Patents Assigned to Epicentre Technologies
  • Publication number: 20220275428
    Abstract: 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: Application
    Filed: April 25, 2022
    Publication date: September 1, 2022
    Applicant: Epicentre Technologies Corporation
    Inventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
  • Patent number: 10184122
    Abstract: 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: Grant
    Filed: July 21, 2015
    Date of Patent: January 22, 2019
    Assignee: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Patent number: 9115396
    Abstract: 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: Grant
    Filed: July 7, 2011
    Date of Patent: August 25, 2015
    Assignee: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Patent number: 9080211
    Abstract: 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: Grant
    Filed: October 24, 2009
    Date of Patent: July 14, 2015
    Assignee: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Publication number: 20140179562
    Abstract: 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: Application
    Filed: September 13, 2013
    Publication date: June 26, 2014
    Applicant: Epicentre Technologies Corporation
    Inventors: Ramesh Vaidyanathan, Scott Kuersten, Ken Doyle
  • Patent number: 8574864
    Abstract: 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: Grant
    Filed: November 3, 2010
    Date of Patent: November 5, 2013
    Assignee: Epicentre Technologies Corporation
    Inventors: Ramesh Vaidyanathan, Scott Kuersten, Ken Doyle
  • Patent number: 8309335
    Abstract: 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: Grant
    Filed: February 29, 2012
    Date of Patent: November 13, 2012
    Assignee: Epicentre Technologies Corporation
    Inventors: Jerome Jendrisak, Ramesh Vaidyanathan, Gary Dahl
  • Patent number: 8163491
    Abstract: 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: Grant
    Filed: February 17, 2010
    Date of Patent: April 24, 2012
    Assignee: Epicentre Technologies Corporation
    Inventors: Jerome Jendrisak, Ramesh Vaidyanathan, Gary Dahl
  • Patent number: 7794971
    Abstract: 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: Grant
    Filed: July 1, 2004
    Date of Patent: September 14, 2010
    Assignee: Epicentre Technologies Corporation
    Inventors: Darin J. Haskins, Leslie M. Hoffman
  • Patent number: 7727744
    Abstract: 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: Grant
    Filed: March 30, 2005
    Date of Patent: June 1, 2010
    Assignee: Epicentre Technologies Corporation
    Inventors: Michael J. Fiandt, Gary A. Dahl
  • Publication number: 20100120098
    Abstract: 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: Application
    Filed: October 24, 2009
    Publication date: May 13, 2010
    Applicant: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Patent number: 7659072
    Abstract: 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: Grant
    Filed: August 5, 2008
    Date of Patent: February 9, 2010
    Assignee: Epicentre Technologies Corporation
    Inventors: Gary A. Dahl, Jerome J. Jendrisak, Agnes J. Radek
  • Publication number: 20090053775
    Abstract: 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: Application
    Filed: June 30, 2008
    Publication date: February 26, 2009
    Applicant: Epicentre Technologies Corporation
    Inventors: Gary Dahl, Roy Rabindranauth Sooknanan
  • Publication number: 20080293107
    Abstract: 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: Application
    Filed: August 5, 2008
    Publication date: November 27, 2008
    Applicant: Epicentre Technologies Corporation
    Inventors: Gary A. Dahl, Jerome J. Jendrisak, Agnes J. Radek
  • Patent number: 7413857
    Abstract: 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: Grant
    Filed: November 21, 2003
    Date of Patent: August 19, 2008
    Assignee: Epicentre Technologies
    Inventors: Gary A. Dahl, Jerome J. Jendrisak, Agnes J. Radek
  • Publication number: 20080044851
    Abstract: 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: Application
    Filed: June 4, 2007
    Publication date: February 21, 2008
    Applicant: Epicentre Technologies
    Inventors: Jerome Jendrisak, Haiying Grunenwald
  • Publication number: 20070281336
    Abstract: 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: Application
    Filed: April 16, 2007
    Publication date: December 6, 2007
    Applicant: Epicentre Technologies
    Inventors: Jerome Jendrisak, Ronald Meis, Gary Dahl
  • Patent number: 7291487
    Abstract: 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: Grant
    Filed: April 1, 2003
    Date of Patent: November 6, 2007
    Assignee: Epicentre Technologies Corporation
    Inventors: Rui Sousa, Jerome J. Jendrisak
  • Publication number: 20070111216
    Abstract: 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: Application
    Filed: September 27, 2005
    Publication date: May 17, 2007
    Applicant: Epicentre Technologies
    Inventors: Jerry Jendrisak, Agnes Radek, Gary Dahl
  • Patent number: 7138267
    Abstract: 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: Grant
    Filed: April 4, 2002
    Date of Patent: November 21, 2006
    Assignee: Epicentre Technologies Corporation
    Inventors: Jerome J. Jendrisak, Leslie M. Hoffman, Michael J. Fiandt, Darin Haskins