krotz
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Patent number: 7271258Abstract: The invention provides methods for synthesizing oligonucleotides using nucleoside monomers having carbonate protected hydroxyl groups that are deprotected with ?-effect nucleophiles. The ?-effect nucleophile irreversibly cleave the carbonate protecting groups while simultaneously oxidizing the internucleotide phosphite triester linkage to a phosphodiester linkage. The procedure may be carried out in aqueous solution at neutral to mildly basic pH. The method eliminates the need for separate deprotection and oxidation steps, and, since the use of acid to remove protecting groups is unnecessary, acid-induced depurination is avoided. Fluorescent or other readily detectable carbonate protecting groups can be used, enabling monitoring of individual reaction steps during oligonucleotide synthesis. The invention is particularly useful in the highly parallel, microscale synthesis of oligonucleotides.Type: GrantFiled: June 15, 2006Date of Patent: September 18, 2007Assignee: Agilent Technologies, Inc.Inventors: Douglas J. Dollinger, Marvin H. Caruthers, Jason R. Betley
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Patent number: 7227016Abstract: Synthetic processes are provided wherein oligomeric compounds are prepared having phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.Type: GrantFiled: December 28, 2004Date of Patent: June 5, 2007Assignee: Isis Pharmaceuticals, Inc.Inventors: Vasulinga T. Ravikumar, Muthiah Manoharan, Daniel C. Capaldi, Achim Krotz, Douglas L. Cole, Andrei Guzaev
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Patent number: 7227015Abstract: Methods for the formation of sulfurized oligonucleotides are provided. The methods allow for the formation of phosphorothioate linkages in the oligonucleotides or derivatives, without the need for complex solvent mixtures and repeated washing or solvent changes. Oligonucleotides having from about 8, and up to about 50, nucleotides can be sulfurized according to the methods of the invention with higher yields than have been previously reported.Type: GrantFiled: January 10, 2001Date of Patent: June 5, 2007Assignee: ISIS Pharmaceuticals, Inc.Inventors: Douglas L. Cole, Vasulinga T. Ravikumar, Zacharia S. Cheruvallath
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Patent number: 7227017Abstract: A process for the synthesis of phosphorothioate oligonucleotides is provided which comprises assembling an oligonucleotide bound to a solid support in the presence of acetonitrile; prior to cleaving the oligonucleotide from the solid support removing the acetonitrile; and cleaving the oligonucleotide from the solid support. The process is particularly suited to the large scale synthesis of nucleotides. The acetonitrile may be removed from the solid support by one or both of drying and by washing with solvents. Preferred washing solvents comprise trialkylamines.Type: GrantFiled: June 5, 2003Date of Patent: June 5, 2007Assignee: Avecia LimitedInventors: Ben James Mellor, Donald Alfred Wellings, Mark Edward Douglas
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Patent number: 7217814Abstract: Provided are methods of producing phosphitylated compounds, including 3?-O-phosphoramidites, comprising the step of reacting a hydroxyl-containing compound with a phosphitylating agent in the presence of a phosphitylation activator selected from the group consisting of: (1) acid-base complexes derived from an amine base of Formula II wherein R3, R4, R5, R6, and R7 are independently hydrogen, C1–C10 alkyl, C3–C10 cycloalkyl, C6–C10 aryl, C7–C10 aralkyl, C1–C10 heteroalkyl, or C1–C10 heteroaryl, and at least one of R3, R4, R5, R6, and R7 is not hydrogen; (2) zwitterionic amine complexes; and (3) combinations of two or more thereof, to produce a phosphitylated compound. Further provided are methods for purifying phosphitylated compounds comprising the steps of providing a phosphitylated compound in a solution solvent, contacting said phosphitylated compound with a precipitation solvent, and precipitating said phosphitylated compound.Type: GrantFiled: November 16, 2004Date of Patent: May 15, 2007Assignee: Honeywell International Inc.Inventors: Christian Werner, Frank Nerenz, Andreas Kanschik-Conradsen, Kalakota S. Reddy
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Patent number: 7199236Abstract: Synthetic processes are provided wherein oligomeric compounds are prepared having phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.Type: GrantFiled: September 14, 2004Date of Patent: April 3, 2007Assignee: Isis Pharmaceuticals, Inc.Inventors: Vasulinga T. Ravikumar, Muthiah Manoharan, Daniel C. Capaldi, Achim Krotz, Douglas L. Cole, Andrei Guzaev
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Patent number: 7193077Abstract: Precursors for use in the synthesis of polynucleotides and methods of using the precursors in synthesizing polynucleotides are disclosed. The precursors include a heterocyclic base having an exocyclic amine group and a substituted or unsubstituted triaryl methyl protecting group bound to the exocyclic amine group.Type: GrantFiled: August 30, 2003Date of Patent: March 20, 2007Assignee: Agilent Technologies, Inc.Inventors: Douglas J. Dellinger, Agnieszka B. Sierzchala, Marvin H. Caruthers
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Patent number: 7186822Abstract: Synthetic processes are provided wherein oligomeric compounds are prepared having phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.Type: GrantFiled: December 28, 2004Date of Patent: March 6, 2007Assignee: Isis Pharmaceuticals, Inc.Inventors: Vasulinga Ravikumar, Muthiah Manoharan, Daniel C. Capaldi, Achim Krotz, Douglas L. Cole, Andrei P. Guzaev
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Patent number: 7169916Abstract: A process of manufacturing oligonucleotides includes a 5?-deblocking step in which the 5-blocking group is removed with dichloroacetic acid that is essentially free of chloral. The process is useful for making oligonucleotides that are substantially free of chloral adducts.Type: GrantFiled: March 31, 2003Date of Patent: January 30, 2007Assignee: Isis Pharmaceuticals, Inc.Inventors: Achim Krotz, Daniel Capaldi, Hans Gaus, Brett Turney
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Patent number: 7153954Abstract: The present invention relates to large scale preparation of LNA phosphoramidites using a 2-cyanoethyl-N,N,N?,N?-tetra-substituted phosphoramidite and a nucleophilic activator, e.g. 2-cyanoethyl-N,N,N?,N?-tetraisopropylphosphoramidite and 4,5-dicyanoimidazole. The method is faster and more cost efficient that previously known methods.Type: GrantFiled: July 12, 2002Date of Patent: December 26, 2006Assignee: Santaris Pharma A/SInventors: Troels Koch, Christoph Rosenbohn, Daniel Sejer Pedersen
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Patent number: 7144700Abstract: Methods, employing a polycyclic hydrocarbon or a polycyclic heteroaromatic compound as sensitizers, are provided to increase the efficiency of removing, by irradiation, photolabile protecting groups that mask reactive sites on synthesis intermediaries. Preferred groups of photolabile protecting moieties include: ((?-methyl-2-nitropiperonyl)-oxy)carbonyl (MeNPOC), ((Phenacyl)-oxy)carbonyl (PAOC), O-(9-phenylxanthen-9-yl) (PIXYL), and ((2-methylene-9,10-anthraquinone)-oxy)carbonyl (MAQOC). In conjunction with using the sensitizers and protecting groups described above, a method of forming, from component molecules, a plurality of compounds on a support, each compound occupying a separate predefined region of the support is provided. These resulting solid-phase arrays are useful, for example, to assay for the presence of biochemical products in biological samples.Type: GrantFiled: July 21, 2000Date of Patent: December 5, 2006Assignee: Affymetrix, Inc.Inventors: Glenn McGall, Daniel E. Falvey, Jacqueline A. Fidanza, Brian M. Feldman
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Patent number: 7135565Abstract: A method of synthesizing a polynucleotide which can, for example, be used during fabrication of an array. A second nucleoside is coupled to a first nucleoside through a phosphite linkage, with the second nucleoside having a hydroxyl protecting group that is a non-carbonate protecting group. The product of the foregoing step is exposed to a composition which both oxidizes the formed phosphite to a phosphate and deprotects the protected hydroxyl of the coupled nucleoside. The method has particular application to fabricating an addressable array of polynucleotides on a substrate which carries substrate bound moieties each with a hydroxyl group.Type: GrantFiled: July 27, 2001Date of Patent: November 14, 2006Assignees: Agilent Technologies, Inc., University of ColoradoInventors: Douglas J. Dellinger, Michael G. M. Perbost, Marvin H. Caruthers, Jason R. Betley
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Patent number: 7135564Abstract: A reusable linker arm for solid support oligonucleotide synthesis, the linker arm comprising formula (a) wherein Z is a linker moiety and T is an organic radical.Type: GrantFiled: June 30, 1999Date of Patent: November 14, 2006Assignee: University Technologies International Inc.Inventors: Richard T. Pon, Shuyuan Yu
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Patent number: 7125982Abstract: The present method describes the use of thio-phosphate as a feed source for micro-organisms and multi-cellular organisms. This compound enters into nucleotide pools and ultimately into polymers of both RNA and DNA forming stable phosphorothioate internucleotide linkages. The method enables the microbial synthesis of both plasmid and phage DNA substituted with phosphorothioate. Furthermore, methods are described for the preparation of phosphorothioate oligo mixtures from recombinant phage DNA grown in modified media for use in antisense studies.Type: GrantFiled: December 5, 2001Date of Patent: October 24, 2006Assignee: Frayne ConsultantsInventor: Elizabeth Gay Frayne
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Patent number: 7098325Abstract: The invention relates to a process for the sulfurization of phosphorus-containing compounds which comprises contacting the phosphorus compound to be sulfurized with a sulfur transfer reagent of formula (I) wherein R1 is aryl which can be substituted by halo, (C1–C6) alkyl or (C1-C6) alkoxy, and R2 is (C1–C6) alkyl, which could also form a cyclic ring together with R1, in a solvent or a mixture of solvents.Type: GrantFiled: October 7, 2002Date of Patent: August 29, 2006Inventors: Pierre Martin, Francois J Natt
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Patent number: 7098326Abstract: The present invention discloses novel methods for the integrated synthesis and purification of oligonucleotides. The methods employ novel capping reagents carrying two functional groups. The first functional group provides for a smooth and efficient capping process and incorporates the second functional group into contaminant oligonucleotides during solid phase oligonucleotide synthesis. The second functional group functions as a chemical purification handle in the trapping of truncated oligonucleotides (failure sequences) on a solid support. The trapping process creates covalent bonds between the solid support and the truncated oligonucleotides and therefore allows the removal of the truncated sequences from the desired full length oligonucleotide product by filtration. The chemical trapping process employed in this invention is based on cycloaddition reactions, particularly Diels-Alder reactions between the truncated oligonucleotides and the trapping agent.Type: GrantFiled: January 22, 2003Date of Patent: August 29, 2006Assignee: Sigma-Aldrich Co.Inventors: Wolfgang Pieken, Andreas Wolter, Michael Leuck
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Patent number: 7049432Abstract: The present invention provides alkylphosphonate dimers and oligonucleotides prepared therefrom. The invention further provides novel methods for the preparation of these alkylphosphonate dimers. Methods for the preparation of substantially diastereomerically pure alkylphosphonate dimers are also provided.Type: GrantFiled: June 4, 2002Date of Patent: May 23, 2006Assignees: ISIS Pharmaceuticals, Inc., McGill UniversityInventors: Muthiah Manoharan, George Just, Andrei Guzaev, Arlène Roland, Jianchao Wang, Michael E. Jung
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Patent number: 7041816Abstract: Synthetic processes are provided wherein oligomeric compounds are prepared having phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.Type: GrantFiled: January 20, 2004Date of Patent: May 9, 2006Assignee: ISIS Pharmaceuticals, Inc.Inventors: Vasulinga T. Ravikumar, Muthiah Manoharan, Daniel C. Capaldi, Achim Krotz, Douglas L. Cole, Andrei Guzaev
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Patent number: 7022833Abstract: A process for the synthesis of a phosphorothioate triester is provided. The process comprises the coupling of an H-phosphonate with an alcohol in the presence of a solution comprising both a coupling agent and a sulfur transfer agent. Preferably, the H-phosphonate and alcohol are protected nucleosides or oligonucleotides.Type: GrantFiled: February 23, 2001Date of Patent: April 4, 2006Assignee: Avecia LimitedInventor: Colin Bernard Reese
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Patent number: 6974865Abstract: The present invention is directed to nucleoside monomers wherein the 3?-O atom is replaced with a methylene group. The present invention also provides oligomers comprising a plurality of such monomers which are linked by methylene phosphonate linkages. Further, methods of preparing monomers and oligomers according to the present invention are provided.Type: GrantFiled: December 18, 2002Date of Patent: December 13, 2005Assignee: ISIS Pharmaceuticals, Inc.Inventors: Phillip Dan Cook, Muthiah Manoharan, Martin Maier, Haoyun An
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Patent number: 6951931Abstract: Compounds having structure (1) wherein R1 is —H a protecting group, a linker or a binding partner; and R2 and R34 are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.Type: GrantFiled: November 14, 2002Date of Patent: October 4, 2005Assignee: ISIS Pharmaceuticals, Inc.Inventors: Kuei-Ying Lin, Mark D. Matteucci
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Patent number: 6936709Abstract: A protected 2?-deoxycytidine is purified by precipitating the protected 2?-deoxycytidine represented by general formula (3) in the form of a hydrated crystal from a solution containing the protected 2?-deoxycytidine and water, and by recovering the protected 2?-deoxycytidine: wherein R1 represents a 4-methoxytrityl, 4, 4?-dimethoxytrityl, or triphenylmethyl group; and B1 represents a cytosine group having a protected amino group. The compound represented by general formula (3) is, in particular, a protected 2?-deoxycytidine represented by formula (4): The 2?-deoxycytidine is used as a raw material for antisense DNA.Type: GrantFiled: June 4, 2003Date of Patent: August 30, 2005Assignee: Mitsui Chemicals, Inc.Inventors: Hiroki Ishibashi, Kiyoteru Nagahara, Yasushi Fukuiri, Yasuko Matsuba
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Patent number: 6936472Abstract: A method for specifically and uniformly synthesizing desired polymers within molecular array elements. Droplets containing a reactive monomer are successively applied to the elements of a molecular array in order to synthesize a substrate-bound polymer. Application of an initial droplet, having a first volume, defines the position and size of a molecular array element. Subsequent droplets are applied, to add successive reactive monomers to growing nascent polymers within the molecular array element, with covering volumes so that, even when application of the subsequent droplets is misregistered, the entire surfaces of the elements of the molecular array are exposed to the subsequently applied droplets. Following application of initial droplets, the surface of the molecular array is exposed to a solution containing a very efficient capping agent in order to chemically cap any unreacted nascent growing polymers and any unreacted substrate molecules.Type: GrantFiled: October 5, 2001Date of Patent: August 30, 2005Assignee: Agilent Technologies, Inc.Inventors: Jonathan P. Earhart, Michel G. M. Perbost
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Patent number: 6919437Abstract: Methods for the preparation of oligonucleotides having bioreversible phosphate blocking groups are disclosed. In one aspect, the present invention provides compounds comprising a sequence of nucleotide units that includes a first segment having at least one internucleoside linkage of formula: 3?-O—P(X)(O?)—O-5? and a second segment having at least one internucleoside linkage of formula: 3?-O—P(X)(Y1—(CH2)q—Y2—Y3—Z)—O-5? wherein each of X, Y1, and Y2 is, independently, O or S; q is 2 to about 4; Y3 is C(?O) or S; and Z is aryl having 6 to about 14 carbon atoms or alkyl having from one to about six carbon atoms.Type: GrantFiled: June 10, 1999Date of Patent: July 19, 2005Assignee: ISIS Pharmaceuticals, Inc.Inventors: Muthiah Manoharan, Andrei Guzaev
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Patent number: 6911540Abstract: Oligomers which have substituents on the 2? position are resistant to oligonucleases and furthermore can be derivatized to deliver reagents or drugs, to carry label, or to provide other properties.Type: GrantFiled: June 27, 2002Date of Patent: June 28, 2005Assignee: ISIS Pharmaceuticals, Inc.Inventors: Chris A. Buhr, Mark Matteucci
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Patent number: 6902900Abstract: The invention comprises novel methods and strategies to detect and/or quantify nucleic acid analytes. The methods involve nucleic acid probes with covalently conjugated dyes, which are attached either at adjacent nucleotides or at the same nucleotide of the probe and novel linker molecules to attach the dyes to the probes. The nucleic acid probes generate a fluorescent signal upon hybridization to complementary nucleic acids based on the interaction of one of the attached dyes, which is either an intercalator or a DNA groove binder, with the formed double stranded DNA. The methods can be applied to a variety of applications including homogeneous assays, real-time PCR monitoring, transcription assays, expression analysis on nucleic acid microarrays and other microarray applications such as genotyping (SNP analysis). The methods further include pH-sensitive nucleic acid probes that provide switchable fluorescence signals that are triggered by a change in the pH of the medium.Type: GrantFiled: October 21, 2002Date of Patent: June 7, 2005Assignee: Prolico, LLCInventors: Martin Davies, Ian Bruce, Andreas Wolter
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Patent number: 6900301Abstract: Therapeutic oligonucleotide analogues which have improved nuclease resistance and improved cellular uptake are provided. Replacement of the normal phosphorodiester inter-sugar linkages found in natural oligomers with four atom linking groups forms unique di- and poly-nucleosides and nucleotides useful in regulating RNA expression and in therapeutics. Methods of synthesis and use are also disclosed.Type: GrantFiled: May 22, 2002Date of Patent: May 31, 2005Assignee: ISIS Pharmaceuticals, Inc.Inventors: Phillip Dan Cook, Yogesh Shantilal Sanghvi, Jean Jacques Vasseur, Francoise Debart
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Patent number: 6894158Abstract: Provided are methods of producing phosphitylated compounds, including 3?-O-phosphoramidites, comprising the step of reacting a hydroxyl-containing compound with a phosphitylating agent in the presence of a phosphitylation activator selected from the group consisting of: (1) acid-base complexes derived from an amine base of Formula I wherein R, R1, and R2 are independently C1-C10 alkyl, C3-C10 cycloalkyl, C6-C10 aryl, C7-C10 aralkyl, C1-C10 heteroalkyl, or C1-C10 heteroaryl, wherein any two adjacent R, R1, and R2 may be connected to form a heterocyclic ring; (2) acid-base complexes derived from a diazabicyclo amine base; and (3) combinations of two or more thereof.Type: GrantFiled: February 24, 2003Date of Patent: May 17, 2005Assignee: Honeywell International Inc.Inventors: Christian Werner, Frank Nerenz, Andreas Kanschik-Conradsen, Kalakota Reddy
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Patent number: 6881836Abstract: Novel compounds are provided which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar—C(R1)(R2)—O—C(O)— wherein: Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative thereof; R1 and R2 are independently H, optionally substituted alkyl, alkenyl or alkynyl, optionally substituted aryl or optionally substituted heteroaromatic, or a vinylogous derivative of the foregoing; and X is a leaving group, a chemical fragment linked to Ar—C(R1)(R2)—O—C(O)— via a heteroatom, or a solid support; provided that when Ar is 1-pyrenyl and R1 and R2 are H, X is not linked to Ar—C(R1)(R2)—O—C(O)— via a nitrogen atom.Type: GrantFiled: January 22, 2003Date of Patent: April 19, 2005Assignee: Affymetrix, IncInventors: Glenn H. McGall, Ngo Q. Nam, Richard P. Rava
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Patent number: 6875859Abstract: The invention concerns compounds of the general formula (I) in which the residues R1 to R7 have the meanings given in the application as well as methods for their preparation.Type: GrantFiled: March 11, 2002Date of Patent: April 5, 2005Assignee: Roche Diagnostics GmbHInventors: Klaus Mühlegger, Herbert Von Der Eltz
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Patent number: 6875750Abstract: Aziridine derivatives of formula (I) are disclosed which can be used as cofactor for S-adenosyl-L-methionine-dependent methyltransferases.Type: GrantFiled: July 28, 1999Date of Patent: April 5, 2005Assignee: Max-Planck-Gesellschaft zur Foerderung der Wissenschaften E.V.Inventors: Marc Pignot, Elmar Weinhold
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Patent number: 6861518Abstract: Methods and Intermediates for the Preparation of Oligomers Containing Diastereomerically Enriched Phosphorothioate Linkages are Disclosed.Type: GrantFiled: September 24, 2002Date of Patent: March 1, 2005Assignee: McGill UniversityInventors: George Just, Zhili Xin, Eric Marsault, Yi Jin, Jianchao Wang
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Patent number: 6858720Abstract: A method of synthesizing polynucleotides is disclosed. The method involves contacting a first nucleotide with a selected reactive group in the presence of an ionic liquid. The selected reactive group may be on a second nucleotide, a polynucleotide, or on a moiety on an insoluble substrate, for example in an oligonucleotide synthesizer.Type: GrantFiled: October 31, 2001Date of Patent: February 22, 2005Assignee: Agilent Technologies, Inc.Inventors: Joel Myerson, Michel G. M. Perobost, Douglas J. Dellinger, Geraldine F Dellinger
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Patent number: 6858722Abstract: Synthetic processes are provided wherein oligomers are prepared using phosphoramidite compositions. Oligomers having phosphodiester, phosphorothioate, phosphorodithioate covalent linkages are prepared that can include other covalent linkages. Also provided are compositions useful in such processes.Type: GrantFiled: May 23, 2003Date of Patent: February 22, 2005Assignee: Isis Pharmaceuticals, Inc.Inventors: Vasulinga T. Ravikumar, Daniel C. Capaldi, Douglas L. Cole
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Patent number: 6858715Abstract: Synthetic processes are provided wherein oligomeric compounds are prepared having phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.Type: GrantFiled: August 30, 2002Date of Patent: February 22, 2005Assignee: ISIS Pharmaceuticals, Inc.Inventors: Vasulinga T. Ravikumar, Muthiah Manoharan, Daniel C. Capaldi, Achim Krotz, Douglas L. Cole, Andrei Guzaev
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Patent number: 6852850Abstract: A method of fabricating polynucleotide arrays includes dissolving a nucleotide monomer, oligonucleotide, or polynucleotide in a solvent containing ionic liquid and depositing the resulting solution on an array substrate. The method has particular application to fabrication of an addressable array of polynucleotides on a substrate that carries substrate bound moieties each with a hydroxyl group. The process may be repeated at specific locations on the array to elongate the polynucleotide deposited on the array.Type: GrantFiled: October 31, 2001Date of Patent: February 8, 2005Assignee: Agilent Technologies, Inc.Inventors: Joel Myerson, Michel G M Perbost, Douglas J Dellinger, Geraldine F. Dellinger
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Patent number: 6846922Abstract: The present invention relates to improved methods for the preparation of nucleoside phosphoramidites and oligonucleotides. In one aspect, the methods of the invention are used to prepare phosphitylating reagents using pyridinium salts as activators. In a further aspect, the methods of the invention are used to prepare internucleoside linkages using activators which include at least one pyridinium salt and at least one substituted imidazole. In a further aspect, methods are provided preparation of internucleoside linkages between nucleosides having 2?-substituents using imidazolium or benzimidazolium salts as an activator. In a further aspect, methods are provided preparation of internucleoside linkages between nucleosides having bioreversible protecting group that confers enhanced chemical and biophysical properties, without exocyclic amine protection, using imidazolium or benzimidazolium salts as an activator.Type: GrantFiled: November 8, 2000Date of Patent: January 25, 2005Assignee: ISIS Pharmaceuticals, Inc.Inventors: Muthia Manoharan, Vasulinga T. Ravikumar
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Patent number: 6825331Abstract: The present invention provides oligomers which are specifically hybridizable with a selected sequence of RNA or DNA wherein at least one of the nucleoside moieties of the oligomer is modified to include an aminooxy linkage. These oligomers are useful for diagnostic, therapeutic and investigative purposes.Type: GrantFiled: September 3, 2002Date of Patent: November 30, 2004Assignee: ISIS Pharmaceuticals, Inc.Inventors: Muthiah Manoharan, Harri Lonnberg, Harri Salo, Pasi Virta
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Patent number: RE39324Abstract: Compounds having structure (1) wherein R1 is —H a protecting group, a linker or a binding partner; and R2 and R34 are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.Type: GrantFiled: February 21, 2002Date of Patent: October 3, 2006Assignee: ISIS Pharmaceuticals, Inc.Inventors: Kuei-Ying Lin, Mark D. Matteucci