Patents by Inventor Steven A. Benner

Steven A. Benner 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).

  • Patent number: 10106837
    Abstract: This invention provides a single process that collects any and all target nucleic acids from a sample that can contain any of a number of biological species, including bacteria, viruses, or fungi, where the first step renders the sample nonhazardous and releases nucleic acids from cell structures, compartments, and molecular complexes that may hold them, the second step concentrates the target nucleic acids from even very highly dilute states, in the third step releases these in a form that, following dilution, makes them compatible with processes that amplify nucleic acids, both standard PCR as well as isothermal amplification protocols. The pre-amplification process involves ammonia solutions no more toxic than those found in the commercial product Windex, requires no electrical power, requires materials no more complex than water desalinization resin and salt, and can be used by inexperienced individuals.
    Type: Grant
    Filed: February 4, 2015
    Date of Patent: October 23, 2018
    Inventor: Steven A Benner
  • Publication number: 20180265537
    Abstract: This invention claims aqueous compositions that comprise triphosphates of 2?-deoxynucleoside derivatives that have, instead of a 3?-OH moiety, a 3?-ONH2 moiety; wherein said compositions contain less than 0.5 mole percent contaminating triphosphate having a 3?-OH moiety, as well as processes for providing such compositions. The compositions further must contain insubstantial amounts of hydroxylamine.
    Type: Application
    Filed: March 16, 2017
    Publication date: September 20, 2018
    Inventor: Steven A. Benner
  • Patent number: 10059735
    Abstract: This application discloses nucleoside analogs that when incorporated into a oligonucleotide, forms a nucleobase pair with either thymidine or cytidine that are present in a complementary strand at the paired position. These analogs are called “purine biversals”. Such compounds and their associated processes have utility in processes that detect complementary oligonucleotides, in particular oligonucleotides from natural sources and in complex biological mixtures, where the sequence of the complementary oligonucleotide being detected is not known precisely. The invention also includes compositions of matter that are oligonucleotides that contain purine biversals of the instant invention, and duplexes of said oligonucleotides.
    Type: Grant
    Filed: December 13, 2016
    Date of Patent: August 28, 2018
    Inventors: Steven A Benner, Hyo-Joong Kim
  • Patent number: 10059737
    Abstract: This invention is for a new molecular recognition system, where DNA-like molecules comprising segments built from nucleotides that carry only a small which comprises process by which one molecule interacts with a specific second molecule, or by which a portion of a single molecule interacts specifically with another portion of the same molecule. Further, this invention relates to molecular recognition that follows simple rules. Further, this invention relates to molecular systems that are linear biopolymers that are analogs of DNA and RNA, in that they are built from a small set of building blocks that are linked together by phosphate groups, where the building blocks comprise a sugar (ribose, 2?-deoxyribose, or an analog) attached to a heterocycle. The molecular recognition that they display differs from that displayed by DNA and RNA, in that the rules governing molecular recognition break the rules of size complementarity followed in molecular recognition displayed between and within strands of DNA and RNA.
    Type: Grant
    Filed: March 16, 2017
    Date of Patent: August 28, 2018
    Inventors: Steven A Benner, Shuichi Hoshika
  • Patent number: 9988659
    Abstract: The instant invention provides for the assembly of large DNA oligonucleotide constructs by the self-assembly of multiple oligonucleotide fragments, wherein the assembly is guided by the hybridization between non-standard nucleotides that form non-standard nucleobase pairs orthogonal to the standard T:A and C:G nucleobase pairs. Adding nucleobase pairs increases the information density of the fragments, minimizing off-target hybridization. The invention further provides rules and methods for converting non-standard pairs into standard pairs using polymerase copying with conversion.
    Type: Grant
    Filed: March 18, 2014
    Date of Patent: June 5, 2018
    Inventors: Steven A Benner, Ryan Shaw
  • Publication number: 20170298356
    Abstract: This invention provides for processes for binding to and/or chemically transforming a preselected target, where the process involves contacting said target to an oligonucleotide molecule that contains one or more “non-standard” nucleotides, which are nucleotide analogs that, when incorporated into oligonucleotides (DNA or RNA, collectively xNA), present to a pattern of hydrogen bonds that is different from the pattern presented by adenine, guanine, cytosine, and uracil. This disclosure provides an example where such an oligonucleotide molecule is built from both D- and L-mirror image carbohydrates in the backbone. It also provides a process for obtaining these binders and/or transformers by a laboratory in vitro selection process that exploits rolling circle amplification rather than the polymerase chain reaction.
    Type: Application
    Filed: June 30, 2017
    Publication date: October 19, 2017
    Inventor: Steven A. Benner
  • Patent number: 9725713
    Abstract: This invention provides for products and processes for binding to a preselected target, where the process involves contacting this target to an oligonucleotide molecule that contains one or more “non-standard” nucleotides, which are nucleotide analogs that, when incorporated into oligonucleotides (DNA or RNA, collectively xNA), present to a complementary strand in a Watson-Crick pairing geometry a pattern of hydrogen bonds that is different from the pattern presented by adenine, guanine, cytosine, and uracil. This disclosure provides an example where such an oligonucleotide molecule contains a single 2-amino-8-(1?-?-D-2?-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)one and a single 6-amino-5-nitro-3-(1?-?-D-2?-deoxyribofuranosyl)-2(1H)-pyridone, and where the target is a cell, and is obtained by a process of in vitro selection.
    Type: Grant
    Filed: November 18, 2013
    Date of Patent: August 8, 2017
    Inventors: Steven A Benner, Zunyi Yang
  • Patent number: 9315842
    Abstract: This invention covers processes for the isothermal amplification of DNA molecules having a preselected sequence. It is based on the unexpected discovery that primers having, at some positions, adenine substituted by 2-aminopurine or diaminopurine, guanine by inosine, thymine by 2-thiothymine, and cytosine by N4-ethylcytosine (“SAMRS nucleotides”) were accepted by enzymes used in the standard helicase-dependent amplification (HDA). Further unexpected was the discovery that target nucleotides are efficiently amplified in an HDA-like process (hereinafter abbreviated as simply HDA) using substituted primers. Also discovered was the diminution of spurious products through the use of SAMRS-substituted primers.
    Type: Grant
    Filed: August 19, 2013
    Date of Patent: April 19, 2016
    Inventors: Steven A Benner, Zunyi Yang
  • Patent number: 9062345
    Abstract: The disclosed invention provides processes to synthesize DNA analogs that contain non-standard nucleotides, defined as those which form nucleobase pairs that fit standard Watson-Crick geometry, but are joined to their complements by hydrogen bonding patterns different from those that join standard A:T and G:C pairs. The disclosed process resembles “rolling circle amplification”, but uses primers that contain non-standard nucleotides, as well as 2?-deoxynucleotide triphosphates whose heterocyclic “nucleobases” are also non-standard. An example is provided that shows this process using 6-amino-5-nitro-3-(1?-beta-D-2?-deoxyribofuranosyl)-2(1H)-pyridone to implement the non-standard “small” donor-donor-acceptor (pyDDA) hydrogen bonding pattern, and 2-amino-8-(1?-beta-D-2?-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one to implement the “large” acceptor-acceptor-donor (puAAD) pattern.
    Type: Grant
    Filed: January 15, 2014
    Date of Patent: June 23, 2015
    Inventor: Steven A Benner
  • Patent number: 9062336
    Abstract: This invention covers methods for isothermal amplification of DNA. It is based on the unexpected discovery that primers having, at some positions, adenine substituted by 2-aminopurine or diaminopurine, guanine by inosine, thymine by 2-thiothymine, and cytosine by N4-ethylcytosine (“substituted primers”) were accepted by enzymes used in the standard recombinase polymerase assay (RPA). Further unexpected was the discovery that target nucleotides are efficiently amplified in an RPA-like process (hereinafter abbreviated as simply RPA) using substituted primers. RPA-like processes were also discovered to amplify target DNA with substituted primers tagged with oligonucleotides incorporating nucleotides from an artificially expanded genetic information system (AEGIS).
    Type: Grant
    Filed: March 7, 2013
    Date of Patent: June 23, 2015
    Inventors: Steven A Benner, Nidhi Sharma
  • Publication number: 20150050695
    Abstract: This invention covers processes for the isothermal amplification of DNA molecules having a preselected sequence. It is based on the unexpected discovery that primers having, at some positions, adenine substituted by 2-aminopurine or diaminopurine, guanine by inosine, thymine by 2-thiothymine, and cytosine by N4-ethylcytosine (“SAMRS nucleotides”) were accepted by enzymes used in the standard helicase-dependent amplification (HDA). Further unexpected was the discovery that target nucleotides are efficiently amplified in an HDA-like process (hereinafter abbreviated as simply HDA) using substituted primers. Also discovered was the diminution of spurious products through the use of SAMRS-substituted primers.
    Type: Application
    Filed: August 19, 2013
    Publication date: February 19, 2015
    Inventors: Steven A. Benner, Zunyi Yang
  • Patent number: 8946397
    Abstract: This invention provides compounds that are of the class of nucleoside analogs, and more specifically nucleoside analogs that have a non-standard nucleobase, and more specifically analogs where a side chain is appended to said non-standard nucleobase, where said side chain can be cleaved so as to leave behind no more than five atoms appended to the nucleobase as a “scar”. The claimed compounds are useful as intermediates in processes that transiently introduce tags, labels, fluorescent molecules, or other species into oligonucleotides, as in sequencing using cyclic reversible termination, in in vitro selection using functionalized nucleotides that must later be PCR amplified, or in nucleotide capture protocols used in diagnostics.
    Type: Grant
    Filed: April 4, 2012
    Date of Patent: February 3, 2015
    Inventor: Steven A. Benner
  • Patent number: 8389703
    Abstract: This invention relates to nucleoside, nucleotide, and oligonucleotide analogs that incorporate non-standard nucleobase analogs, defined to be those that present a pattern of hydrogen bonds to a paired nucleobase analog in a complementary strand that is different from the pattern presented by adenine, guanine, cytosine, and thymine. The invention is specifically concerned with nucleotide analogs that present the donor-donor-acceptor, hydrogen bonding patterns on pyrimidine analogs, and especially those that are analogs of ribonucleotides, including protected ribonucleotides suitable for phosphoramidite-based synthesis of RNA. The heterocycles on these nucleoside analogs are aminopyridones that have electron withdrawing groups attached to the position analogous to the 5-position of the ring in standard pyrimidines, including nitro, cyano, and carboxylic acid derivatives.
    Type: Grant
    Filed: November 2, 2011
    Date of Patent: March 5, 2013
    Inventors: Steven A. Benner, Hyo-Joong Kim
  • Publication number: 20110319298
    Abstract: This patent application claims processes and compositions of matter that enable the discovery of single nucleotide polymorphisms (SNPs) that distinguish the genomes of two individual organisms in the same species, as well as that distinguish the paternal and maternal genetic inheritance of a single individual, as well as distinguish the genomes of cells in special tissues (e.g. cancer tissues) within an individual from the genomes of the standard cells in the same individuals, as well as the SNPs that are discovered using these processes and compositions. Two steps are essential to the invention disclosed in this application. The first step provides four sets of primers, which are designated “T-extendable”, “A-extendable”, “C-extendable”, and “G-extendable”. These primers, when targeted against a reference genome as a template, add (respectively) T, A, C, and G to their 3?-ends in a template-directed primer extension reaction.
    Type: Application
    Filed: April 21, 2009
    Publication date: December 29, 2011
    Inventors: Steven A. Benner, Shuichi Hoshika, Nicole Leal
  • Publication number: 20110275124
    Abstract: 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: Application
    Filed: March 23, 2009
    Publication date: November 10, 2011
    Inventors: Steven A. Benner, Daniel Hutter, Nicole Aurora Leal, Fei Chen
  • Patent number: 6941317
    Abstract: A computer research tool is provided for searching and displaying biological data. Specifically, the invention provides a computer research tool for performing computerized research of biological data from various databases and for providing a novel graphical user interface that significantly enhances biological data representation, progressive querying and cross-navigation of windows and databases. The invention can be implemented in numerous ways, including as a system, a device, a method, or a computer readable medium.
    Type: Grant
    Filed: September 14, 1999
    Date of Patent: September 6, 2005
    Assignee: Eragen Biosciences, Inc.
    Inventors: Stephen Chamberlin, Steven A. Benner, Lukas Knecht
  • Patent number: 6063571
    Abstract: The present invention relates to a novel advantageous process for amplifying nucleic acids using DNA/PNA primers and a temperature-stable polymerase enzyme.
    Type: Grant
    Filed: September 11, 1997
    Date of Patent: May 16, 2000
    Assignee: Hoechst Aktiengesellschaft
    Inventors: Eugen Uhlmann, Gerhard Breipohl, Steven A. Benner, Michael Lutz
  • Patent number: 5432272
    Abstract: The disclosure describes a method for incorporating into double stranded DNA and RNA base pairs composed of pairing units that fit the Watson-Crick geometry in that they involve a monocyclic six membered ring pairing with a fused bicyclic heterocyclic ring system composed of a five member ring fused with a six membered ring, with the orientation of the heterocycles with respect to each other and with respect to the backbone chain analogous to that found in DNA and RNA, but with a pattern of hydrogen bonds holding the base pair together different from that found in the AT and GC base pairs (a "non-standard base pair").
    Type: Grant
    Filed: October 9, 1990
    Date of Patent: July 11, 1995
    Inventor: Steven A. Benner
  • Patent number: 5216141
    Abstract: Analogs of DNA containing sulfides, sulfoxides, and sulfones as linking groups between subunits capable of forming bonds with natural oligonucleotides are described. The analogs are lipophilic, stable to chemical degradation under a wide range of conditions and stable to enzymatic degradation in vivo.
    Type: Grant
    Filed: June 6, 1988
    Date of Patent: June 1, 1993
    Inventor: Steven A. Benner
  • Patent number: 4638032
    Abstract: A support system for organic synthesis comprising magnetic particles in a dispersion medium covalently attached to functional groups having affinity for polymer subunits, and methods for making and using the support system, e.g. for synthesis of oligodeoxynucleotides and polypeptides.
    Type: Grant
    Filed: August 10, 1984
    Date of Patent: January 20, 1987
    Assignee: Genetics Institute, Inc.
    Inventor: Steven A. Benner