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Klabenkova KV, Zhdanova PV, Burakova EA, Bizyaev SN, Fokina AA, Stetsenko DA. A Convenient Oligonucleotide Conjugation via Tandem Staudinger Reaction and Amide Bond Formation at the Internucleotidic Phosphate Position. Int J Mol Sci 2024; 25:2007. [PMID: 38396686 PMCID: PMC10889076 DOI: 10.3390/ijms25042007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Staudinger reaction on the solid phase between an electronodeficit organic azide, such as sulfonyl azide, and the phosphite triester formed upon phosphoramidite coupling is a convenient method for the chemical modification of oligonucleotides at the internucleotidic phosphate position. In this work, 4-carboxybenzenesulfonyl azide, either with a free carboxy group or in the form of an activated ester such as pentafluorophenyl, 4-nitrophenyl, or pentafluorobenzyl, was used to introduce a carboxylic acid function to the terminal or internal internucleotidic phosphate of an oligonucleotide via the Staudinger reaction. A subsequent treatment with excess primary alkyl amine followed by the usual work-up, after prior activation with a suitable peptide coupling agent such as a uronium salt/1-hydroxybenzotriazole in the case of a free carboxyl, afforded amide-linked oligonucleotide conjugates in good yields including multiple conjugations of up to the exhaustive modification at each phosphate position for a weakly activated pentafluorobenzyl ester, whereas more strongly activated and, thus, more reactive aryl esters provided only single conjugations at the 5'-end. The conjugates synthesized include those with di- and polyamines that introduce a positively charged side chain to potentially assist the intracellular delivery of the oligonucleotide.
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Affiliation(s)
- Kristina V. Klabenkova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia;
| | - Ekaterina A. Burakova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Sergei N. Bizyaev
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Alesya A. Fokina
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Dmitry A. Stetsenko
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
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2
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Hari Y, Fuchi Y, Yamamoto K, Ito Y. Benzo-Fused 7-Oxabicyclo[2.2.1]heptane-2,3-diol Derivatives as Universal Linkers for Solid-Phase Oligonucleotide Synthesis. SYNTHESIS-STUTTGART 2023. [DOI: 10.1055/s-0042-1751405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
AbstractIn solid-phase oligonucleotide (ON) synthesis, especially for 3′-modified ONs, a universal linker attached to a solid support is widely used. In this study, benzo-fused 7-oxabicyclo[2.2.1]heptane-2,3-diol derivatives are designed, synthesized, and evaluated as universal linkers. The designed linkers show reactivity comparable to that of a conventional universal linker for releasing the desired ONs. Additionally, these materials exhibit a more robust structure under basic conditions, as generally used in ON synthesis, and hydrophobic properties relative to the conventional universal linker. Notably, when diphenyl-substituted (terphenyl) and phenanthrene-type (PT) linkers are used, cyclic phosphodiesters derived from linker units as byproducts, which are produced by release of ONs from the linker units, are detected in the HPLC chromatograms. The PT linker is applicable to various ON syntheses using controlled pore glass (CPG) and polystyrene (PS) resins. These results demonstrate that the PT linker can serve as an alternative to conventional universal linkers.
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3
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Borths CJ, Burr T, Figuccia A, Ford JG, Guan B, Jones MT, Klingeleers D, Lochner S, Rodriguez AA, Wetter C. Nitrosamine Risk Assessments in Oligonucleotides. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Tracey Burr
- Ionis Pharmaceuticals Inc., Carlsbad, California 92010, United States
| | - Aude Figuccia
- Novartis AG, Lichtstrasse 35, CH-4056 Basel, Switzerland
| | - J. Gair Ford
- AstraZeneca, Macclesfield SK10 2NA, United Kingdom
| | - Bing Guan
- Biogen, Cambridge, Massachusetts 02142, United States
| | - Michael T. Jones
- Pfizer, 875 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | | | | | | | - Christian Wetter
- F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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4
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Knouse KW, Flood DT, Vantourout JC, Schmidt MA, Mcdonald IM, Eastgate MD, Baran PS. Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies. ACS CENTRAL SCIENCE 2021; 7:1473-1485. [PMID: 34584948 PMCID: PMC8461637 DOI: 10.1021/acscentsci.1c00487] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 05/27/2023]
Abstract
Phosphate linkages govern life as we know it. Their unique properties provide the foundation for many natural systems from cell biology and biosynthesis to the backbone of nucleic acids. Phosphates are ideal natural moieties; existing as ionized species in a stable P(V)-oxidation state, they are endowed with high stability but exhibit enzymatically unlockable potential. Despite intense interest in phosphorus catalysis and condensation chemistry, organic chemistry has not fully embraced the potential of P(V) reagents. To be sure, within the world of chemical oligonucleotide synthesis, modern approaches utilize P(III) reagent systems to create phosphate linkages and their analogs. In this Outlook, we present recent studies from our laboratories suggesting that numerous exciting opportunities for P(V) chemistry exist at the nexus of organic synthesis and biochemistry. Applications to the synthesis of stereopure antisense oligonucleotides, cyclic dinucleotides, methylphosphonates, and phosphines are reviewed as well as chemoselective modification to peptides, proteins, and nucleic acids. Finally, an outlook into what may be possible in the future with P(V) chemistry is previewed, suggesting these examples represent just the tip of the iceberg.
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Affiliation(s)
- Kyle W. Knouse
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julien C. Vantourout
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael A. Schmidt
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ivar M. Mcdonald
- Small
Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Martin D. Eastgate
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Phil S. Baran
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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5
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Huang Y, Knouse KW, Qiu S, Hao W, Padial NM, Vantourout JC, Zheng B, Mercer SE, Lopez-Ogalla J, Narayan R, Olson RE, Blackmond DG, Eastgate MD, Schmidt MA, McDonald IM, Baran PS. A P(V) platform for oligonucleotide synthesis. Science 2021; 373:1265-1270. [PMID: 34516793 PMCID: PMC8579956 DOI: 10.1126/science.abi9727] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The promise of gene-based therapies is being realized at an accelerated pace, with more than 155 active clinical trials and multiple U.S. Food and Drug Administration approvals for therapeutic oligonucleotides, by far most of which contain modified phosphate linkages. These unnatural linkages have desirable biological and physical properties but are often accessed with difficulty using phosphoramidite chemistry. We report a flexible and efficient [P(V)]–based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can install not only stereodefined or racemic thiophosphates but any combination of (S, R or rac)–PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotide polymers. This platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable P(V) reagents.
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Affiliation(s)
- Yazhong Huang
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Kyle W. Knouse
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Elsie Biotechnologies, 4955 Directors Pl, San Diego, CA 92121
| | - Shenjie Qiu
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Wei Hao
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Natalia M. Padial
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Julien C. Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Bin Zheng
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Stephen E. Mercer
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Javier Lopez-Ogalla
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Rohan Narayan
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Richard E. Olson
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Donna G. Blackmond
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Martin D. Eastgate
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Michael A. Schmidt
- Chemical Process Development, Bristol Myers Squibb, One Squibb Dr., New Brunswick, NJ 08903
| | - Ivar M. McDonald
- Small Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney St., Cambridge, MA 02142
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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6
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Lu H, Cai J, Zhang K. Synthetic Approaches for Copolymers Containing Nucleic Acids and Analogues: Challenges and Opportunities. Polym Chem 2021; 12:2193-2204. [PMID: 34394751 PMCID: PMC8356553 DOI: 10.1039/d0py01707h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A deep integration of nucleic acids with other classes of materials have become the basis of many useful technologies. Among these biohybrids, nucleic acid-containing copolymers has seen rapid development in both chemistry and application. This review focuses on the various synthetic approaches to access nucleic acid-polymer biohybrids spanning post-polymerization conjugation, nucleic acids in polymerization, solid-phase synthesis, and nucleoside/nucleobase-functionalized polymers. We highlight the challenges associated with working with nucleic acids with each approach and the ingenuity of the solutions, with the hope of lowering the entry barrier and inpsiring further investigations in this exciting area.
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Affiliation(s)
- Hao Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jiansong Cai
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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7
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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8
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Guo X, Stolee JA, Fillon YA, Zou L. Trace-Level Determination of Acrylonitrile Generated in the Manufacturing Process of Oligonucleotides by Static Headspace Gas Chromatography with an Electron Impact(+) Mass Detector. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.0c00527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xun Guo
- Analytical Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
| | - Jessica A. Stolee
- Analytical Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
| | - Yannick A. Fillon
- Antisense Oligonucleotide Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
| | - Lanfang Zou
- Analytical Development, Biogen Inc., Cambridge, Massachusetts 02142, United States
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9
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Sutton JM, Guimaraes GJ, Annavarapu V, van Dongen WD, Bartlett MG. Current State of Oligonucleotide Characterization Using Liquid Chromatography-Mass Spectrometry: Insight into Critical Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1775-1782. [PMID: 32812756 DOI: 10.1021/jasms.0c00179] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As interests increase in oligonucleotide therapeutics, there has been a greater need for analytical techniques to properly analyze and quantitate these biomolecules. This article looks into some of the existing chromatographic approaches for oligonucleotide analysis, including anion exchange, hydrophilic interaction liquid chromatography, and ion pair chromatography. Some of the key advantages and challenges of these chromatographic techniques are discussed. Colloid formation in mobile phases of alkylamines and fluorinated alcohols, a recently discovered analytical challenge, is discussed. Mass spectrometry is the method of choice to directly obtain structural information about oligonucleotide therapeutics. Mass spectrometry sensitivity challenges are reviewed, including comparison to other oligonucleotide techniques, salt adduction, and the multiple charge state envelope. Ionization of oligonucleotides through the charge residue model, ion evaporation model, and chain ejection model are analyzed. Therapeutic oligonucleotides have to undergo approval from major regulatory agencies, and the impurities and degradation products must be well-characterized to be approved. Current accepted thresholds for oligonucleotide impurities are reported. Aspects of the impurities and degradation products from these types of molecules are discussed as well as optimal analytical strategies to determine oligonucleotide related substances. Finally, ideas are proposed on how the field of oligonucleotide therapeutics may improve to aid in future analysis.
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Affiliation(s)
- J Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | - Guilherme J Guimaraes
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | - Vidya Annavarapu
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | | | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
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10
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Catani M, De Luca C, Medeiros Garcia Alcântara J, Manfredini N, Perrone D, Marchesi E, Weldon R, Müller-Späth T, Cavazzini A, Morbidelli M, Sponchioni M. Oligonucleotides: Current Trends and Innovative Applications in the Synthesis, Characterization, and Purification. Biotechnol J 2020; 15:e1900226. [PMID: 32298041 DOI: 10.1002/biot.201900226] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Oligonucleotides (ONs) are gaining increasing importance as a promising novel class of biopharmaceuticals. Thanks to their fundamental role in gene regulation, they can be used to develop custom-made drugs (also called N-to-1) able to act on the gene expression at pre-translational level. With recent approvals of ON-based therapeutics by the Food and Drug Administration (FDA), a growing demand for high-quality chemically modified ONs is emerging and their market is expected to impressively prosper in the near future. To satisfy this growing market demand, a scalable and economically sustainable ON production is needed. In this paper, the state of the art of the whole ON production process is illustrated with the aim of highlighting the most promising routes toward the auspicated market-size production. In particular, the most recent advancements in both the upstream stage, mainly based on solid-phase synthesis and recombinant technology, and the downstream one, focusing on chromatographic techniques, are reviewed. Since ON production is projected to expand to the large scale, automatized multicolumn countercurrent technologies will reasonably be required soon to replace the current ones based on batch single-column operations. This consideration is supported by a recent cutting-edge application of continuous chromatography for the ON purification.
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Affiliation(s)
- Martina Catani
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Chiara De Luca
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - João Medeiros Garcia Alcântara
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Nicolò Manfredini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Daniela Perrone
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Elena Marchesi
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Richard Weldon
- ChromaCon AG, Technoparkstrasse 1, Zürich, 8005, Switzerland
| | | | - Alberto Cavazzini
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Massimo Morbidelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Mattia Sponchioni
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
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11
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Goyon A, Yehl P, Zhang K. Characterization of therapeutic oligonucleotides by liquid chromatography. J Pharm Biomed Anal 2020; 182:113105. [PMID: 32004766 DOI: 10.1016/j.jpba.2020.113105] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/21/2019] [Accepted: 01/08/2020] [Indexed: 12/27/2022]
Abstract
Marketed therapies in the pharmaceutical landscape are rapidly evolving and getting more diverse. Small molecule medicines have dominated in the past while antibodies have grown dramatically in recent years. However, the failure of traditional small and large molecules in accessing certain targets has led to increased R&D efforts to develop alternative modalities. Therapeutic oligonucleotides (ONs) can accurately be directed against their ribonucleic acid (RNA) target and represent a promising approach in previously untreated diseases. Established automated synthesis of ONs coupled with chemical improvements and the advance of new drug delivery technologies has recently brought ONs to a heightened level of interest. The first part of the present review describes the different classes of oligonucleotides, namely antisense oligonucleotide (ASO), small interfering RNA (siRNA), microRNA (miRNA), aptamer and immunostimulatory ON, with a focus on their delivery systems relevant for future analytical characterization. The second part reviews the typical impurities in therapeutic ON products. The third part discusses the use of historical methods anion exchange chromatography (AEX), ion-pair reversed phase liquid chromatography (IP-RP), mixed-mode chromatography (MMC) and recent analytical methodologies of hydrophilic interaction liquid chromatography (HILIC), two-dimensional liquid chromatography (2D-LC) mass spectrometry for the characterization of ASO and siRNA modalities. The effects of physicochemical properties of RPLC columns and ion-pair agents on ON separation are specifically addressed with possible future directions for method development provided. Finally, some innovative analytical developments for the analysis of siRNAs and their delivery materials to pave the way toward the use of multi-attribute methods in the near future are discussed.
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Affiliation(s)
- Alexandre Goyon
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Peter Yehl
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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12
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Kim TW, Papagiannis C, Capaldi D, McPherson AK, Mahdi F, Luu N, Rodriguez AA, Hoffmaster C, Serota D, Henry SP. Impurity Qualification Toxicology Study for a 2'-O-Methoxyethyl-Modified Antisense Inhibitor in Mice. Nucleic Acid Ther 2019; 30:14-21. [PMID: 31687889 DOI: 10.1089/nat.2019.0780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Safety assessment of drug impurities is a routine part of the drug development process. For oligonucleotide-based drugs, impurities can arise from impurities in starting materials, as by-products of the manufacturing process or from degradation, and are generally structurally similar to the parent oligonucleotide. To study the potential impact of impurities, a representative batch of a 2'-O-methoxyethyl (MOE) antisense oligonucleotide (ASO) was compared to batches of drug that were enriched with nine of the common impurities encountered with the chemical class. Mice were treated for 3 months with weekly subcutaneous injection of 10 or 30 mg/kg. The impurity content of the parent batch was 0.25%-2.5% of total drug substance. The enriched impurity mixtures contained from 3% to 10% of the various impurities. The expected common class effects were observed at the 30 mg/kg/week dose level in hematology, serum chemistry, and histopathology. However, there were no differences between the representative batch of material and those enriched with impurities. Based on these data, common oligonucleotide impurity studies do not appear to contribute to the overall toxicology profile.
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Affiliation(s)
- Tae-Won Kim
- Ionis Pharmaceuticals, Inc., Carlsbad, California
| | | | | | | | - Farah Mahdi
- Ionis Pharmaceuticals, Inc., Carlsbad, California
| | - Nhuy Luu
- Ionis Pharmaceuticals, Inc., Carlsbad, California
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13
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Roussis SG, Pearce M, Rentel C. Small alkyl amines as ion-pair reagents for the separation of positional isomers of impurities in phosphate diester oligonucleotides. J Chromatogr A 2019; 1594:105-111. [PMID: 30819437 DOI: 10.1016/j.chroma.2019.02.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
In an effort to improve separation of impurities in oligonucleotide drugs, alkyl amines of different length and carbon content were evaluated as reagents in ion pair-reversed phase (IP-RP) HPLC with mass spectrometric detection. A range of columns was tested in combination with different buffers, ion-pair modifiers and varying pH adjustments. For phosphorothioate oligonucleotides, larger amines, like tributyl and hexyl amine provided the best chromatography, as small amines tended to broaden peaks due to the separation of diastereoisomers. For phosphate diester oligonucleotides, the best separations were obtained using small alkyl amines, like propyl-, isopropyl- and diethylamine. Conditions optimized for oligonucleotide sequence and type of impurity enabled full separation of the individual components of composite impurities, such as n-1, N3-(2-cyanoethyl)thymine (CNET), deaminated and 3-(2-oxopropyl)imidazopyrimidinone (OPC) impurities. The addition of long-chain alkyl acids like hexanoic acid to the IP buffer resulted in further improvements in peak separation.
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Affiliation(s)
| | - Megan Pearce
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Claus Rentel
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, CA 92010, United States.
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14
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O'Shea J, Theile CS, Das R, Babu IR, Charisse K, Manoharan M, Maier MA, Zlatev I. An efficient deprotection method for 5′-[O,O-bis(pivaloyloxymethyl)]-(E)-vinylphosphonate containing oligonucleotides. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Two-dimensional liquid chromatography-mass spectrometry for the characterization of modified oligonucleotide impurities. Anal Biochem 2018; 556:45-52. [PMID: 29936097 DOI: 10.1016/j.ab.2018.06.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
A 2D-LC system coupled with a TOF mass spectrometer has been evaluated for its capabilities to provide enhanced characterization of oligonucleotide impurities. To address loop limitations in the total volume (40 μL) sampled across 1D peaks, a column trap was incorporated between the 1D and 2D columns. The main advantages of the column trap include reduction of the total number of sequential 2D runs required to fully sample broad 1D peaks, and most importantly, reduction of the error in quantitative determination of the components in broad 1D peaks by avoiding the numerical stitching of data from several 2D runs. Comprehensive RP x IP provided orthogonal separation despite its lower 1D resolution. In contrast, IP x IP did not provide orthogonal separation. RP x IP using the direct on-line extended heart-cutting system with the column trap showed additional benefits, in the elimination of off-line fractionation and sample handling errors and was successfully applied in a pH stability study of a crude oligonucleotide. SAX x IP successfully separated the isobaric "n+16" doublet of the "n + O" and "[n + S-O]" impurity species, a feat not currently possible by mass spectrometry alone or 1D-LC, demonstrating the importance of the added capabilities of the 2D-LC approach.
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16
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Roussis SG, Koch C, Capaldi D, Rentel C. Rapid Oligonucleotide Drug Impurity Determination by Direct Spectral Comparison of Ion Pair-Reversed Phase HPLC ESI MS Data. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1099-1106. [PMID: 29575209 DOI: 10.1002/rcm.8125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Quantitative Ion-Pair (IP)-HPLC MS methods are employed to determine the complex impurity profiles of oligonucleotide therapeutics. While impurities that co-elute with the main product are routinely monitored, the large number of early and late eluting impurities makes their individual measurements tedious and time-consuming. An improved method is needed for routine analyses. METHODS A Combined Ranking (CR) index is developed to provide a composite value for both qualitative and quantitative impurity changes. Positive and Negative Impurity Change (PIC/NIC) indices are developed to determine the degree and direction of change. Optimized experimental conditions are determined for the characterization of trace levels of impurities. Replicate analysis, blank subtraction, and signal processing approaches are used to enhance the S/N. Dot-product and Euclidean distance equations monitor spectral changes. RESULTS Spiking experiments with individual and complex impurity mixtures show the method can distinguish among samples differing in impurity content by 0.2% wt. The method has been applied to monitor changes in impurity profile among different batches of the same oligonucleotide and changes in the same batch over time (stability analysis). The method permits rapid determination of changes in the types and amounts (increases and decreases) of impurities present. CONCLUSIONS A novel approach for the rapid determination of changes in the impurity profile of oligonucleotide therapeutics has been developed. The straightforward data treatment and the speed and simplicity of the approach make the method easy to implement and use. Possible quality control applications include drug substance and drug product stability studies, and the assessment of batch-to-batch variability.
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Affiliation(s)
| | - Charlie Koch
- Ionis Pharmaceuticals, Carlsbad, California, 92010
| | | | - Claus Rentel
- Ionis Pharmaceuticals, Carlsbad, California, 92010
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17
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Capaldi D, Teasdale A, Henry S, Akhtar N, den Besten C, Gao-Sheridan S, Kretschmer M, Sharpe N, Andrews B, Burm B, Foy J. Impurities in Oligonucleotide Drug Substances and Drug Products. Nucleic Acid Ther 2017; 27:309-322. [PMID: 29125795 DOI: 10.1089/nat.2017.0691] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This white paper, which is the 10th in a series intended to address issues associated with the development of therapeutic oligonucleotides, examines the subject of product-related impurities. The authors consider chemistry and safety aspects and advance arguments in favor of platform approaches to impurity identification and qualification. Reporting, identification, and qualification thresholds suitable for product-related impurities of therapeutic oligonucleotides are proposed.
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Affiliation(s)
| | - Andy Teasdale
- 2 AstraZeneca UK Ltd. , Macclesfield, United Kingdom
| | - Scott Henry
- 1 Ionis Pharmaceuticals, Inc. , Carlsbad, California
| | - Nadim Akhtar
- 2 AstraZeneca UK Ltd. , Macclesfield, United Kingdom
| | | | | | | | - Neal Sharpe
- 5 Anavex Life Sciences Corp. , New York, New York
| | - Ben Andrews
- 6 GlaxoSmithKline , Stevenage, United Kingdom
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18
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Michaelides IN, Tago N, Viverge B, Carell T. Synthesis of RNA Containing 5-Hydroxymethyl-, 5-Formyl-, and 5-Carboxycytidine. Chemistry 2017; 23:15894-15898. [PMID: 28906048 DOI: 10.1002/chem.201704216] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Indexed: 12/17/2022]
Abstract
5-Hydroxymethyl-, 5-formyl-, and 5-carboxy-2'-deoxycytidine are new epigenetic bases (hmdC, fdC, cadC) that were recently discovered in the DNA of higher eukaryotes. The same bases (5-hydroxymethyl-, 5-formyl-, and 5-carboxycytidine; hmC, fC, and caC) have now also been detected in mammalian RNA with a high abundance in mRNA. While DNA phosphoramidites (PAs) that allow the synthesis of xdC-containing oligonucleotides for deeper biological studies are available, the corresponding silyl-protected RNA PAs for fC and caC have not yet been disclosed. Here, we report novel RNA PAs for hmC, fC, and caC that can be used in routine RNA synthesis. The new building blocks are compatible with the canonical PAs and also with themselves, which enables even the synthesis of RNA strands containing all three of these bases. The study will pave the way for detailed physical, biochemical, and biological studies to unravel the function of these non-canonical modifications in RNA.
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Affiliation(s)
- Iacovos N Michaelides
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.,Current address: AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0FZ, UK
| | - Nobuhiro Tago
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Bastien Viverge
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
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19
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El Zahar NM, Magdy N, El-Kosasy AM, Bartlett MG. Chromatographic approaches for the characterization and quality control of therapeutic oligonucleotide impurities. Biomed Chromatogr 2017; 32. [PMID: 28869310 DOI: 10.1002/bmc.4088] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/13/2017] [Accepted: 08/28/2017] [Indexed: 12/16/2022]
Abstract
Phosphorothioate (PS) oligonucleotides are a rapidly rising class of drugs with significant therapeutic applications. However, owing to their complex structure and multistep synthesis and purification processes, generation of low-level impurities and degradation products are common. Therefore, they require significant investment in quality control and impurity identification. This requires the development of advanced methods for analysis, characterization and quantitation. In addition, the presence of the PS linkage leads to the formation of chiral centers which can affect their biological properties and therapeutic efficiency. In this review, the different types of oligonucleotide impurities and degradation products, with an emphasis on their origin, mechanism of formation and methods to reduce, prevent or even eliminate their production, will be extensively discussed. This review will focus mainly on the application of chromatographic techniques to determine these impurities but will also discuss other approaches such as mass spectrometry, capillary electrophoresis and nuclear magnetic resonance spectroscopy. Finally, the chirality and formation of diastereomer mixtures of PS oligonucleotides will be covered as well as approaches used for their characterization and the application for the development of stereochemically-controlled PS oligonucleotides.
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Affiliation(s)
- N M El Zahar
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - N Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - A M El-Kosasy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, USA
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20
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Brooks JL, Olsen P, Chen L, Rodriguez AA. UnyLinker dimer impurity characterization and process improvement. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.01.101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Rodriguez AA, Cedillo I, McPherson AK. Conversion of adenine to 5-amino-4-pyrimidinylimidazole caused by acetyl capping during solid phase oligonucleotide synthesis. Bioorg Med Chem Lett 2016; 26:3468-71. [PMID: 27353533 DOI: 10.1016/j.bmcl.2016.06.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
The acetyl capping reaction used throughout solid phase oligonucleotide synthesis is meant to minimize n-1 deletionmer impurities by terminating sequences that fail to couple to a phosphoramidite. However, the reaction is also responsible for the formation of a number of impurities. One capping-related impurity has an additional mass of 98amu from the parent oligonucleotide. The n+98 amu impurity was found to result from modification of an adenine nucleobase. The structure of the impurity was determined by preparation of an oligonucleotide enriched in n+98 amu, enzymatic digestion to individual nucleosides, isolation of the pure nucleoside+98 amu species, crystallization, and X-ray crystallographic analysis. The n+98 amu impurity is an oligonucleotide in which one adenine residue has been converted to 5-amino-4-pyrimidinylimidazole. The mechanism of formation of the impurity was investigated, and a mechanism is proposed.
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Affiliation(s)
| | - Isaiah Cedillo
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, USA
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22
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Roussis SG. A Novel and Intuitive Method of Displaying and Interacting with Mass Difference Information: Application to Oligonucleotide Drug Impurities. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1150-1164. [PMID: 25836378 DOI: 10.1007/s13361-015-1115-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/26/2015] [Accepted: 02/23/2015] [Indexed: 06/04/2023]
Abstract
A new method is presented for determining relationships between components in complex analytical systems. The method uses the mass differences between peaks in high resolution electrospray ionization (ESI) mass spectra. It relates peaks that share common mass differences. The method is based on the fundamental assumption that peaks in the spectra having the same exact mass difference are related by the same chemical moiety/substructure. Moreover, the presence (or absence/loss) of the same chemical moiety from a series of molecules may reflect similarities in the mechanisms of formation of each molecule. The determined mass differences in the spectra are used to automatically differentiate the types of components in the samples. Contour plots and summary plots of the summed total ion signal as a function of the mass difference are generated, which form powerful tools for the rapid and automated determination of the components in the samples and for comparisons with other samples. For the first time, in this work a unique profile contour plot has been developed that permits the interactive interrogation of the mass range by mass difference data matrix to obtain valuable information about components that share a common mechanism of formation, and all possible mechanisms of formation linked to a selected precursor molecule. The method can be used as an additional and complementary method to the existing analytical methods to determine relationships between components in complex chemical systems.
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23
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Yamada T, Masaki Y, Okaniwa N, Kanamori T, Ohkubo A, Tsunoda H, Seio K, Sekine M. Synthesis and properties of oligonucleotides modified with 2'-O-(2-carboxyethyl)nucleotides and their carbamoyl derivatives. Org Biomol Chem 2015; 12:6457-64. [PMID: 25019462 DOI: 10.1039/c4ob01260g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
2'-O-Methyl oligoribonucleotides with four kinds of 2'-O-modified uridine derivatives were synthesised. Their duplex stability, hydration behavior and exonuclease resistance were studied by spectroscopic analyses and molecular dynamics simulations. Consequently, 2'-O-modification of the uridine residue with 2-carbamoylethyl or 2-(N-methylcarbamoyl)ethyl groups resulted in a significant improvement of the exonuclease resistance without the loss of duplex stability.
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Affiliation(s)
- Takeshi Yamada
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta-cho, Midoriku, Yokohama, Japan.
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24
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Leszczynska G, Pięta J, Wozniak K, Malkiewicz A. Site-selected incorporation of 5-carboxymethylaminomethyl(-2-thio)uridine into RNA sequences by phosphoramidite chemistry. Org Biomol Chem 2014; 12:1052-6. [PMID: 24407195 DOI: 10.1039/c3ob42302f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5-Carboxymethylaminomethyluridine (cmnm(5)U) and 5-carboxymethylaminomethyl-2-thiouridine (cmnm(5)s(2)U) are located at the wobble position in several cytosolic and mitochondrial tRNA sequences. In this paper, we report the first site-selected incorporation of cmnm(5)U and cmnm(5)s(2)U into RNA sequences by phosphoramidite chemistry on a CPG solid support. Trifluoroacetyl and 2-(trimethylsilyl)ethyl were selected for the protection of the amine and carboxyl functions, respectively.
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25
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Rydzak JW, White DE, Airiau CY, Sterbenz JT, York BD, Clancy DJ, Dai Q. Real-Time Process Analytical Technology Assurance for Flow Synthesis of Oligonucleotides. Org Process Res Dev 2014. [DOI: 10.1021/op500035j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- James W. Rydzak
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - David E. White
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Christian Y. Airiau
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Jeffrey T. Sterbenz
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Brian D. York
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Donald J. Clancy
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Qunying Dai
- Product Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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26
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Rodriguez AA, Cedillo I, Mowery BP, Gaus HJ, Krishnamoorthy SS, McPherson AK. Formation of the N(2)-acetyl-2,6-diaminopurine oligonucleotide impurity caused by acetyl capping. Bioorg Med Chem Lett 2014; 24:3243-6. [PMID: 24980055 DOI: 10.1016/j.bmcl.2014.06.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 11/25/2022]
Abstract
The acetyl 'capping' reaction routinely employed during phosphorothioate oligonucleotide synthesis has been implicated in the formation of an impurity species with a mass 41 amu greater than the expected oligonucleotide molecule. The impurity has been found to arise by conversion of a protected guanine nucleobase to N(2)-acetyl-2,6-diaminopurine. A two-part mechanism is proposed consisting of transamidation of the protecting group on guanine and substitution of guanine's O(6) atom.
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Affiliation(s)
- Andrew A Rodriguez
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States.
| | - Isaiah Cedillo
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Brendan P Mowery
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | - Hans J Gaus
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
| | | | - Andrew K McPherson
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, United States
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27
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Leszczynska G, Leonczak P, Wozniak K, Malkiewicz A. Chemical synthesis of the 5-taurinomethyl(-2-thio)uridine modified anticodon arm of the human mitochondrial tRNA(Leu(UUR)) and tRNA(Lys). RNA (NEW YORK, N.Y.) 2014; 20:938-947. [PMID: 24757169 PMCID: PMC4024646 DOI: 10.1261/rna.044412.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
5-Taurinomethyluridine (τm(5)U) and 5-taurinomethyl-2-thiouridine (τm(5)s(2)U) are located at the wobble position of human mitochondrial (hmt) tRNA(Leu(UUR)) and tRNA(Lys), respectively. Both hypermodified units restrict decoding of the third codon letter to A and G. Pathogenic mutations in the genes encoding hmt-tRNA(Leu(UUR)) and hmt-tRNA(Lys) are responsible for the loss of the discussed modifications and, as a consequence, for the occurrence of severe mitochondrial dysfunctions (MELAS, MERRF). Synthetic oligoribonucleotides bearing modified nucleosides are a versatile tool for studying mechanisms of genetic message translation and accompanying pathologies at nucleoside resolution. In this paper, we present site-specific chemical incorporation of τm(5)U and τm(5)s(2)U into 17-mers related to the sequence of the anticodon arms hmt-tRNA(Leu(UUR)) and hmt-tRNA(Lys), respectively employing phosphoramidite chemistry on CPG support. Selected protecting groups for the sulfonic acid (4-(tert-butyldiphenylsilanyloxy)-2,2-dimethylbutyl) and the exoamine function (-C(O)CF3) are compatible with the blockage of the canonical monomeric units. The synthesis of τm(5)s(2)U-modified RNA fragment was performed under conditions eliminating the formation of side products of 2-thiocarbonyl group oxidation and/or oxidative desulphurization. The structure of the final oligomers was confirmed by mass spectroscopy and enzymatic cleavage data.
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28
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Capaldi D, Ackley K, Brooks D, Carmody J, Draper K, Kambhampati R, Kretschmer M, Levin D, McArdle J, Noll B, Raghavachari R, Roymoulik I, Sharma BP(B, Thürmer R, Wincott F. Quality Aspects of Oligonucleotide Drug Development: Specifications for Active Pharmaceutical Ingredients. ACTA ACUST UNITED AC 2012. [DOI: 10.1177/0092861512445311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Guga P, Koziołkiewicz M. Phosphorothioate nucleotides and oligonucleotides - recent progress in synthesis and application. Chem Biodivers 2012; 8:1642-81. [PMID: 21922655 DOI: 10.1002/cbdv.201100130] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, PL-90-363 Łódź.
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30
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Sanghvi YS. A status update of modified oligonucleotides for chemotherapeutics applications. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.1.1-22. [PMID: 21901670 DOI: 10.1002/0471142700.nc0401s46] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This unit presents an update of recent developments and clinical progress in chemically modified oliogonucleotides useful for therapeutic applications. During the last decade, the number of therapeutic oligonucleotides in clinical trials has nearly tripled. This is primarily due to advances in the synthesis protocols, better understanding of the biology, improved delivery, and better formulation technologies. Currently, over 100 clinical trials with oligonucleotide-based drugs are ongoing in the United States for potential treatment of a variety of life-threatening diseases. Among various oligonucleotides, antisense technology has been at the forefront, with one product on the market. Antisense technologies represent about half of the active clinical trials. Similarly, siRNA, aptamers, spiegelmers microRNA, shRNA, IMO, and CpG have been other active classes of oligonucleotides that are also undergoing clinical trials. This review attempts to summarize the current status of synthesis, chemical modifications, purification, and analysis in light of the rapid progress with multitude of oligonucleotides pursued as therapeutic modality.
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31
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Lartia R, Murat P, Dumy P, Defrancq E. Versatile introduction of azido moiety into oligonucleotides through diazo transfer reaction. Org Lett 2011; 13:5672-5. [PMID: 21958022 DOI: 10.1021/ol202397e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of a diazo transfer (DZT) reagent enables clean and efficient conversion of aminated oligodeoxyribonucleotides (ODNs) into their azido counterparts under mild conditions. ODNs bearing an amino tether at the 3', 5', or any internal position could be modified in this manner thus demonstrating the versatility of this reaction. Easy access to such azido-modified ODNs is of great interest for conjugation in particular through copper catalyzed 1,3-dipolar cycloaddition (CuAAC reaction).
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Affiliation(s)
- Rémy Lartia
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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32
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Nikcevic I, Wyrzykiewicz TK, Limbach PA. DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY - HIGH RESOLUTION MASS SPECTROMETRY. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 304:98-104. [PMID: 21811394 PMCID: PMC3146765 DOI: 10.1016/j.ijms.2010.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described.Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3'-terminal phosphate monoester and 3'-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N(3) (2-cyanoethyl) adducts of the full length product. When compared with low resolution LC-MS, ~60% more impurities can be identified when charge state and isotopic distribution information is available and used for impurity profiling.
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Affiliation(s)
- Irena Nikcevic
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172
| | | | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172
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33
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Terrazas M, Aviñó A, Siddiqui MA, Marquez VE, Eritja R. A Direct, Efficient Method for the Preparation of siRNAs Containing Ribo-like North Bicyclo[3.1.0]hexane Pseudosugars. Org Lett 2011; 13:2888-91. [DOI: 10.1021/ol200909j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Anna Aviñó
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Maqbool A. Siddiqui
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Victor E. Marquez
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Ramon Eritja
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
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Jensen MA, Anderson KM, Davis RW. Gas-phase cleavage and dephosphorylation of universal linker-bound oligodeoxynucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 29:867-78. [PMID: 21128173 DOI: 10.1080/15257770.2010.534757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
While base-specific support is commonly used for single-column oligodeoxynucleotide synthesis, the universal linker is critical for high-throughput synthesis of potentially thousands of samples in a single run. Here, we report conditions for cleavage and complete dephosphorylation of two commercial universal linkers, UnySupport and UnyLinker, processed in the gas phase (NH(3)) using our custom device. First, we compared the average yield of T10mers over time (15, 30, 60, 120, and 240 minutes, 40 psi, 80°C and 90°C). For samples processed with water added prior to incubation, we discovered a substantial increase in yield compared to those left dry (up to 55%). This was also the case for samples subjected to increases in chamber pressure (10, 20, 30 and 40 psi, 120 minutes, 80°C and 90°C). Next, we compared the effects of increased temperature, pressure and incubation times on the rates of dephosphorylation. We found the optimum conditions to be either 10 psi, 120 minutes at 80°C or 60 minutes at 90°C; in both cases, water added to columns prior to incubation had a substantial effect on rate of reaction as well as overall yield compared with those left dry. Finally, performance between the two linkers was similar enough to conclude each fulfills the desired requirements for mainstream, high-throughput oligodeoxynucleotide cleavage/deprotection and dephosphorylation in the gas phase.
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Affiliation(s)
- Michael A Jensen
- Stanford Genome Technology Center, Stanford University, 855 S. California Ave, Palo Alto, CA 94304, USA.
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35
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Seiffert S, Debelak H, Hadwiger P, Jahn-Hofmann K, Roehl I, Vornlocher HP, Noll B. Characterization of side reactions during the annealing of small interfering RNAs. Anal Biochem 2011; 414:47-57. [PMID: 21376008 DOI: 10.1016/j.ab.2011.02.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 02/25/2011] [Accepted: 02/25/2011] [Indexed: 10/18/2022]
Abstract
Small interfering RNAs (siRNAs) are emerging as a novel therapeutic modality for the specific inhibition of target gene expression. The development of siRNA-based therapeutics requires in-depth knowledge of the manufacturing process as well as adequate analytical methods to characterize this class of molecules. Here the impurity formation during the annealing of siRNA was investigated. Two siRNAs containing common chemical RNA modifications (2'-O-methyl, 2'-deoxy-2'-fluoro, 2'-deoxy-ribose, and phosphorothioate linkages) were used to determine major side reactions-such as 2',3'-isomerization, strand scission, and HF elimination-depending on annealing parameters such as RNA concentration, presence of cations, temperature, and time. Individual impurities were characterized using analytical size exclusion chromatography, denaturing and nondenaturing ion-pair reversed-phase high-performance liquid chromatography, differential scanning calorimetry, and ultraviolet spectrometry. The degradation pathways described in this work can lead to significantly reduced product quality and compromised drug activity. The data reported here provide background to successfully address challenges associated with the manufacture of siRNAs and other nucleic acid therapeutics such as aptamers, spiegelmers, and decoy and antisense oligonucleotides.
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36
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Tedebark U, Scozzari A, Werbitzky O, Capaldi D, Holmberg L. Industrial-scale manufacturing of a possible oligonucleotide cargo CPP-based drug. Methods Mol Biol 2011; 683:505-24. [PMID: 21053153 DOI: 10.1007/978-1-60761-919-2_36] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
This chapter describes the manufacturing process to a certain level for a possible oligonucleotide cargo and a peptide API in a multi-kilogram scale from a manufacture's point of view. In the concluding remarks, possible conjugation methods will be discussed from an industrial-scale perspective.
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37
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Tsunoda H, Kudo T, Ohkubo A, Seio K, Sekine M. Synthesis of oligodeoxynucleotides using fully protected deoxynucleoside 3'-phosphoramidite building blocks and base recognition of oligodeoxynucleotides incorporating N3-cyano-ethylthymine. Molecules 2010; 15:7509-31. [PMID: 21030906 PMCID: PMC6259151 DOI: 10.3390/molecules15117509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/08/2010] [Accepted: 10/14/2010] [Indexed: 11/16/2022] Open
Abstract
Oligodeoxynucleotide (ODN) synthesis, which avoids the formation of side products, is of great importance to biochemistry-based technology development. One side reaction of ODN synthesis is the cyanoethylation of the nucleobases. We suppressed this reaction by synthesizing ODNs using fully protected deoxynucleoside 3'-phosphoramidite building blocks, where the remaining reactive nucleobase residues were completely protected with acyl-, diacyl-, and acyl-oxyethylene-type groups. The detailed analysis of cyanoethylation at the nucleobase site showed that N3-protection of the thymine base efficiently suppressed the Michael addition of acrylonitrile. An ODN incorporating N3-cyanoethylthymine was synthesized using the phosphoramidite method, and primer extension reactions involving this ODN template were examined. As a result, the modified thymine produced has been proven to serve as a chain terminator.
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Affiliation(s)
- Hirosuke Tsunoda
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
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38
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Ravikumar VT, Kumar RK, Olsen P, Moore MN, Carty RL, Andrade M, Gorman D, Zhu X, Cedillo I, Wang Z, Mendez L, Scozzari AN, Aguirre G, Somanathan R, Berneès S. UnyLinker: An Efficient and Scaleable Synthesis of Oligonucleotides Utilizing a Universal Linker Molecule: A Novel Approach To Enhance the Purity of Drugs. Org Process Res Dev 2008. [DOI: 10.1021/op8000178] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vasulinga T. Ravikumar
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - R. Krishna Kumar
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Phil Olsen
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Max N. Moore
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Recaldo L. Carty
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Mark Andrade
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Dennis Gorman
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Xuefeng Zhu
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Isaiah Cedillo
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Zhiwei Wang
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Lucio Mendez
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Anthony N. Scozzari
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Gerardo Aguirre
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Ratnasamy Somanathan
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
| | - Sylvain Berneès
- Isis Pharmaceuticals, Inc. 2282 Faraday Avenue, Carlsbad, California 92008 U.S.A., Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, Tijuana, B.C., México, and DEP, Facultad de Ciencias Quı́micas, UANL, Guerrero y Progreso S/N, Col. Treviño, 64570, Monterrey, N.L., México
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39
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Saneyoshi H, Ando K, Seio K, Sekine M. Chemical synthesis of RNA via 2′-O-cyanoethylated intermediates. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.07.102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Højland T, Kumar S, Babu BR, Umemoto T, Albaek N, Sharma PK, Nielsen P, Wengel J. LNA (locked nucleic acid) and analogs as triplex-forming oligonucleotides. Org Biomol Chem 2007; 5:2375-9. [PMID: 17637956 DOI: 10.1039/b706101c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The triplex-forming abilities of some conformationally restricted nucleotide analogs are disclosed and compared herein. 2'-Amino-LNA monomers proved to be less stabilising to triplexes than LNA monomers when incorporated into a triplex-forming third strand. N2'-functionalisation of 2'-amino-LNA monomers with a glycyl unit induced the formation of exceptionally stable triplexes. Nucleotide analogs containing a C2',C3'-oxymethylene linker (E-type furanose conformation) or a C2',C4'-propylene linker (N-type furanose conformation) had no significant effect on triplex stability proving that conformational restriction per se is insufficient to stabilise triplexes.
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Affiliation(s)
- Torben Højland
- Nucleic Acid Center, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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41
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Wang Z, Olsen P, Ravikumar VT. A novel universal linker for efficient synthesis of phosphorothioate oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:259-69. [PMID: 17454735 DOI: 10.1080/15257770701257277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A versatile and conformationally preorganized universal linker molecule is reported here for efficient synthesis of phosphorothioate oligonucleotides. With respect to nucleoside loaded support, comparable yield and quality based on ion-pair LC-MS are obtained for both deoxy and 2'-O-methoxyethyl modified phosphorothioate oligonucleotides. No 3'-phosphate or phosphorothioate monoester or any modification of universal molecule still attached to oligonucleotide was observed. [structure: see text]
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Affiliation(s)
- Zhiwei Wang
- Isis Pharmaceuticals, Carlsbad, California 92008. USA
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42
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Kumar RK, Olsen P, Ravikumar VT. An alternative advantageous protocol for efficient synthesis of phosphorothioate oligonucleotides utilizing phenylacetyl disulfide (PADS). NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:181-8. [PMID: 17365796 DOI: 10.1080/15257770601112739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Phosphorothioate oligonucleotides could be synthesized using a 0.2 M solution of phenylacetyl disulfide (PADS) in a mixture of pyridine and acetonitrile (1:1, v/v) with > 99.9% step-wise efficiency. Unlike most other sulfurizing reagents that need to be stable in solution for performance, PADS needs to degrade and "age" in solution and hence performs efficiently even after storing the solution at room temperature for over a month. High yield and quality of oligonucleotides are produced thereby offering an alternative attractive protocol for use of this efficient sulfurizing reagent.
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43
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Semenyuk A, Ahnfelt M, Estmer Nilsson C, Yong Hao X, Földesi A, Kao YS, Chen HH, Kao WC, Peck K, Kwiatkowski M. Cartridge-based high-throughput purification of oligonucleotides for reliable oligonucleotide arrays. Anal Biochem 2006; 356:132-41. [PMID: 16769031 DOI: 10.1016/j.ab.2006.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Revised: 05/03/2006] [Accepted: 05/05/2006] [Indexed: 10/24/2022]
Abstract
A novel, cartridge-based procedure for the efficient and irreversible detritylation of oligonucleotides is reported. This method, combined with a process for the elimination of depurinated fragments produces, in a highly parallel fashion, oligonucleotides with better purity than those traditionally obtained using reversed-phase high-performance liquid chromotography purification. Our combined detritylation and purification methodology compares favorably with commercial cartridge-based purification systems. The benefits of working with pure oligonucleotides, with regard to higher signal and better signal linearity, are shown in array-based hybridization experiments.
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Affiliation(s)
- Andrey Semenyuk
- Department of Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
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44
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Kumar RK, Guzaev AP, Rentel C, Ravikumar VT. Efficient synthesis of antisense phosphorothioate oligonucleotides using a universal solid support. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.02.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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45
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Cheruvallath ZS, Eleuteri A, Turney B, Ravikumar VT. (2-Acetoxyphenoxy)ethyl (APOE) as a Phosphate Protecting Group in Solid-Phase Synthesis of Oligonucleotides via the Phosphoramidite Approach. Org Process Res Dev 2006. [DOI: 10.1021/op0502147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Alessandra Eleuteri
- Isis Pharmaceuticals, Inc., 2282 Faraday Avenue, Carlsbad, California 92008, U.S.A
| | - Brett Turney
- Isis Pharmaceuticals, Inc., 2282 Faraday Avenue, Carlsbad, California 92008, U.S.A
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46
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Ravikumar VT, Andrade M, Carty RL, Dan A, Barone S. Development of siRNA for therapeutics: efficient synthesis of phosphorothioate RNA utilizing phenylacetyl disulfide (PADS). Bioorg Med Chem Lett 2006; 16:2513-7. [PMID: 16481168 DOI: 10.1016/j.bmcl.2006.01.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 01/20/2006] [Accepted: 01/20/2006] [Indexed: 12/01/2022]
Abstract
Efficient synthesis of phosphorothioate RNA (PS-RNA) is demonstrated by using phenylacetyl disulfide (PADS) in a mixture of pyridine and acetonitrile (1:1, v/v) for 3 min. Sulfurization is achieved with >99.8% stepwise efficiency. This reagent also performs efficiently during synthesis of RNA containing PS:PO mixed backbone.
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47
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Gaus H, Olsen P, Sooy KV, Rentel C, Turney B, Walker KL, McArdle JV, Capaldi DC. Trichloroacetaldehyde modified oligonucleotides. Bioorg Med Chem Lett 2005; 15:4118-24. [PMID: 16002284 DOI: 10.1016/j.bmcl.2005.06.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 06/02/2005] [Accepted: 06/02/2005] [Indexed: 11/18/2022]
Abstract
Some commercial batches of dichloroacetic acid (DCA) contain traces of chloral (trichloroacetaldehyde). Using such DCA to effect detritylation during solid-phase oligonucleotide synthesis results in the formation of a family of process impurities in which the atoms of chloral (Cl3CCHO) are incorporated between the 5'-oxygen and phosphorus atoms of an internucleotide linkage. The structure was elucidated by HPLC with UV and MS detection, digestion of the oligonucleotide, synthesis of model compounds, and 1H and 31P NMR spectroscopy. By understanding the chemistry behind its formation, we are now able to limit levels of this impurity in synthetic oligonucleotides by limiting chloral in DCA.
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Affiliation(s)
- Hans Gaus
- Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad, CA 92008, USA
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48
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Kurata C, Bradley K, Gaus H, Luu N, Cedillo I, Ravikumar VT, Van Sooy K, McArdle JV, Capaldi DC. Characterization of high molecular weight impurities in synthetic phosphorothioate oligonucleotides. Bioorg Med Chem Lett 2005; 16:607-14. [PMID: 16274991 DOI: 10.1016/j.bmcl.2005.10.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 10/13/2005] [Accepted: 10/14/2005] [Indexed: 11/16/2022]
Abstract
Phosphorothioate oligonucleotides manufactured by standard phosphoramidite techniques using 2'-deoxyadenosine- or 2'-O-(2-methoxyethyl)-5-methylcytosine-loaded solid supports contain branched impurities consisting of two chains linked through the exocyclic amino group of the 3'-terminal nucleoside of one chain and the 3'-terminal hydroxyl group of another via a P(O)SH group. These impurities are not produced when a universal, non-nucleoside derivatized support is used.
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Affiliation(s)
- Christine Kurata
- Isis Pharmaceuticals Inc., 1896 Rutherford Road, Carlsbad, CA 92008, USA
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49
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Krishna Kumar R, Ravikumar VT. 4,4'-Dimethoxytrityl group derived from secondary alcohols: are they removed slowly under acidic conditions? Bioorg Med Chem Lett 2005; 15:3426-9. [PMID: 15946845 DOI: 10.1016/j.bmcl.2005.05.018] [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] [Received: 04/12/2005] [Revised: 05/04/2005] [Accepted: 05/04/2005] [Indexed: 11/15/2022]
Abstract
Removal of 4,4'-dimethoxytrityl (DMT) groups from primary and secondary hydroxyl functionality was investigated. It was observed that deblocking of DMT group from secondary hydroxyl group of molecules attached to solid support under acidic conditions occurred relatively slowly compared to primary hydroxyl group. Marginal difference in rate of detritylation was observed between DMT group attached to 5'-hydroxyl group of deoxyribonucleoside and 2'-O-methoxyethylribonucleoside when attached to one kind of support. Removal of DMT from nucleoside attached to OligoPrep solid support was found to be slow.
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Affiliation(s)
- R Krishna Kumar
- Department of Chemistry, Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, CA 92008, USA
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50
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Nitromethane as a scavenger of acrylonitrile in the deprotection of synthetic oligonucleotides. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.04.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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