Abstract: Activity-based probes that can be used to selectively identify and characterize enzymes that are involved in different phases of xenobiotic metabolism in a host and its microbiota population(s) are described. The activity-based probes described specifically label only their target active enzymes involved in xenobiotic metabolism and therefore provide a measurement of true protein functional activity rather than transcript or protein abundance. The activity-based probes also provide multimodal profiling of these active enzymes. Methods for preparing the activity based probes and exemplary methods for their use also are disclosed.
Type:
Grant
Filed:
October 3, 2018
Date of Patent:
May 31, 2022
Assignee:
Battelle Memorial Institute
Inventors:
Aaron T. Wright, Susan Ramos-Hunter, Christopher Whidbey
Abstract: Embodiments may include a method of determining a nucleic acid sequence. The nucleic acid may be DNA. The method may include forming, by a polymerase, a double-stranded nucleic acid molecule from a first nucleic acid strand and a second nucleic acid strand. Forming the double-stranded nucleic acid molecule may include adding a first compound to the second nucleic acid strand. The first compound may include a nucleotide attached to a third nucleic acid strand. The third nucleic acid strand may be attached to a moiety. The method may also include detaching the nucleotide from the third nucleic acid strand and the moiety. The method may further include measuring a change in an electrical characteristic of a transistor resulting from the moiety. Additionally, the method may include identifying the nucleotide based on the measured change in the electrical characteristic.
Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using renewable initiators coupled to a solid support. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template.
Type:
Grant
Filed:
January 29, 2019
Date of Patent:
May 17, 2022
Assignee:
Molecular Assemblies, Inc.
Inventors:
J. William Efcavitch, Matthew T. Holden
Abstract: Described herein are recognition modules that bind specifically to a template nucleic acid and which ligate together in a reducing environment to produce a gamma peptide nucleic acid (?PNA) oligomer. Also provided are methods of synthesizing a ?PNA oligomer on a template using the recognition modules.
Abstract: The present disclosure relates to a composition for analysis of DNA sequences and a method for analysis of DNA sequences by using the same and, more particularly, to a composition comprising the compound represented by Chemical Formula 1 and a method for analysis of DNA sequences, the method comprising a step of treating a sample with the same. The compound represented by Chemical Formula 1 in which TAMRA is linked to polypyrrole specifically binds an A/T base pair (W) to fluoresce alone without causing DNA photocleavage. Therefore, the compound is useful for DNA analysis particularly at the single DNA molecule level.
Type:
Grant
Filed:
June 20, 2019
Date of Patent:
April 19, 2022
Assignee:
Sogang University Research Foundation
Inventors:
Kyu Bong Jo, Seong Hyun Lee, Hiroshi Sugiyama
Abstract: The present disclosure provides a solid phase method of making oligonucleotides via sequential coupling cycles including at least one coupling of a dinucleotide dimer subunit to a free 3?-terminal group of a growing chain. The oligonucleotides include at least two nucleoside subunits joined by a N3??P5? phosphoramidate linkage. The method may include the steps of (a) deprotecting the protected 3? amino group of a terminal nucleoside attached to a solid phase support, said deprotecting forming a free 3? amino group; (b) contacting the free 3? amino group with a 3?-protected amino-dinucleotide-5?-phosphoramidite dimer in the presence of a nucleophilic catalyst to form an internucleoside N3??P5? phosphoramidite linkage; and (c) oxidizing (e.g., sulfurizing) the linkage. The compositions produced by the subject methods may include a reduced amount of one or more (N?x) oligonucleotide products. Also provided are pharmaceutical compositions including the subject oligonucleotide compositions.
Abstract: The present invention relates to improving the processing rate of a sequencing reaction, for example in a nanopore sequencing reaction, by means of using improved nucleoside-tags. The tags are linked to the nucleoside phosphate via a Pictet Spengler reaction. Exemplary sequencing reactions that are improved by the present methods include nanopore-based nucleic acid sequencing-by-synthesis reactions.
Type:
Grant
Filed:
October 8, 2019
Date of Patent:
April 5, 2022
Assignee:
Roche Sequencing Solutions, Inc.
Inventors:
Frank Bergmann, Ian Quang Chau, Peter Crisalli, Hannah Marie Kallewaard-Lum, Hannes Kuchelmeister, Sebastian Johannes Pomplun, Hasham Saqib, Christian Wellner
Abstract: Embodiments of the present disclosure relate to sequencing methods using nucleotide molecules with a 3? AOM blocking group, which can provide reduced phasing and pre-phasing values. Also provided herein are kits related to such sequencing methods.
Type:
Grant
Filed:
December 20, 2019
Date of Patent:
April 5, 2022
Assignee:
Illumina Cambridge Limited
Inventors:
Antoine Francais, Elena Cressina, Adam Culley, Angelica Mariani, Xiaolin Wu, Xiaohai Liu
Abstract: Disclosed are a method for marking 5-formyl cytosine and the use thereof in single base resolution sequencing. The method for marking the 5-formyl cytosine comprises the following steps of: (1) preparing a DNA or RNA sample; and (2) mixing the DNA or RNA sample with a buffer solution and a compound R1—CH2—CN to obtain a marking reaction system; and reacting the compound R1—CH2—CN therein with the 5-formyl cytosine in DNA and RNA molecules, and thereby achieving the marking of the 5-formyl cytosine; the reaction process is as in (I) below: wherein, R1 is an electron withdrawing group next to the CH2 group, preferably —CN, (II) or (III), and more preferably —CN; R is a DNA or RNA molecule connected to the 5-formyl cytosine; and the pH value of the marking reaction system is 7.5-9. On this basis, also provided in the present invention is a sequencing analysis method for the 5-formyl cytosine.
Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.
Type:
Grant
Filed:
June 24, 2021
Date of Patent:
March 29, 2022
Assignee:
ELEMENT BIOSCIENCES, INC.
Inventors:
Michael Previte, Molly Min He, Junhua Zhao, Hui Zhen Mah, Chunhong Zhou, Sinan Arslan, Matthew Kellinger, Lorenzo Berti, Steve Xiangling Chen
Abstract: The present invention relates to ?-PNA monomers according to Formula I where substituent groups R1, R2, R3, R4, R5, R6, B and P are defined as set forth in the specification. The invention also provides methodology for synthesizing compounds according to Formula I and methodology for synthesizing PNA oligomers that incorporate one or more Formula I monomers.
Type:
Grant
Filed:
August 26, 2020
Date of Patent:
March 22, 2022
Assignee:
CARNEGIE MELLON UNIVERSITY
Inventors:
Danith H. Ly, Srinivas Rapireddy, Bichismita Sahu
Abstract: Emulsion compositions are provided herein. Also provided herein are kits containing one or more emulsion compositions or components for making such emulsion compositions. Also provided herein are methods of using such emulsion compositions, such as for amplification of target nucleic acids in emulsion droplets.
Abstract: The invention relates to an oligonucleotide including one or more modified nucleoside bases having the structure -B-L-A wherein for each of the modified nucleosides A is independently a monosaccharide or oligosaccharide, Lisa linker molecule, and B is independently a pyrimidine or pyridine base linked to the sugar-phosphate backbone of the oligonucleotide; and wherein the oligonucleotide binds specifically to a carbohydrate-binding monoclonal antibody with an affinity of less than 100 nM. Immunogenic conjugates that include the oligonucleotide, and pharmaceutical compositions that include the oligonucleotide or the immunogenic conjugate are also disclosed. Various method of using the oligonucleotides, immunogenic conjugates, and pharmaceutical compositions are disclosed, including inducing an immune response, inhibiting viral or bacterial infection, treating a cancerous condition, and detecting a neutralizing antibody.
Abstract: Fluorescent dyes, ink compositions comprising the dyes, methods and devices for printing the ink compositions, images printed using the ink compositions and methods for authenticating the printed images are provided. The fluorescent dyes are heterorotaxanes that include large macrocyclic rings around fluorophores and are capable of emitting solid-state fluorescence. When the heterorotaxanes are combined with encapsulating agents and competitive binding agents in aqueous solution, the resulting ink composition exhibits a complex, dynamic equilibrium that provides a tunable fluorescence emission spectrum with a non-linear response to the dye concentration.
Type:
Grant
Filed:
February 6, 2019
Date of Patent:
March 8, 2022
Assignees:
Northwestern University, Innotune LLC
Inventors:
James Fraser Stoddart, Xisen Hou, Chenfeng Ke, Roger B. Pettman
Abstract: A method for processing a nucleic acid, in which the nucleic acid is exposed to an aqueous medium which includes a polyol in sufficient proportion for at least a portion of the nucleic acid to enter or remain in an extra-solution phase. Thus, a polyol may be used to bind a nucleic acid which is in solution to a solid support or to wash a nucleic acid on a solid support whilst maintaining it on the support. The polyol may for example be a C2-C10 alkanediol.
Abstract: The present invention provides, among other aspects, functionalized chromophoric polymer dots comprising a hydrophobic core and a hydrophilic cap, and bioconjugates thereof. Also provided are improved methods for preparing functionalized chromophoric polymer dots. Methods for in vivo imaging and molecular labeling are also disclosed.
Type:
Grant
Filed:
December 4, 2018
Date of Patent:
February 15, 2022
Assignee:
UNIVERSITY OF WASHINGTON
Inventors:
Daniel T. Chiu, Changfeng Wu, Jason McNeill, Jiangbo Yu
Abstract: This invention provides a process for sequencing nucleic acids using 3? modified deoxynucleotide analogues or 3? modified deoxyinosine triphosphate analogues, and 3? modified dideoxynucleotide analogues having a detectable marker attached thereto.
Type:
Grant
Filed:
April 15, 2019
Date of Patent:
February 8, 2022
Assignee:
THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
Inventors:
Jingyue Ju, Dae Hyun Kim, Jia Guo, Qinglin Meng, Zengmin Li, Huanyan Cao