Patents Assigned to Epicentre Technologies
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Publication number: 20220275428Abstract: Presented herein are methods and compositions for analyzing rare nucleic acid species. Some methods presented herein use DNA reassociation kinetics following thermal denaturation to define populations of nucleic acid sequences, e.g., highly abundant (e.g., cDNA from rRNA), moderately abundant, and less abundant or rare sequences (e.g., cDNA from mRNA).Type: ApplicationFiled: April 25, 2022Publication date: September 1, 2022Applicant: Epicentre Technologies CorporationInventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
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Patent number: 10184122Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing).Type: GrantFiled: July 21, 2015Date of Patent: January 22, 2019Assignee: Epicentre Technologies CorporationInventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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Patent number: 9115396Abstract: Compositions of transposome complexes for generating DNA fragments with specific 5?- and 3?-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components.Type: GrantFiled: July 7, 2011Date of Patent: August 25, 2015Assignee: Epicentre Technologies CorporationInventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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Patent number: 9080211Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next-generation sequencing.).Type: GrantFiled: October 24, 2009Date of Patent: July 14, 2015Assignee: Epicentre Technologies CorporationInventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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Publication number: 20140179562Abstract: The present innovation provides methods and kits that enable rapid and efficient dual end-tagging of RNA to prepare libraries for analysis by applications such as next-generation RNA sequencing, qPCR, microarray analysis, or cloning. The methods do not require time-consuming and inefficient gel-purification steps that are common to methods known in the art. In addition, the present invention provides methods and kits for rapid, high-throughput enzymatic preparation of 5?-activated, 3?-blocked DNA oligonucleotides from standard, single-stranded DNA oligonucleotides.Type: ApplicationFiled: September 13, 2013Publication date: June 26, 2014Applicant: Epicentre Technologies CorporationInventors: Ramesh Vaidyanathan, Scott Kuersten, Ken Doyle
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Patent number: 8574864Abstract: The present innovation provides methods and kits that enable rapid and efficient dual end-tagging of RNA to prepare libraries for analysis by applications such as next-generation RNA sequencing, qPCR, microarray analysis, or cloning. The methods do not require time-consuming and inefficient gel-purification steps that are common to methods known in the art. In addition, the present invention provides methods and kits for rapid, high-throughput enzymatic preparation of 5?-activated, 3?-blocked DNA oligonucleotides from standard, single-stranded DNA oligonucleotides.Type: GrantFiled: November 3, 2010Date of Patent: November 5, 2013Assignee: Epicentre Technologies CorporationInventors: Ramesh Vaidyanathan, Scott Kuersten, Ken Doyle
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Patent number: 8309335Abstract: The present invention provides novel compositions, kits and methods employing RNA 5? polyphosphatases, RNA 5? monophosphatases, capping enzymes, decapping enzymes, nucleic acid pyrophosphatases and RNA ligases, as well as other enzymes, for selective 5? ligation tagging of desired classes of RNA molecules that differ with respect to particular chemical moieties on their 5? ends. The 5? tagged RNA molecules can be used for synthesis of tagged first-stand cDNA, double-stranded cDNA, and sense or antisense RNA for a variety of uses.Type: GrantFiled: February 29, 2012Date of Patent: November 13, 2012Assignee: Epicentre Technologies CorporationInventors: Jerome Jendrisak, Ramesh Vaidyanathan, Gary Dahl
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Patent number: 8163491Abstract: The present invention provides novel compositions, kits and methods employing RNA 5? polyphosphatases, RNA 5? monophosphatases, capping enzymes, decapping enzymes, nucleic acid pyrophosphatases and RNA ligases, as well as other enzymes, for selective 5? ligation tagging of desired classes of RNA molecules that differ with respect to particular chemical moieties on their 5? ends. The 5?tagged RNA molecules can be used for synthesis of tagged first-stand cDNA, double-stranded cDNA, and sense or antisense RNA for a variety of uses.Type: GrantFiled: February 17, 2010Date of Patent: April 24, 2012Assignee: Epicentre Technologies CorporationInventors: Jerome Jendrisak, Ramesh Vaidyanathan, Gary Dahl
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Patent number: 7794971Abstract: The present invention provides compositions and methods for controlling the copy number for a broad range of plasmids and uses thereof. Disclosed is a host cell for conditional control of copy number of a plasmid, which host cell comprises a poly(A) polymerase gene that is operably joined to a conditionally inducible promoter, and a method for cloning and stably maintaining a DNA sequence encoding a heterologous polypeptide in the host cell.Type: GrantFiled: July 1, 2004Date of Patent: September 14, 2010Assignee: Epicentre Technologies CorporationInventors: Darin J. Haskins, Leslie M. Hoffman
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Patent number: 7727744Abstract: Methods, compositions and kits are disclosed for obtaining directionally truncated polypeptides by inserting a transposon. Preferably the transposon comprises a selectable marker and an ori, and optionally a promoter, a ribosome binding site and a translation start codon, into a target sequence in vitro or in vivo. Amplification products, varying in length depending on the transposon insertion site, are obtained using one primer that anneals to the target sequence and a second primer that anneals to the transposon. Amplification products are ligated to circular dsDNA, transformed into host cells, and individual colonies, each containing a directionally truncated clone of the target sequence, are obtained by plating on medium for which the selectable marker encodes resistance. Directionally truncated polypeptides encoded by the target sequence are obtained in vivo by inducing an RNAP in the host cells that uses the promoter or, in vitro by cell-free transcription and translation.Type: GrantFiled: March 30, 2005Date of Patent: June 1, 2010Assignee: Epicentre Technologies CorporationInventors: Michael J. Fiandt, Gary A. Dahl
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Publication number: 20100120098Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next-generation sequencing.Type: ApplicationFiled: October 24, 2009Publication date: May 13, 2010Applicant: Epicentre Technologies CorporationInventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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Patent number: 7659072Abstract: Methods, compositions and kits for amplifying a target sequence by strand displacement replication using strand-displacing primers. The method uses primers that have only ribonucleotides or purine ribonucleotides and at least one 2?-substituted pyrimidine-2?-deoxyribonucleotide.Type: GrantFiled: August 5, 2008Date of Patent: February 9, 2010Assignee: Epicentre Technologies CorporationInventors: Gary A. Dahl, Jerome J. Jendrisak, Agnes J. Radek
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Publication number: 20090053775Abstract: The present invention relates generally to methods, compositions and kits for synthesizing sense RNA molecules from one or more RNA molecules of interest in a sample. In exemplary embodiments, the methods use a terminal tagging oligoribonucleotide (rTTO) to join a DNA sequence tag to the 3?-termini of first-strand cDNA molecules. The use of an rTTO comprising ribonucleotides results in decreased oligonucleotide-derived background synthesis of RNA in the absence of sample RNA and, surprisingly and unexpectedly, also results in significantly increased yields of sense RNA molecules that exhibit sequences that are substantially identical to those of the RNA molecules of interest in the sample. The sense RNA molecules also have an RNA sequence tag on their 5?-termini that is useful for fixing the lengths of sense RNA molecules that are synthesized in a second or subsequent round.Type: ApplicationFiled: June 30, 2008Publication date: February 26, 2009Applicant: Epicentre Technologies CorporationInventors: Gary Dahl, Roy Rabindranauth Sooknanan
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Publication number: 20080293107Abstract: Methods, compositions and kits for amplifying a target sequence by strand displacement replication using strand-displacing primers. The method uses primers that have only ribonucleotides or purine ribonucleotides and at least one 2?-substituted pyrimidine-2?-deoxyribonucleotide.Type: ApplicationFiled: August 5, 2008Publication date: November 27, 2008Applicant: Epicentre Technologies CorporationInventors: Gary A. Dahl, Jerome J. Jendrisak, Agnes J. Radek
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Patent number: 7413857Abstract: Methods, compositions and kits for amplifying a target sequence by strand displacement replication using strand-displacing primers. The method uses primers that have only ribonucleotides or purine ribonucleotides and at least one 2?-substituted pyrimidine-2?-deoxyribonucleotide.Type: GrantFiled: November 21, 2003Date of Patent: August 19, 2008Assignee: Epicentre TechnologiesInventors: Gary A. Dahl, Jerome J. Jendrisak, Agnes J. Radek
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Publication number: 20080044851Abstract: The present invention provides compositions and methods for digesting DNA. In particular, the present invention provides enzymes mixtures that provide enhanced DNA digestion and methods of using the enzyme mixtures to eliminate or reduce undesired DNA molecules from a sample of interest.Type: ApplicationFiled: June 4, 2007Publication date: February 21, 2008Applicant: Epicentre TechnologiesInventors: Jerome Jendrisak, Haiying Grunenwald
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Publication number: 20070281336Abstract: The present invention relates to kits and methods for efficiently generating 5? capped RNA having a modified cap nucleotide and for use of such modified-nucleotide-capped RNA molecules. The invention is used to obtain novel compositions of such modified-nucleotide-capped RNA molecules. In particular, the present invention provides kits and methods for capping RNA using a modified cap nucleotide and a capping enzyme system, such as poxvirus capping enzyme. The present invention finds use for in vitro production of 5?-capped RNA having a modified cap nucleotide and for in vitro or in vivo production of polypeptides by in vitro or in vivo translation of such modified-nucleotide-capped RNA for a variety of research, therapeutic, and commercial applications.Type: ApplicationFiled: April 16, 2007Publication date: December 6, 2007Applicant: Epicentre TechnologiesInventors: Jerome Jendrisak, Ronald Meis, Gary Dahl
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Patent number: 7291487Abstract: A method for synthesizing a nucleic acid molecule comprising at least one non-canonical nucleoside triphosphate using a mutant polymerase having a reduced discrimination between canonical and non-canonical substrates is disclosed. The method comprises incubating a template nucleic acid in a reaction mixture comprising the mutant nucleic acid polymerase and the appropriate canonical and non-canonical nucleoside triphosphates which are desired substrates for the mutant nucleic acid polymerase. The present invention is also a method of determining the sequence of a nucleic acid molecule using the mutant polymerase to create a nucleic acid molecule comprising at least one non-canonical nucleoside triphosphate.Type: GrantFiled: April 1, 2003Date of Patent: November 6, 2007Assignee: Epicentre Technologies CorporationInventors: Rui Sousa, Jerome J. Jendrisak
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Publication number: 20070111216Abstract: The present invention relates to methods and compositions for the identification of enzyme inhibitors. In particular, the present invention relates to the identification of nucleic acid polymerase inhibitors.Type: ApplicationFiled: September 27, 2005Publication date: May 17, 2007Applicant: Epicentre TechnologiesInventors: Jerry Jendrisak, Agnes Radek, Gary Dahl
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Patent number: 7138267Abstract: A method for retrofitting DNA in a single-copy or high-copy vector, such as a fosmid or BAC, whereby an artificial transposon is used to introduce a conditional multi-copy origin of replication (“ori”) into the DNA in said vector. Following random in vitro or in vivo transposition of the ori-containing transposon into DNA in the single-copy or low-copy vector, the resulting insertion clones are introduced into a special host strain that contains a gene which encodes a polypeptide required for replication from the multi-copy ori. However, since the gene for this polypeptide is expressed from a tightly-regulated inducible promoter, the polypeptide is not expressed in the absence of inducer. On addition of inducer to the culture medium, the host cell synthesizes the polypeptide, which in turn activates replication from the multi-copy ori, thereby increasing the amount of clone DNA synthesized by the cell.Type: GrantFiled: April 4, 2002Date of Patent: November 21, 2006Assignee: Epicentre Technologies CorporationInventors: Jerome J. Jendrisak, Leslie M. Hoffman, Michael J. Fiandt, Darin Haskins