IL267216B2 - Using biological RNA scaffolds with in vitro selection to generate robust small molecule-binding aptamers for genetically encoded biosensors - Google Patents

Using biological RNA scaffolds with in vitro selection to generate robust small molecule-binding aptamers for genetically encoded biosensors

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Publication number
IL267216B2
IL267216B2 IL267216A IL26721619A IL267216B2 IL 267216 B2 IL267216 B2 IL 267216B2 IL 267216 A IL267216 A IL 267216A IL 26721619 A IL26721619 A IL 26721619A IL 267216 B2 IL267216 B2 IL 267216B2
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IL
Israel
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library
ligand
domain
rna
sequence
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IL267216A
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English (en)
Hebrew (he)
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IL267216A (en
IL267216B1 (en
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Univ Colorado Regents
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Publication of IL267216A publication Critical patent/IL267216A/en
Publication of IL267216B1 publication Critical patent/IL267216B1/en
Publication of IL267216B2 publication Critical patent/IL267216B2/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/28—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Vibrionaceae (F)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/32—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Bacillus (G)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1044—Preparation or screening of libraries displayed on scaffold proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1058—Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/115—Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/16—Aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed
    • C12N2310/531—Stem-loop; Hairpin
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/11—Applications; Uses in screening processes for the determination of target sites, i.e. of active nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2330/00—Production
    • C12N2330/30—Production chemically synthesised
    • C12N2330/31—Libraries, arrays
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Plant Pathology (AREA)
  • Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Ecology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
IL267216A 2016-12-12 2017-12-11 Using biological RNA scaffolds with in vitro selection to generate robust small molecule-binding aptamers for genetically encoded biosensors IL267216B2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201662432879P 2016-12-12 2016-12-12
PCT/US2017/065526 WO2018111745A1 (en) 2016-12-12 2017-12-11 Use of biological rna scaffolds with in vitro selection to generate robust small molecule binding aptamers for genetically encodable biosensors

Publications (3)

Publication Number Publication Date
IL267216A IL267216A (en) 2019-08-29
IL267216B1 IL267216B1 (en) 2024-12-01
IL267216B2 true IL267216B2 (en) 2025-04-01

Family

ID=62559449

Family Applications (1)

Application Number Title Priority Date Filing Date
IL267216A IL267216B2 (en) 2016-12-12 2017-12-11 Using biological RNA scaffolds with in vitro selection to generate robust small molecule-binding aptamers for genetically encoded biosensors

Country Status (14)

Country Link
US (2) US20200208142A1 (enExample)
EP (1) EP3551755A4 (enExample)
JP (2) JP7418210B2 (enExample)
KR (1) KR102612226B1 (enExample)
CN (1) CN110462039A (enExample)
AU (1) AU2017378078B2 (enExample)
BR (1) BR112019012012A2 (enExample)
CA (1) CA3056218A1 (enExample)
EA (1) EA201991446A1 (enExample)
IL (1) IL267216B2 (enExample)
MX (1) MX2019006825A (enExample)
MY (1) MY205553A (enExample)
PH (1) PH12019501302A1 (enExample)
WO (1) WO2018111745A1 (enExample)

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10852274B2 (en) 2017-03-09 2020-12-01 Auburn University Differential circuit for background correction in electrochemical measurements
US11505799B2 (en) 2017-07-07 2022-11-22 Innamed, Inc. Aptamers for measuring lipoprotein levels
US11560565B2 (en) 2018-06-13 2023-01-24 Auburn University Electrochemical detection nanostructure, systems, and uses thereof
WO2020264444A2 (en) * 2019-06-27 2020-12-30 Innamed, Inc. Assay method for point of care quantification of an immunophilin-binding immunosuppressant drug
CN113430203A (zh) * 2020-03-23 2021-09-24 华东理工大学 一种新型rna检测与定量的方法
WO2021256582A1 (ko) * 2020-06-17 2021-12-23 포항공과대학교 산학협력단 전사 활성 인자 및 토홀드 스위치를 포함하는 트립토판 검출용 바이오센서
WO2022006042A1 (en) * 2020-06-29 2022-01-06 President And Fellows Of Harvard College Methods, compositions, and kits for nucleic acid barcoding of biomolecules
CN115177740A (zh) * 2021-04-01 2022-10-14 安升（上海）医药科技有限公司 核酸自组装介导的adc药物的构建方法及应用
CN113512089B (zh) * 2021-06-30 2023-06-13 兰州大学 一种水溶性量子点的多肽稳定剂及应用
CN115704029A (zh) * 2021-08-06 2023-02-17 纳莹(上海)生物科技有限公司 一种rna检测与定量的方法
CN114518359B (zh) * 2022-03-08 2024-08-20 山东理工大学 一种基于g-四联体的双模式卡那霉素适配体传感器的制备方法
CN115791726B (zh) * 2022-11-25 2024-11-15 海南大学 一种基于g-四联体dna超灵敏高选择性检测锶离子的方法
WO2024118806A1 (en) * 2022-11-29 2024-06-06 The Johns Hopkins University Aptamer regulated transcription for in-vitro sensing and transduction
CN116170470B (zh) * 2023-02-28 2023-07-04 北京科易为科技有限公司 移液器系统的数据通讯方法及其通讯系统

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20050019916A1 (en) * 2003-04-14 2005-01-27 Stojanovic Milan N. Cross reactive arrays of three-way junction sensors for steriod determination
US20150031754A1 (en) * 2011-08-16 2015-01-29 Research Foundation of State University of New York at Albany Aptamer modulators of estrogen receptors
US20150141282A1 (en) * 2013-09-06 2015-05-21 Cornell University Rna sequences that induce fluorescence of small molecule fluorophores

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060121510A1 (en) * 1998-11-03 2006-06-08 Breaker Ronald R Multidomain polynucleotide molecular sensors
US20030162190A1 (en) * 2001-11-15 2003-08-28 Gorenstein David G. Phosphoromonothioate and phosphorodithioate oligonucleotide aptamer chip for functional proteomics
US20060121466A1 (en) * 2002-06-13 2006-06-08 Amgen Inc. Hammerhead ribozymes
MX2007005491A (es) * 2004-11-08 2007-09-27 Univ Yale Diseno de compuesto basado en la estructura que involucra riboconmutadores.
SG174103A1 (en) * 2007-05-29 2011-09-29 Univ Yale Riboswitches and methods and compositions for use of and with riboswitches
WO2012021554A1 (en) * 2010-08-09 2012-02-16 Yale University Cyclic di-gmp-ii riboswitches, motifs, and compounds, and methods for their use
US8383794B2 (en) * 2010-10-08 2013-02-26 Li Niu Conformation-selective nucleic acid inhibitors of AMPA glutamate receptors
US20120248666A1 (en) * 2011-03-30 2012-10-04 Firestone Industrial Products Company, Llc Gas spring and damper assembly and suspension system including same
CN104293793B (zh) * 2014-07-24 2018-05-18 江南大学 一种特异识别t-2毒素的寡核苷酸适配体

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20050019916A1 (en) * 2003-04-14 2005-01-27 Stojanovic Milan N. Cross reactive arrays of three-way junction sensors for steriod determination
US20150031754A1 (en) * 2011-08-16 2015-01-29 Research Foundation of State University of New York at Albany Aptamer modulators of estrogen receptors
US20150141282A1 (en) * 2013-09-06 2015-05-21 Cornell University Rna sequences that induce fluorescence of small molecule fluorophores

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
KENT, ALEXANDRA D., NICHOLAS G. SPIROPULOS, AND JENNIFER M. HEEMSTRA., GENERAL APPROACH FOR ENGINEERING SMALL-MOLECULE-BINDING DNA SPLIT APTAMERS., 13 September 2013 (2013-09-13) *
PORTER, ELY B., JOAN G. MARCANO-VEL?ZQUEZ, AND ROBERT T. BATEY., THE PURINE RIBOSWITCH AS A MODEL SYSTEM FOR EXPLORING RNA BIOLOGY AND CHEMISTRY., 1 October 2014 (2014-10-01) *
VILLA, ALESSANDRA, JENS W?HNERT, AND GERHARD STOCK., MOLECULAR DYNAMICS SIMULATION STUDY OF THE BINDING OF PURINE BASES TO THE APTAMER DOMAIN OF THE GUANINE SENSING RIBOSWITCH., 10 June 2009 (2009-06-10) *
YANG, XIAOJUAN, ET AL., CHARACTERIZATION AND APPLICATION OF A DNA APTAMER BINDING TO L-TRYPTOPHAN., 16 October 2010 (2010-10-16) *

Also Published As

Publication number Publication date
EP3551755A4 (en) 2020-06-24
JP2023093572A (ja) 2023-07-04
JP2020504096A (ja) 2020-02-06
MY205553A (en) 2024-10-25
US20200208142A1 (en) 2020-07-02
AU2017378078B2 (en) 2024-06-13
EP3551755A1 (en) 2019-10-16
KR102612226B1 (ko) 2023-12-12
PH12019501302A1 (en) 2019-10-28
EA201991446A1 (ru) 2020-03-03
JP7418210B2 (ja) 2024-01-19
CN110462039A (zh) 2019-11-15
BR112019012012A2 (pt) 2019-10-29
MX2019006825A (es) 2019-10-30
WO2018111745A1 (en) 2018-06-21
AU2017378078A1 (en) 2019-07-25
KR20190100227A (ko) 2019-08-28
IL267216A (en) 2019-08-29
CA3056218A1 (en) 2018-06-21
IL267216B1 (en) 2024-12-01
US20220170009A1 (en) 2022-06-02

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