1
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Jadhav V, Vaishnaw A, Fitzgerald K, Maier MA. RNA interference in the era of nucleic acid therapeutics. Nat Biotechnol 2024; 42:394-405. [PMID: 38409587 DOI: 10.1038/s41587-023-02105-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/15/2023] [Indexed: 02/28/2024]
Abstract
Two decades of research on RNA interference (RNAi) have transformed a breakthrough discovery in biology into a robust platform for a new class of medicines that modulate mRNA expression. Here we provide an overview of the trajectory of small-interfering RNA (siRNA) drug development, including the first approval in 2018 of a liver-targeted siRNA interference (RNAi) therapeutic in lipid nanoparticles and subsequent approvals of five more RNAi drugs, which used metabolically stable siRNAs combined with N-acetylgalactosamine ligands for conjugate-based liver delivery. We also consider the remaining challenges in the field, such as delivery to muscle, brain and other extrahepatic organs. Today's RNAi therapeutics exhibit high specificity, potency and durability, and are transitioning from applications in rare diseases to widespread, chronic conditions.
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Affiliation(s)
- Vasant Jadhav
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Akshay Vaishnaw
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Kevin Fitzgerald
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Martin A Maier
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
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2
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Zhang HJ, Ociepa M, Nassir M, Zheng B, Lewicki SA, Salmaso V, Baburi H, Nagel J, Mirza S, Bueschbell B, Al-Hroub H, Perzanowska O, Lin Z, Schmidt MA, Eastgate MD, Jacobson KA, Müller CE, Kowalska J, Jemielity J, Baran PS. Stereocontrolled access to thioisosteres of nucleoside di- and triphosphates. Nat Chem 2024; 16:249-258. [PMID: 37857844 DOI: 10.1038/s41557-023-01347-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Nucleoside diphosphates and triphosphates impact nearly every aspect of biochemistry; however, the use of such compounds as tools or medicinal leads for nucleotide-dependent enzymes and receptors is hampered by their rapid in vivo metabolism. Although a successful strategy to address the instability of the monophosphate moiety in oligonucleotide therapeutics has been accomplished by their isosteric replacement with phosphorothioates, no practical methods exist to rapidly and controllably access stereopure di- and triphosphate thioisosteres of both natural and unnatural nucleosides. Here we show how a modular, reagent-based platform can enable the stereocontrolled and scalable synthesis of a library of such molecules. This operationally simple approach provides access to pure stereoisomers of nucleoside α-thiodiphosphates and α-thiotriphosphates, as well as symmetrical or unsymmetrical dinucleoside thiodiphosphates and thiotriphosphates (including RNA cap reagents). We demonstrate that ligand-receptor interactions can be dramatically influenced by P-stereochemistry, showing that such thioisosteric replacements can have profound effects on the potency and stability of lead candidates.
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Affiliation(s)
- Hai-Jun Zhang
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Michał Ociepa
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Molhm Nassir
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Bin Zheng
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Sarah A Lewicki
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helay Baburi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Jessica Nagel
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Salahuddin Mirza
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Beatriz Bueschbell
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Haneen Al-Hroub
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Olga Perzanowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ziqin Lin
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Michael A Schmidt
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Martin D Eastgate
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany.
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| | - Phil S Baran
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
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3
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Skelly JD, Chen F, Chang SY, Ujjwal RR, Ghimire A, Ayers DC, Song J. Modulating On-Demand Release of Vancomycin from Implant Coatings via Chemical Modification of a Micrococcal Nuclease-Sensitive Oligonucleotide Linker. ACS APPLIED MATERIALS & INTERFACES 2023; 15:37174-37183. [PMID: 37525332 PMCID: PMC10421633 DOI: 10.1021/acsami.3c05881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Periprosthetic infections are one of the most serious complications in orthopedic surgeries, and those caused by Staphylococcus aureus (S. aureus) are particularly hard to treat due to their tendency to form biofilms on implants and their notorious ability to invade the surrounding bones. The existing prophylactic local antibiotic deliveries involve excessive drug loading doses that could risk the development of drug resistance strains. Utilizing an oligonucleotide linker sensitive to micrococcal nuclease (MN) cleavage, we previously developed an implant coating capable of releasing covalently tethered vancomycin, triggered by S. aureus-secreted MN, to prevent periprosthetic infections in the mouse intramedullary (IM) canal. To further engineer this exciting platform to meet broader clinical needs, here, we chemically modified the oligonucleotide linker by a combination of 2'-O-methylation and phosphorothioate modification to achieve additional modulation of its stability/sensitivity to MN and the kinetics of MN-triggered on-demand release. We found that when all phosphodiester bonds within the oligonucleotide linker 5'-carboxy-mCmGTTmCmG-3-acrydite, except for the one between TT, were replaced by phosphorothioate, the oligonucleotide (6PS) stability significantly increased and enabled the most sustained release of tethered vancomycin from the coating. By contrast, when only the peripheral phosphodiester bonds at the 5'- and 3'-ends were replaced by phosphorothioate, the resulting oligonucleotide (2PS) linker was cleaved by MN more rapidly than that without any PS modifications (0PS). Using a rat femoral canal periprosthetic infection model where 1000 CFU S. aureus was inoculated at the time of IM pin insertion, we showed that the prophylactic implant coating containing either 0PS- or 2PS-modified oligonucleotide linker effectively eradicated the bacteria by enabling the rapid on-demand release of vancomycin. No bacteria were detected from the explanted pins, and no signs of cortical bone changes were detected in these treatment groups throughout the 3 month follow-ups. With an antibiotic tethering dose significantly lower than conventional antibiotic-bearing bone cements, these coatings also exhibited excellent biocompatibility. These chemically modified oligonucleotides could help tailor prophylactic anti-infective coating strategies to meet a range of clinical challenges where the risks for S. aureus prosthetic infections range from transient to long-lasting.
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Affiliation(s)
- Jordan D Skelly
- Department of Orthopedics and Physical Rehabilitation, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
| | - Feiyang Chen
- Department of Orthopedics and Physical Rehabilitation, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
| | - Shing-Yun Chang
- Department of Orthopedics and Physical Rehabilitation, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
| | - Rewati R Ujjwal
- Department of Orthopedics and Physical Rehabilitation, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
| | - Ananta Ghimire
- Department of Orthopedics and Physical Rehabilitation, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
| | - David C Ayers
- Department of Orthopedics and Physical Rehabilitation, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
| | - Jie Song
- Department of Orthopedics and Physical Rehabilitation, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
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4
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Klootwyk B, Ryan AE, Lopez A, McCloskey MJR, Janosko CP, Deiters A, Floreancig PE. Peroxide-Mediated Release of Organophosphates from Boron-Containing Phosphotriesters: A New Class of Organophosphate Prodrugs. Org Lett 2023; 25:5530-5535. [PMID: 37463277 PMCID: PMC10391626 DOI: 10.1021/acs.orglett.3c02036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Indexed: 07/20/2023]
Abstract
Phosphate mono- and diesters can be liberated efficiently from boryl allyloxy (BAO) and related phosphotriesters by H2O2. This protocol was applied to the release of a phosphorylated serine derivative and the nucleotide analogue AZT monophosphate. Nucleotide release in the presence of ATP and a kinase provides a diphosphate, demonstrating that this method can be applied to biological processes.
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Affiliation(s)
- Brittany
M. Klootwyk
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Amy E. Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Arbil Lopez
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mitchell J. R. McCloskey
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chasity P. Janosko
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Paul E. Floreancig
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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5
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Nassir M, Ociepa M, Zhang HJ, Grant LN, Simmons BJ, Oderinde MS, Kawamata Y, Cauley AN, Schmidt MA, Eastgate MD, Baran PS. Stereocontrolled Radical Thiophosphorylation. J Am Chem Soc 2023. [PMID: 37399078 DOI: 10.1021/jacs.3c05655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
The first practical, fully stereoselective P(V)-radical hydrophosphorylation is presented herein by using simple, limonene-derived reagent systems. A set of reagents have been developed that upon radical initiation react smoothly with olefins and other radical acceptors to generate P-chiral products, which can be further diversified (with conventional 2e- chemistry) to a range of underexplored bioisosteric building blocks. The reactions have a wide scope with excellent chemoselectivity, and the unexpected stereochemical outcome has been supported computationally and experimentally. Initial ADME studies are suggestive of the promising properties of this rarely explored chemical space.
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Affiliation(s)
- Molhm Nassir
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michał Ociepa
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hai-Jun Zhang
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lauren N Grant
- Small Molecule Drug Discovery, Bristol Myers Squibb, Princeton, New Jersey 08543, United States
| | - Bryan J Simmons
- Small Molecule Drug Discovery, Bristol Myers Squibb, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Martins S Oderinde
- Small Molecule Drug Discovery, Bristol Myers Squibb, Princeton, New Jersey 08543, United States
| | - Yu Kawamata
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anthony N Cauley
- Small Molecule Drug Discovery, Bristol Myers Squibb, Princeton, New Jersey 08543, United States
| | - Michael A Schmidt
- Chemical Process Development, Bristol Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Martin D Eastgate
- Chemical Process Development, Bristol Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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6
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Kim H, Jeong IH, Choi YK, Lee YK, Moon E, Huh YH, Im W, Jin JO, Kwak M, Lee PCW. Suppression of Lung Cancer Malignancy by Micellized siRNA through Cell Cycle Arrest. Adv Healthc Mater 2023; 12:e2202358. [PMID: 36644959 DOI: 10.1002/adhm.202202358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/03/2023] [Indexed: 01/17/2023]
Abstract
UBA6-specific E2 conjugation enzyme 1 (USE1) is frequently overexpressed in lung cancer patients. Moreover, the critical role of USE1 in the progression of human lung cancer is also indicated. As the next step, the authors aim to develop USE1-targeted therapeutic agents based on RNA interference (RNAi). In this study, a lipid-modified DNA carrier, namely U4T, which consists of four consecutive dodec-1-ynyluracil (U) nucleobases to increase the cell permeability of siRNA targeting of USE1 is introduced. The U4Ts aggregate to form micelles, and the USE1-silencing siRNA-incorporated soft spherical nucleic acid aggregate (siSNA) can be created simply through base-pairing with siRNA. Treatment with siSNA is effective in suppressing tumor growth in vivo as well as cell proliferation, migration, and invasion of lung cancer cells. Furthermore, siSNA inhibited tumor cell growth by inducing cell cycle arrest in the G1 phase and apoptosis. Thus, the anti-tumor efficacy of siSNA in lung cancer cell lines and that siSNA possesses effective cell-penetrating ability without using cationic transfection moieties are confirmed. Collectively, these results suggest that siSNA can be applied to the clinical application of RNAi-based therapeutics for lung cancer treatment.
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Affiliation(s)
- Haejoo Kim
- Department of Chemistry and Industry 4.0 Convergence Bionics Engineering, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 48513, Republic of Korea.,Smart Gym-based Translational Research Center for Active Senior's Healthcare, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 48513, Republic of Korea
| | - In-Ho Jeong
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.,Lung Cancer Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Yeol Kyo Choi
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Yeon Kyung Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Eunyoung Moon
- Center for Electron Microscopy Research, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Yang Hoon Huh
- Center for Electron Microscopy Research, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Jun-O Jin
- Department of Microbiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Minseok Kwak
- Department of Chemistry and Industry 4.0 Convergence Bionics Engineering, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 48513, Republic of Korea.,Smart Gym-based Translational Research Center for Active Senior's Healthcare, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 48513, Republic of Korea
| | - Peter Chang-Whan Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.,Lung Cancer Research Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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7
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White LK, Hesselberth JR. Modification mapping by nanopore sequencing. Front Genet 2022; 13:1037134. [PMID: 36386798 PMCID: PMC9650216 DOI: 10.3389/fgene.2022.1037134] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 06/26/2024] Open
Abstract
Next generation sequencing (NGS) has provided biologists with an unprecedented view into biological processes and their regulation over the past 2 decades, fueling a wave of development of high throughput methods based on short read DNA and RNA sequencing. For nucleic acid modifications, NGS has been coupled with immunoprecipitation, chemical treatment, enzymatic treatment, and/or the use of reverse transcriptase enzymes with fortuitous activities to enrich for and to identify covalent modifications of RNA and DNA. However, the majority of nucleic acid modifications lack commercial monoclonal antibodies, and mapping techniques that rely on chemical or enzymatic treatments to manipulate modification signatures add additional technical complexities to library preparation. Moreover, such approaches tend to be specific to a single class of RNA or DNA modification, and generate only indirect readouts of modification status. Third generation sequencing technologies such as the commercially available "long read" platforms from Pacific Biosciences and Oxford Nanopore Technologies are an attractive alternative for high throughput detection of nucleic acid modifications. While the former can indirectly sense modified nucleotides through changes in the kinetics of reverse transcription reactions, nanopore sequencing can in principle directly detect any nucleic acid modification that produces a signal distortion as the nucleic acid passes through a nanopore sensor embedded within a charged membrane. To date, more than a dozen endogenous DNA and RNA modifications have been interrogated by nanopore sequencing, as well as a number of synthetic nucleic acid modifications used in metabolic labeling, structure probing, and other emerging applications. This review is intended to introduce the reader to nanopore sequencing and key principles underlying its use in direct detection of nucleic acid modifications in unamplified DNA or RNA samples, and outline current approaches for detecting and quantifying nucleic acid modifications by nanopore sequencing. As this technology matures, we anticipate advances in both sequencing chemistry and analysis methods will lead to rapid improvements in the identification and quantification of these epigenetic marks.
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Affiliation(s)
| | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
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8
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Bhat MY, Ahmed S, Ahmed QN. Tf 2O- and Cu(OTf) 2-Assisted Acylamination Reaction of Unactivated Alcohols with Nitriles: A One-Pot P(IV) Activation, Stereoretention in Cycloalkanols and Deprotection Approach. J Org Chem 2022; 87:11608-11624. [PMID: 35973064 DOI: 10.1021/acs.joc.2c01251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Described herein is a simple, novel, one-pot acylamination reaction of unactivated alcohols. This reaction employs the combination of PCl3 and triflic anhydride (Tf2O) or copper triflate Cu(OTf)2, which serves as a source of P(IV)-activated complex for nitriles to react under the Ritter-type mechanism. The synthetic utility of Tf2O-promoted reactions was demonstrated by its effectiveness to generate different acylaminated products. By employing Cu(OTf)2, this method represents a rare example of α-selective acylamination reaction. With chiral cycloalkanols, using the Cu(OTf)2-promoted procedure, acylaminated products are formed with complete retention of configuration. The synthetic utility of the copper-assisted reaction in acetonitrile was readily demonstrated as a mild deprotection strategy.
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Affiliation(s)
- Mohammad Yaqoob Bhat
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sajjad Ahmed
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Qazi Naveed Ahmed
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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9
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Dinesen A, Winther A, Wall A, Märcher A, Palmfeldt J, Chudasama V, Wengel J, Gothelf KV, Baker JR, Howard KA. Albumin Biomolecular Drug Designs Stabilized through Improved Thiol Conjugation and a Modular Locked Nucleic Acid Functionalized Assembly. Bioconjug Chem 2022; 33:333-342. [PMID: 35129956 DOI: 10.1021/acs.bioconjchem.1c00561] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Albumin-nucleic acid biomolecular drug designs offer modular multifunctionalization and extended circulatory half-life. However, stability issues associated with conventional DNA nucleotides and maleimide bioconjugation chemistries limit the clinical potential. This work aims to improve the stability of this thiol conjugation and nucleic acid assembly by employing a fast-hydrolyzing monobromomaleimide (MBM) linker and nuclease-resistant nucleotide analogues, respectively. The biomolecular constructs were formed by site-selective conjugation of a 12-mer oligonucleotide to cysteine 34 (Cys34) of recombinant human albumin (rHA), followed by annealing of functionalized complementary strands bearing either a fluorophore or the cytotoxic drug monomethyl auristatin E (MMAE). Formation of conjugates and assemblies was confirmed by gel shift analysis and mass spectrometry, followed by investigation of serum stability, neonatal Fc receptor (FcRn)-mediated cellular recycling, and cancer cell killing. The MBM linker afforded rapid conjugation to rHA and remained stable during hydrolysis. The albumin-nucleic acid biomolecular assembly composed of stabilized oligonucleotides exhibited high serum stability and retained FcRn engagement mediating FcRn-mediated cellular recycling. The MMAE-containing assembly exhibited cytotoxicity in the human MIA PaCa-2 pancreatic cancer cell line with an IC50 of 342 nM, triggered by drug release from breakdown of an acid-labile linker. In summary, this work presents rHA-nucleic acid module-based assemblies with improved stability and retained module functionality that further promotes the drug delivery potential of this biomolecular platform.
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Affiliation(s)
- Anders Dinesen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Alexander Winther
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Archie Wall
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Anders Märcher
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University, DK-8200 Aarhus N, Denmark
| | - Vijay Chudasama
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - James R Baker
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
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10
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Tee HS, Wood SA, Bouma-Gregson K, Lear G, Handley KM. Genome Streamlining, Plasticity, and Metabolic Versatility Distinguish Co-occurring Toxic and Nontoxic Cyanobacterial Strains of Microcoleus. mBio 2021; 12:e0223521. [PMID: 34700377 PMCID: PMC8546630 DOI: 10.1128/mbio.02235-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 01/21/2023] Open
Abstract
Harmful cyanobacterial bloom occurrences have increased worldwide due to climate change and eutrophication, causing nuisance and animal deaths. Species from the benthic cyanobacterial genus Microcoleus are ubiquitous and form thick mats in freshwater systems, such as rivers, that are sometimes toxic due to the production of potent neurotoxins (anatoxins). Anatoxin-producing (toxic) strains typically coexist with non-anatoxin-producing (nontoxic) strains in mats, although the reason for this is unclear. To determine the genetic mechanisms differentiating toxic and nontoxic Microcoleus, we sequenced and assembled genomes from 11 cultures and compared these to another 31 Microcoleus genomes. Average nucleotide identities (ANI) indicate that toxic and nontoxic strains are distinct species (ANI, <95%), and only 6% of genes are shared across all 42 genomes, suggesting a high level of genetic divergence among Microcoleus strains. Comparative genomics showed substantial genome streamlining in toxic strains and a potential dependency on external sources for thiamine and sucrose. Toxic and nontoxic strains are further differentiated by an additional set of putative nitrate transporter (nitrogen uptake) and cyanophycin (carbon and nitrogen storage) genes, respectively. These genes likely confer distinct competitive advantages based on nutrient availability and suggest nontoxic strains are more robust to nutrient fluctuations. Nontoxic strains also possess twice as many transposable elements, potentially facilitating greater genetic adaptation to environmental changes. Our results offer insights into the divergent evolution of Microcoleus strains and the potential for cooperative and competitive interactions that contribute to the co-occurrence of toxic and nontoxic species within mats. IMPORTANCE Microcoleus autumnalis, and closely related Microcoleus species, compose a geographically widespread group of freshwater benthic cyanobacteria. Canine deaths due to anatoxin-a poisoning, following exposure to toxic proliferations, have been reported globally. While Microcoleus proliferations are on the rise, the mechanisms underpinning competition between, or coexistence of, toxic and nontoxic strains are unknown. This study identifies substantial genetic differences between anatoxin-producing and non-anatoxin-producing strains, pointing to reduced metabolic flexibility in toxic strains, and potential dependence on cohabiting nontoxic strains. Results provide insights into the metabolic and evolutionary differences between toxic and nontoxic Microcoleus, which may assist in predicting and managing aquatic proliferations.
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Affiliation(s)
- Hwee Sze Tee
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Keith Bouma-Gregson
- U.S. Geological Survey, California Water Science Center, Sacramento, California, USA
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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11
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Zheng B, Hang C, Zhu J, Purdum GE, Sezen-Edmonds M, Treitler DS, Yu M, Yuan C, Zhu Y, Freitag A, Guo S, Zhu G, Hritzko B, Paulson J, Shackman JG, He BL, Fu W, Tai HC, Ayers S, Park H, Eastgate MD, Cohen B, Rogers A, Wang Q, Schmidt MA. P(III) vs P(V): A P(V) Reagent for Thiophosphoramidate Linkages and Application to an Asymmetric Synthesis of a Cyclic Dinucleotide STING Agonist. J Org Chem 2021; 87:1934-1940. [PMID: 34232659 DOI: 10.1021/acs.joc.1c01055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A highly stereoselective synthesis of a cyclic dinucleotide (CDN) STING agonist containing two chiral thiophosphoramidate linkages is described. These rare yet key functional groups were, for the first time, installed efficiently and with high diastereoselectivity using a specially designed P(V) reagent. By utilizing this strategy, the CDN was prepared in greater than 16-fold higher yield than the prior P(III) approach, with fewer hazardous reagents and chromatographic purifications.
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Affiliation(s)
- Bin Zheng
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Chao Hang
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Jason Zhu
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Geoffrey E Purdum
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Melda Sezen-Edmonds
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Daniel S Treitler
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Miao Yu
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Changxia Yuan
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ye Zhu
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Adam Freitag
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Siwei Guo
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Guanghui Zhu
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ben Hritzko
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - James Paulson
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Jonathan G Shackman
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Brian L He
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Weiqing Fu
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Hua Chia Tai
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Sloan Ayers
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Hyunsoo Park
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin D Eastgate
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ben Cohen
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Amanda Rogers
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Qinggang Wang
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael A Schmidt
- Bristol Myers Squibb, Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
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12
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Scharner J, Aznarez I. Clinical Applications of Single-Stranded Oligonucleotides: Current Landscape of Approved and In-Development Therapeutics. Mol Ther 2020; 29:540-554. [PMID: 33359792 PMCID: PMC7854307 DOI: 10.1016/j.ymthe.2020.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/19/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded oligonucleotides have been explored as a therapeutic modality for more than 20 years. Only during the last 5 years have single-stranded oligonucleotides become a modality of choice in the fields of precision medicine and targeted therapeutics. Recently, there have been a number of development efforts involving this modality that have led to treatments for genetic diseases that were once untreatable. This review highlights key applications of single-stranded oligonucleotides that function in a sequence-dependent manner when applied to modulate precursor (pre-)mRNA splicing, gene expression, and immune pathways. These applications have been used to address diseases that range from neurological to muscular to metabolic, as well as to develop vaccines. The wide range of applications denotes the versatility of single-stranded oligonucleotides as a robust therapeutic platform. The focus of this review is centered on approved single-stranded oligonucleotide therapies and the evolution of oligonucleotide therapeutics into novel applications currently in clinical development.
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13
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Salehi Marzijarani N, Lam YH, Wang X, Klapars A, Qi J, Song Z, Sherry BD, Liu Z, Ji Y. New Mechanism for Cinchona Alkaloid-Catalysis Allows for an Efficient Thiophosphorylation Reaction. J Am Chem Soc 2020; 142:20021-20029. [PMID: 33180475 DOI: 10.1021/jacs.0c09192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An efficient synthesis of nucleoside 5'-monothiophosphates under mild reaction conditions using commercially available thiophosphoryl chloride was achieved with a cinchona alkaloid catalyst. A detailed mechanistic study of the reaction was undertaken, employing a combination of reaction kinetics, NMR spectroscopy, and computational modeling, to better understand the observed reactivity. Taken collectively, the results support an unprecedented mechanism for this class of organocatalyst.
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Affiliation(s)
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xiao Wang
- Department of Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Artis Klapars
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ji Qi
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States.,Department of Process Research and Development, MSD R&D (China) Co., Ltd., Building 21 Rongda Road, Wangjing R&D Base, Zhongguancun Electronic Zone West Zone, Beijing 100012, China
| | - Zhiyan Song
- Department of Synthetic Chemistry, Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, China
| | - Benjamin D Sherry
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhijian Liu
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yining Ji
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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14
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Highly efficient library preparation for Ion Torrent sequencing using Y-adapters. Biotechniques 2019; 67:229-237. [PMID: 31621374 DOI: 10.2144/btn-2019-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Library preparation is a crucial step in next-generation sequencing workflows. Key determinants of successful library preparation are the available amount of input DNA and the efficiency of the conversion of this DNA into functional library molecules. While the standard blunt-end ligation protocol for Ion Torrent libraries has a theoretical maximum efficiency of 25%, Y-adapters enable highly efficient library preparation by (i) sticky-end ligation and (ii) rendering both DNA strands functional for sequencing, hence resulting in a theoretical efficiency of up to 100%. Moreover, the generation of adapter dimers is reduced. Therefore, we designed, optimized and validated Y-adapters compatible with Ion Torrent sequencing. These facilitate higher library yields combined with overall high sequencing performance regarding the key characteristics read-length, base quality, and library complexity.
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15
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Phosphorothioated DNA Is Shielded from Oxidative Damage. Appl Environ Microbiol 2019; 85:AEM.00104-19. [PMID: 30737351 DOI: 10.1128/aem.00104-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 02/05/2019] [Indexed: 11/20/2022] Open
Abstract
DNA is the carrier of genetic information. DNA modifications play a central role in essential physiological processes. Phosphorothioation (PT) modification involves the replacement of an oxygen atom on the DNA backbone with a sulfur atom. PT modification can cause genomic instability in Salmonella enterica under hypochlorous acid stress. This modification restores hydrogen peroxide (H2O2) resistance in the catalase-deficient Escherichia coli Hpx- strain. Here, we report biochemical characterization results for a purified PT modification protein complex (DndCDE) from S. enterica We observed multiplex oligomeric states of DndCDE by using native PAGE. This protein complex bound avidly to PT-modified DNA. DndCDE with an intact iron-sulfur cluster (DndCDE-FeS) possessed H2O2 decomposition activity, with a V max of 10.58 ± 0.90 mM min-1 and a half-saturation constant, K 0.5S, of 31.03 mM. The Hill coefficient was 2.419 ± 0.59 for this activity. The protein's activity toward H2O2 was observed to be dependent on the intact DndCDE and on the formation of an iron-sulfur (Fe-S) cluster on the DndC subunit. In addition to cysteine residues that mediate the formation of this Fe-S cluster, other cysteine residues play a catalytic role. Finally, catalase activity was also detected in DndCDE from Pseudomonas fluorescens Pf0-1. The data and conclusions presented suggest that DndCDE-FeS is a short-lived catalase. Our experiments also indicate that the complex binds to PT sites, shielding PT DNA from H2O2 damage. This catalase shield might be able to extend from PT sites to the entire bacterial genome.IMPORTANCE DNA phosphorothioation has been reported in many bacteria. These PT-hosting bacteria live in very different environments, such as the human body, soil, or hot springs. The physiological function of DNA PT modification is still elusive. A remarkable property of PT modification is that purified genomic PT DNA is susceptible to oxidative cleavage. Among the oxidants, hypochlorous acid and H2O2 are of physiological relevance for human pathogens since they are generated during the human inflammation response to bacterial infection. However, expression of PT genes in the catalase-deficient E. coli Hpx- strain restores H2O2 resistance. Here, we seek to solve this obvious paradox. We demonstrate that DndCDE-FeS is a short-lived catalase that binds tightly to PT DNA. It is thus possible that by docking to PT sites the catalase activity protects the bacterial genome against H2O2 damage.
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16
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Ash J, Huang H, Kang JY. Metal- and chloride reagent-free synthesis of mixed thiophosphates. Org Biomol Chem 2019; 17:3812-3818. [DOI: 10.1039/c9ob00370c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Systematic synthesis of mixed thiophosphates from thiophosphates was developed.
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Affiliation(s)
- Jeffrey Ash
- Department of Chemistry and Biochemistry
- University of Nevada Las Vegas
- Las Vegas
- USA
| | - Hai Huang
- Department of Chemistry and Biochemistry
- University of Nevada Las Vegas
- Las Vegas
- USA
- Department of Applied Chemistry
| | - Jun Yong Kang
- Department of Chemistry and Biochemistry
- University of Nevada Las Vegas
- Las Vegas
- USA
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17
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Knouse KW, deGruyter JN, Schmidt MA, Zheng B, Vantourout JC, Kingston C, Mercer SE, Mcdonald IM, Olson RE, Zhu Y, Hang C, Zhu J, Yuan C, Wang Q, Park P, Eastgate MD, Baran PS. Unlocking P(V): Reagents for chiral phosphorothioate synthesis. Science 2018; 361:1234-1238. [PMID: 30072577 DOI: 10.1126/science.aau3369] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/12/2018] [Indexed: 12/21/2022]
Abstract
Phosphorothioate nucleotides have emerged as powerful pharmacological substitutes of their native phosphodiester analogs with important translational applications in antisense oligonucleotide (ASO) therapeutics and cyclic dinucleotide (CDN) synthesis. Stereocontrolled installation of this chiral motif has long been hampered by the systemic use of phosphorus(III) [P(III)]-based reagent systems as the sole practical means of oligonucleotide assembly. A fundamentally different approach is described herein: the invention of a P(V)-based reagent platform for programmable, traceless, diastereoselective phosphorus-sulfur incorporation. The power of this reagent system is demonstrated through the robust and stereocontrolled synthesis of various nucleotidic architectures, including ASOs and CDNs, via an efficient, inexpensive, and operationally simple protocol.
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Affiliation(s)
- Kyle W Knouse
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Justine N deGruyter
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael A Schmidt
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA.
| | - Bin Zheng
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Julien C Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Cian Kingston
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Stephen E Mercer
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ivar M Mcdonald
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Richard E Olson
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ye Zhu
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Chao Hang
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Jason Zhu
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Changxia Yuan
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Qinggang Wang
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Peter Park
- Department of Discovery Chemistry, Bristol-Myers Squibb, P.O. Box 5400, Princeton, NJ 08543, USA
| | - Martin D Eastgate
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA.
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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18
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Wang H, Li J, Jewett MC. Development of a Pseudomonas putida cell-free protein synthesis platform for rapid screening of gene regulatory elements. Synth Biol (Oxf) 2018; 3:ysy003. [PMID: 32995512 PMCID: PMC7445763 DOI: 10.1093/synbio/ysy003] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/12/2018] [Accepted: 04/19/2018] [Indexed: 12/21/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems enable the production of protein without the use of living, intact cells. An emerging area of interest is to use CFPS systems to characterize individual elements for genetic programs [e.g. promoters, ribosome binding sites (RBS)]. To enable this research area, robust CFPS systems must be developed from new chassis organisms. One such chassis is the Gram-negative Pseudomonas bacteria, which have been studied extensively for their diverse metabolism with promises in the field of bioremediation and biosynthesis. Here, we report the development and optimization of a high-yielding (198 ± 5.9 µg/ml) batch CFPS system from Pseudomonas putida ATCC 12633. Importantly, both circular and linear DNA templates can be applied directly to the CFPS reaction to program protein synthesis. Therefore, it is possible to prepare hundreds or even thousands of DNA templates without time-consuming cloning work. This opens the possibility to rapidly assess and validate genetic part performance in vitro before performing experiments in cells. To validate the P. putida CFPS system as a platform for prototyping genetic parts, we designed and constructed a library consisting of 15 different RBSs upstream of the reporter protein sfGFP, which covered an order of magnitude range in expression. Looking forward, our P. putida CFPS platform will not only expand the protein synthesis toolkit for synthetic biology but also serve as a platform in expediting the screening and prototyping of gene regulatory elements.
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Affiliation(s)
- He Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Master of Biotechnology Program, Northwestern University, Evanston, IL, 60208, USA
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Master of Biotechnology Program, Northwestern University, Evanston, IL, 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
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19
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Jin H, Roy U, Lee G, Schärer OD, Cho Y. Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease. J Biol Chem 2018; 293:6482-6496. [PMID: 29514982 PMCID: PMC5925792 DOI: 10.1074/jbc.ra118.002171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/05/2018] [Indexed: 01/04/2023] Open
Abstract
DNA interstrand cross-links (ICLs) block the progress of the replication and transcription machineries and can weaken chromosomal stability, resulting in various diseases. FANCD2-FANCI-associated nuclease (FAN1) is a conserved structure-specific nuclease that unhooks DNA ICLs independently of the Fanconi anemia pathway. Recent structural studies have proposed two different mechanistic features for ICL unhooking by human FAN1: a specific basic pocket that recognizes the terminal phosphate of a 1-nucleotide (nt) 5' flap or FAN1 dimerization. Herein, we show that despite lacking these features, Pseudomonas aeruginosa FAN1 (PaFAN1) cleaves substrates at ∼3-nt intervals and resolves ICLs. Crystal structures of PaFAN1 bound to various DNA substrates revealed that its conserved basic Arg/Lys patch comprising Arg-228 and Lys-260 recognizes phosphate groups near the 5' terminus of a DNA substrate with a 1-nt flap or a nick. Substitution of Lys-260 did not affect PaFAN1's initial endonuclease activity but significantly decreased its subsequent exonuclease activity and ICL unhooking. The Arg/Lys patch also interacted with phosphates at a 3-nt gap, and this interaction could drive movement of the scissile phosphates into the PaFAN1-active site. In human FAN1, the ICL-resolving activity was not affected by individual disruption of the Arg/Lys patch or basic pocket. However, simultaneous substitution of both FAN1 regions significantly reduced its ICL-resolving activity, suggesting that these two basic regions play a complementary role in ICL repair. On the basis of these findings, we propose a conserved role for two basic regions in FAN1 to guide ICL unhooking and to maintain genomic stability.
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Affiliation(s)
- Hyeonseok Jin
- From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Upasana Roy
- the Departments of Chemistry and Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794
| | - Gwangrog Lee
- the Department of Biology, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Orlando D Schärer
- the Departments of Chemistry and Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, South Korea, and
- the Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Yunje Cho
- From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea,
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20
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Ba S, Zhang H, Lee JY, Wu H, Ye R, Huang D, Li T. Investigation of human flap structure-specific endonuclease 1 (FEN1) activity on primer-template models and exploration of a substrate-based FEN1 inhibitor. Bioorg Med Chem 2016; 24:1988-92. [PMID: 27020684 DOI: 10.1016/j.bmc.2016.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
Abstract
Flap structure-specific endonuclease 1 (FEN1) is one of the enzymes that involve in Eukaryotic DNA replication and repair. Recent studies have proved that FEN1 is highly over-expressed in various types of cancer cells and is a drug target. However, a limited number of FEN1 inhibitors has been identified and approved. Herein, we investigate the catalytic activity of FEN1, and propose a substrate-based inhibitor. As a consequence, one of the phosphorothioate-modified substrates is proved to exhibit the most efficient inhibitory effect in our in vitro examinations. A novelly-designed substrate-based FEN1 inhibitor was accordingly constructed and determined a remarkable IC50 value.
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Affiliation(s)
- Sai Ba
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Hao Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jasmine Yiqin Lee
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Haixia Wu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Ruijuan Ye
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Dejian Huang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Tianhu Li
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
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21
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Wan WB, Migawa MT, Vasquez G, Murray HM, Nichols JG, Gaus H, Berdeja A, Lee S, Hart CE, Lima WF, Swayze EE, Seth PP. Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages. Nucleic Acids Res 2014; 42:13456-68. [PMID: 25398895 PMCID: PMC4267618 DOI: 10.1093/nar/gku1115] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 12/19/2022] Open
Abstract
Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity (Tm), nuclease stability, activity in vitro and in vivo, RNase H activation and cleavage patterns (both human and E. coli) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro, while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo, the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.
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Affiliation(s)
- W Brad Wan
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Michael T Migawa
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Guillermo Vasquez
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Heather M Murray
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Josh G Nichols
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Hans Gaus
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Andres Berdeja
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Sam Lee
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | | | - Walt F Lima
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
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22
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Joneja A, Huang X. Linear nicking endonuclease-mediated strand-displacement DNA amplification. Anal Biochem 2011; 414:58-69. [PMID: 21342654 DOI: 10.1016/j.ab.2011.02.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 02/17/2011] [Accepted: 02/17/2011] [Indexed: 11/30/2022]
Abstract
We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to 5000 nucleotides can be linearly amplified using a nicking endonuclease with 7-bp recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length is linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly.
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Affiliation(s)
- Aric Joneja
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
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Eckstein F. Phosphorothioatanaloga von Nucleotiden - Werkzeuge zur Untersuchung biochemischer Prozesse. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.19830950603] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mathew KM, Ravi S, Sontakke CV, Chander H. Synthesis of deoxyadenosine-5?-(35S)-thiomonophosphate [dAMP(35S)] of high specific activity - a key intermediate for the synthesis of Sp-deoxyadenosine-5?-(alpha;-35S)-thiotriphosphate [Sp-dATP (?-35S)]. J Labelled Comp Radiopharm 2002. [DOI: 10.1002/jlcr.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Products of Partial Digestion withHaeIII. Part 1. Characterization, Casework Experience and Confirmation of the Theory of Three-, Four- and Five-Banded RFLP Pattern Origins Using Partial Digestion. J Forensic Sci 1997. [DOI: 10.1520/jfs14220j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Banfalvi G, Sarkar N. Effect of mercury substitution of DNA on its susceptibility to cleavage by restriction endonucleases. DNA Cell Biol 1995; 14:445-50. [PMID: 7748494 DOI: 10.1089/dna.1995.14.445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Mercurated DNA was synthesized in vitro by substituting Hg-dCTP or Hg-dUMP for dCTP in one strand of M13mp8DNA in a DNA polymerase I reaction. Restriction enzymes, including Sma I, Pst I, Bam HI, Hind III, and Hinc II, were completely inactive when their recognition sites were fully substituted with Hg-dCMP, while Hg-dUMP containing DNA was hydroxlyzed to some extent. Under conditions favoring star activities, or when DNA was substituted with a low level of mercury-nucleotide, DNA was cleaved by restriction enzymes. Susceptibility to degrading and synthesizing enzymes and insensitivity to restriction endonucleases of fully mercurated DNA makes mercuration an attractive molecular "tag" for in vitro manipulation and selective isolation of Hg-DNA.
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Affiliation(s)
- G Banfalvi
- Department I, Semmelweis University Medical School, Budapest, Hungary
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Steczko J, Donoho GP, Clemens JC, Dixon JE, Axelrod B. Conserved histidine residues in soybean lipoxygenase: functional consequences of their replacement. Biochemistry 1992; 31:4053-7. [PMID: 1567851 DOI: 10.1021/bi00131a022] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Sequences of 13 lipoxygenases from various plant and mammalian species, thus far reported, display a motif of 38 amino acid residues which includes 5 conserved histidines and a 6th histidine about 160 residues downstream. These residues occur at positions 494, 499, 504, 522, 531, and 690 in soybean lipoxygenase isozyme L-1. Since the participation of iron in the lipoxygenase reaction has been established and existing evidence based on Mössbauer and EXAFS spectroscopy suggests that histidines may be involved in iron binding, the effect of the above residues has been examined in soybean lipoxygenase L-1. Six singly mutated lipoxygenases have been produced in which each of the His residues has been replaced with glutamine. Two additional mutants have been constructed wherein the codons for His-494 and His-504 have been replaced by serine codons. All of the mutant lipoxygenases, which were obtained by expression in Escherichia coli, have mobilities identical to that of the wild-type enzyme on denaturing gel electrophoresis and respond to lipoxygenase antibodies. The mutated proteins H499Q, H504Q, H504S, and H690Q are virtually inactive, while H522Q has about 1% of the wild-type activity. H494Q, H494S, and H531Q are about 37%, 8%, and 20% as active as the wild type, respectively. His-517 is conserved in the several lipoxygenase isozymes but not in the animal isozymes. The mutant H517Q has about 33% of the wild-type activity. The inactive mutants, H499Q, H504Q, H504S, and H690Q, become insoluble when heated for 3 min at 65 degrees C, as does H522Q. The other mutants and the wild-type are stable under these conditions.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J Steczko
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-1153
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Steczko J, Donoho GA, Dixon JE, Sugimoto T, Axelrod B. Effect of ethanol and low-temperature culture on expression of soybean lipoxygenase L-1 in Escherichia coli. Protein Expr Purif 1991; 2:221-7. [PMID: 1821792 DOI: 10.1016/1046-5928(91)90075-t] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have constructed a full-length cDNA that encodes soybean seed lipoxygenase L-1 and have expressed it in Escherichia coli. This gene was inserted into a pT7-7 expression vector, containing the T7 RNA polymerase promoter. E. coli, strain BL21 (DE3), which carries the T7 promoter in its genome, was transfected with the plasmid. Expression of this gene when the cells were cultured at 37 degrees C yielded polypeptide that was recognized by anti-L-1 antibody, but had very little lipoxygenase activity. Yields of active enzyme were markedly increased when cells were cultured at 15-20 degrees C. When ethanol, which has been reported to be an excellent elicitor of heat-shock proteins in E. coli, was also present at a level of 3% the yield was further increased by 40%. Under optimum conditions 22-30 mg of soluble active enzyme was obtained per liter of culture.
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Affiliation(s)
- J Steczko
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-1153
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Koziolkiewicz M, Uznanski B, Stec WJ. Phosphate-Modified Oligonucleotides. The Synthesis, Stereochemistry and ECO Ri Endonuclease Substrate Ability of Decanucleotides d[GGGAATTCCC] Bearing Altered Internucleotide Phosphate Function Between A and A1. ACTA ACUST UNITED AC 1989. [DOI: 10.1080/07328318908054167] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Relaxation of supercoiled phosphorothioate DNA by mammalian topoisomerases is inhibited in a base-specific manner. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89292-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Potter BV, Eckstein F. Cleavage of phosphorothioate-substituted DNA by restriction endonucleases. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)89884-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Eckstein F. Phosphorothioate Analogues of Nucleotides?Tools for the Investigation of Biochemical Processes. ACTA ACUST UNITED AC 1983. [DOI: 10.1002/anie.198304233] [Citation(s) in RCA: 162] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Bartlett PA, Eckstein F. Stereochemical course of polymerization catalyzed by avian myeloblastosis virus reverse transcriptase. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34212-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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