Patents by Inventor Joseph Alan Walder

Joseph Alan Walder has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20140106433
    Abstract: The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3? end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.
    Type: Application
    Filed: August 5, 2013
    Publication date: April 17, 2014
    Applicant: INTEGRATED DNA TECHNOLOGIES
    Inventors: Joseph Alan Walder, Mark Aaron Behlke, Scott Rose, Joesph Dobosy
  • Publication number: 20130288245
    Abstract: The invention provides a provides improvements to assays that employ RNase H cleavage for biological applications related to nucleic acid amplification and detection, where the RNase H has been reversibly inactivated.
    Type: Application
    Filed: March 15, 2013
    Publication date: October 31, 2013
    Applicant: Integrated DNA Technologies
    Inventors: Joseph Alan WALDER, Mark Aaron BEHLKE, Scott D. ROSE, Joseph DOBOSY, Susan Marie RUPP
  • Publication number: 20130236967
    Abstract: The invention pertains to modifications for antisense oligonucleotides, wherein the modifications are used to improve stability and provide protection from nuclease degradation. The modifications could also be incorporated into double-stranded nucleic acids, such as synthetic siRNAs and miRNAs.
    Type: Application
    Filed: February 25, 2013
    Publication date: September 12, 2013
    Applicant: INTEGRATED DNA TECHNOLOGIES, INC.
    Inventors: Mark Aaron Behlke, Kimberly Ann Lennox, Ashley Mae Jacobi, Richard Owczarzy, Joseph Alan Walder
  • Patent number: 8399197
    Abstract: The invention provides compositions and methods for amplifying nucleic acid polymer sequences in a high complexity nucleic acid sample. The unique compositions of the invention include a primer set composed of a mixture of two types of primers for DNA synthesis. For extension in one direction, the primers all contain modifications that destroy their ability to serve as templates that can be copied by DNA polymerases. For extension in the opposite direction the set includes at least one primer that can serve as a template and be replicated by DNA polymerases throughout its length. The method can be carried out by mixing the nucleic acid polymer sequence of interest with the set of DNA synthesis primers in an amplification reaction mixture. The reaction mixture is then subjected to temperature cycling analogous to the temperature cycling in PCR reactions. At least one primer in the primer set hybridizes to the nucleic acid polymer.
    Type: Grant
    Filed: September 9, 2009
    Date of Patent: March 19, 2013
    Assignee: Integrated DNA Technologies, Inc.
    Inventors: Mark Aaron Behlke, Joseph Alan Walder, Jeffrey A. Manthey
  • Publication number: 20120258455
    Abstract: The present invention provides methods of cleaving a nucleic acid strand to initiate, assist, monitor or perform biological assays.
    Type: Application
    Filed: March 23, 2012
    Publication date: October 11, 2012
    Applicant: INTEGRATED DNA TECHNOLOGIES, INC.
    Inventors: Mark Aaron Behlke, Scott D. Rose, Joseph Dobosy, Joseph Alan Walder
  • Publication number: 20120123751
    Abstract: The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, in the presence of divalent cations, particularly duplexes of oligonucleotides which may be used as, for example, but not limited to primers or probes in PCR and/or hybridization assays. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of divalent cation salt conditions on the melting temperature.
    Type: Application
    Filed: November 7, 2011
    Publication date: May 17, 2012
    Applicant: INTEGRATED DNA TECHNOLOGIES, INC.
    Inventors: Richard Owczarzy, Bernardo Moreira, Yong You, Mark Aaron Behlke, Joseph Alan Walder
  • Publication number: 20120108799
    Abstract: The invention pertains to modifications for antisense oligonucleotides, wherein the modifications are used to improve stability and provide protection from nuclease degradation. The modifications could also be incorporated into double-stranded nucleic acids, such as synthetic siRNAs and miRNAs.
    Type: Application
    Filed: September 7, 2011
    Publication date: May 3, 2012
    Applicant: INTEGRATED DNA TECHNOLOGIES, INC.
    Inventors: Mark Aaron Behlke, Richard Owczarzy, Yong You, Joseph Alan Walder, Kim Lennox
  • Patent number: 8055451
    Abstract: The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, in the presence of divalent cations, particularly duplexes of oligonucleotides which may be used as, for example, but not limited to primers or probes in PCR and/or hybridization assays. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of divalent cation salt conditions on the melting temperature.
    Type: Grant
    Filed: January 7, 2008
    Date of Patent: November 8, 2011
    Assignee: Integrated DNA Technologies, Inc.
    Inventors: Richard Owczarzy, Bernardo Moreira, Yong You, Mark Aaron Behlke, Joseph Alan Walder
  • Publication number: 20100167353
    Abstract: The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3? end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.
    Type: Application
    Filed: July 22, 2009
    Publication date: July 1, 2010
    Applicant: INTEGRATED DNA TECHNOLOGIES, INC.
    Inventors: Joseph Alan Walder, Mark Aaron Behlke, Scott Rose, Joseph Dobosy
  • Publication number: 20090325169
    Abstract: The present invention pertains to novel oligonucleotide compounds for use in various biological assays, such as nucleic acid amplification, ligation and sequencing reactions. The novel oligonucleotides comprise a ribonucleic acid domain and a blocking group at or near the 3? end of the oligonucleotide. These compounds offer an added level of specificity previously unseen. Methods for performing nucleic acid amplification, ligation and sequencing are also provided. Additionally, kits containing the oligonucleotides are also disclosed herein.
    Type: Application
    Filed: April 30, 2009
    Publication date: December 31, 2009
    Applicant: Integrated DNA Technologies, Inc.
    Inventors: Joseph Alan Walder, Mark Aaron Behlke, Scott Rose, Joseph Dobosy
  • Publication number: 20090198453
    Abstract: The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, in the presence of divalent cations, particularly duplexes of oligonucleotides which may be used as, for example, but not limited to primers or probes in PCR and/or hybridization assays. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of divalent cation salt conditions on the melting temperature.
    Type: Application
    Filed: January 7, 2008
    Publication date: August 6, 2009
    Applicant: Integrated DNA Technologies, Inc
    Inventors: Richard Owczarzy, Bernardo Moreira, Yong You, Mark Aaron Behlke, Joseph Alan Walder
  • Patent number: 7276337
    Abstract: The present invention relates to methods for detecting the presence of ribonuclease enzymes, more specifically to methods that provide for a visual detection assay. The methods entail contacting a test sample suspected of containing ribonuclease activity with a substrate containing a ribonuclease-sensitive internucleotide linkage flanked directly or indirectly by a fluorescence reporter group and a dark quencher, such that if a ribonuclease activity is present in the sample, the ribonuclease-sensitive internucleotide linkage is cleaved and the fluorescence reporter group emits a visually detectable signal. The present invention further provides novel nucleic acid compositions used as substrates for such assays and encompasses kits for performing the methods of the invention.
    Type: Grant
    Filed: October 27, 2003
    Date of Patent: October 2, 2007
    Assignee: Integrated DNA Technologies, Inc.
    Inventors: Joseph Alan Walder, Mark Aaron Behlke, Eric Jeffrey Devor, Lingyan Huang
  • Patent number: 7135284
    Abstract: The present invention provides novel nucleic acid labeling techniques that generate nucleic acid probes with specific activities at least ten fold higher than the levels obtained using standard labeling methods. Specifically, the methods of the invention provides methods of producing nucleic acid probes that each comprises multiple labeled nucleotides. The methods can be used to generate RNA, DNA or hybrid probes. The invention also provides reaction mixtures and kits for the practice of the methods of the invention and compositions comprising the probes generated according to the methods of the invention.
    Type: Grant
    Filed: February 4, 2000
    Date of Patent: November 14, 2006
    Assignee: Integrated DNA Technologies, Inc.
    Inventors: Mark Aaron Behlke, Eric Jeffrey Devor, Shale Anthony James, Joseph Alan Walder
  • Patent number: 7112406
    Abstract: The invention provides methods and compositions for the amplification and replication of nucleic acid molecules. In particular, novel amplification methods, referred to herein as polynomial amplification, are provided. According to these methods, a nucleic acid molecule to be amplified is contacted with at least two primers; a non-replicable primer which may hybridize to the nucleic acid molecule being amplified, and a replicable primer which may hybridize to a primer extension product generated from extension of the non-replicable primer.
    Type: Grant
    Filed: February 28, 2003
    Date of Patent: September 26, 2006
    Assignee: Integrated DNA Technologies, Inc.
    Inventors: Mark Aaron Behlke, Joseph Alan Walder, Jeffrey A. Manthey
  • Patent number: 6889143
    Abstract: The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, particularly duplexes of oligonucleotides which may be used, for example, as primers or probes in PCR and/or hybridization assays. The invention also relates to methods and systems for designing and selecting oligonucleotide probes and primers having a predicted melting temperature which is optimized for such assays. To this end, algorithms and methods are provided for predicting the melting temperature of a nucleic acid having a predetermined sequence. These methods and algorithms estimate the melting temperature of a nucleic acid duplex under particular salt conditions. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of particular salt conditions on the melting temperature.
    Type: Grant
    Filed: September 11, 2003
    Date of Patent: May 3, 2005
    Assignee: Intergrated DNA Technologies, Inc.
    Inventors: Mark Aaron Behlke, Lingyan Huang, Richard Owczarzy, Joseph Alan Walder
  • Publication number: 20040248095
    Abstract: The invention provides methods and compositions for the amplification and replication of nucleic acid molecules. In particular, novel amplification methods, referred to herein as polynomial amplification, are provided. According to these methods, a nucleic acid molecule to be amplified is contacted with at least two primer; a non-replicable primer which may hybridize to the nucleic acid molecule being amplified, and a replicable primer which may hybridize to a primer extension product generated from extension of the non-replicable primer.
    Type: Application
    Filed: February 28, 2003
    Publication date: December 9, 2004
    Applicant: Integrated DNA Technologies
    Inventors: Mark Aaron Behlke, Joseph Alan Walder, Jeffrey A. Manthey
  • Patent number: 6773885
    Abstract: The present invention relates to methods for detecting the presence of ribonuclease enzymes, more specifically to methods that provide for a visual detection assay. The methods entail contacting a test sample suspected of containing ribonuclease activity with a substrate containing a ribonuclease-sensitive internucleotide linkage flanked directly or indirectly by a fluorescence reporter group and a dark quencher, such that if a ribonuclease activity is present in the sample, the ribonuclease-sensitive internucleotide linkage is cleaved and the fluorescence reporter group emits a visually detectable signal. The present invention further provides novel nucleic acid compositions used as substrates for such assays and encompasses kits for performing the methods of the invention.
    Type: Grant
    Filed: October 1, 2001
    Date of Patent: August 10, 2004
    Assignee: Integrated DNA Technologies, Inc.
    Inventors: Joseph Alan Walder, Mark Aaron Behlke, Eric Jeffrey Devor, Lingyan Huang
  • Publication number: 20040137479
    Abstract: The present invention relates to methods for detecting the presence of ribonuclease enzymes, more specifically to methods that provide for a visual detection assay. The methods entail contacting a test sample suspected of containing ribonuclease activity with a substrate containing a ribonuclease-sensitive internucleotide linkage flanked directly or indirectly by a fluorescence reporter group and a dark quencher, such that if a ribonuclease activity is present in the sample, the ribonuclease-sensitive internucleotide linkage is cleaved and the fluorescence reporter group emits a visually detectable signal. The present invention further provides novel nucleic acid compositions used as substrates for such assays and encompasses kits for performing the methods of the invention.
    Type: Application
    Filed: October 27, 2003
    Publication date: July 15, 2004
    Applicant: Integrated DNA Technologies, Inc.
    Inventors: Joseph Alan Walder, Mark Aaron Behlke, Eric Jeffrey Devor, Lingyan Huang
  • Publication number: 20040115705
    Abstract: The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, particularly duplexes of oligonucleotides which may be used, for example, as primers or probes in PCR and/or hybridization assays. The invention also relates to methods and systems for designing and selecting oligonucleotide probes and primers having a predicted melting temperature which is optimized for such assays. To this end, algorithms and methods are provided for predicting the melting temperature of a nucleic acid having a predetermined sequence. These methods and algorithms estimate the melting temperature of a nucleic acid duplex under particular salt conditions. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of particular salt conditions on the melting temperature.
    Type: Application
    Filed: September 11, 2003
    Publication date: June 17, 2004
    Inventors: Mark Aaron Behlke, Lingyan Huang, Richard Owczarzy, Joseph Alan Walder