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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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2
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Martin Somer A, Macaluso V, Barnes GL, Yang L, Pratihar S, Song K, Hase WL, Spezia R. Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2-24. [PMID: 32881516 DOI: 10.1021/jasms.9b00062] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.
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Affiliation(s)
- Ana Martin Somer
- Departamento de Química, Facultad de Ciencias, Módulo 13 Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain
| | - Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Evry, France
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Li Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P.R. China
| | - Subha Pratihar
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Kihyung Song
- Department of Chemistry, Korea National University of Education, Chungbuk 28644, Republic of Korea
| | - William L Hase
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, 4, Place Jussieu, Paris, 75252 Cedex 05, France
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Pourshahian S, Gryaznov SM. Sequencing of Phosphoramidate Oligonucleotides by Acid Hydrolysis and Mass Spectrometry. Anal Chem 2019; 91:11154-11161. [PMID: 31386344 DOI: 10.1021/acs.analchem.9b01858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrolysis of N3'-P5' phosphoramidate and thiophosphoramidate oligonucleotides with 0.1% formic acid leads to the cleavage of the 3' N-P bond and generates two products, one of which contains a 5'-phosphate. Analysis of the hydrolytic products by liquid chromatography, coupled with mass spectrometry, reveals the mass ladder from both termini, which is used to determine the sequence. While acid hydrolysis does not result in depurination, internal fragments especially in the low mass range are detected. The method is applied to DNA and RNA analogues with and without modifications at the 2'-position. This approach enables rapid sequence confirmation of synthetic phosphoramidate oligonucleotides for quality control as well as denovo sequencing.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson , South San Francisco , California 94080 , United States
| | - Sergei M Gryaznov
- Janssen Pharmaceutical Companies of Johnson & Johnson , South San Francisco , California 94080 , United States
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4
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Goto R, Miyakawa S, Inomata E, Takami T, Yamaura J, Nakamura Y. De novo sequencing of highly modified therapeutic oligonucleotides by hydrophobic tag sequencing coupled with LC-MS. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:78-93. [PMID: 27935159 DOI: 10.1002/jms.3902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 06/06/2023]
Abstract
Correct sequences are prerequisite for quality control of therapeutic oligonucleotides. However, there is no definitive method available for determining sequences of highly modified therapeutic RNAs, and thereby, most of the oligonucleotides have been used clinically without direct sequence determination. In this study, we developed a novel sequencing method called 'hydrophobic tag sequencing'. Highly modified oligonucleotides are sequenced by partially digesting oligonucleotides conjugated with a 5'-hydrophobic tag, followed by liquid chromatography-mass spectrometry analysis. 5'-Hydrophobic tag-printed fragments (5'-tag degradates) can be separated in order of their molecular masses from tag-free oligonucleotides by reversed-phase liquid chromatography. As models for the sequencing, the anti-VEGF aptamer (Macugen) and the highly modified 38-mer RNA sequences were analyzed under blind conditions. Most nucleotides were identified from the molecular weight of hydrophobic 5'-tag degradates calculated from monoisotopic mass in simple full mass data. When monoisotopic mass could not be assigned, the nucleotide was estimated using the molecular weight of the most abundant mass. The sequences of Macugen and 38-mer RNA perfectly matched the theoretical sequences. The hydrophobic tag sequencing worked well to obtain simple full mass data, resulting in accurate and clear sequencing. The present study provides for the first time a de novo sequencing technology for highly modified RNAs and contributes to quality control of therapeutic oligonucleotides. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- R Goto
- Bioanalysis Business Department, CMIC Pharma Science Co., Ltd., 17-18, Nakahata-cho, Nishiwaki-shi, Hyogo, 677-0032, Japan
| | - S Miyakawa
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - E Inomata
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - T Takami
- Bioanalysis Department, CMIC, Inc., Hoffman Estates, Illinois, 60192-3702, USA
| | - J Yamaura
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Y Nakamura
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
- Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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5
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Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YLJ, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. Methods Enzymol 2015; 560:29-71. [PMID: 26253965 DOI: 10.1016/bs.mie.2015.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
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Affiliation(s)
- Weiling Maggie Cai
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yok Hian Chionh
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chee Sheng Ng
- Singapore-MIT Alliance for Research and Technology, Singapore; School of Biological Sciences, Nanyang Technological Institute, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Engineering and Science, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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6
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Abstract
Recent findings have elucidated numerous novel biological functions for oligonucleotides. Current standard methods for the study of oligonucleotides (i.e., hybridization and PCR) are not fully equipped to deal with the experimental needs arising from these new discoveries. More importantly, as the intracellular capacity of oligonucleotides is being harnessed for biomedical applications, alternative bioanalytical techniques become indispensable in order to comply with ever-increasing regulatory requirements. Owing to its ability to detect oligonucleotides independent of their sequence, LC-MS is emerging as the analytical method of choice for oligonucleotides. In this article, the current applications of LC-MS in the analysis of oligonucleotides, with an emphasis on RNA therapeutics and biomarkers, will be examined. In addition, the theoretical framework of oligonucleotide ESI is carefully inspected with the purpose of identifying the contributing factors to MS signal intensity.
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7
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Dudley E, Bond L. Mass spectrometry analysis of nucleosides and nucleotides. MASS SPECTROMETRY REVIEWS 2014; 33:302-31. [PMID: 24285362 DOI: 10.1002/mas.21388] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.
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Affiliation(s)
- Ed Dudley
- Institute of Mass Spectrometry, College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
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Gao Y, Yang J, Cancilla MT, Meng F, McLuckey SA. Top-down interrogation of chemically modified oligonucleotides by negative electron transfer and collision induced dissociation. Anal Chem 2013; 85:4713-20. [PMID: 23534847 DOI: 10.1021/ac400448t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two sets of synthetic 21-23mer oligonucleotides with various types of 2'-position modifications have been studied with tandem mass spectrometry using ion trap collision-induced dissociation (IT-CID) and negative electron transfer (NET)-CID. A systematic study has been conducted to define the limitations of IT-CID in sequencing such 2'-chemically modified oligonucleotides. We found that IT-CID is sufficient in characterizing oligonucleotide sequences that do not contain DNA residues, where high sequence coverage can be achieved by performing IT-CID on multiple charge states. However, oligonucleotides containing DNA residues gave limited backbone fragmentation with IT-CID, largely due to dominant fragmentation at the DNA residue sites. To overcome this limitation, we employed the negative electron transfer to strip an electron from the multiply charged oligonucleotide anion. Then, the radical anion species formed in this reaction can fragment via an alternative radical-directed dissociation mechanism. Unlike IT-CID, NET-CID mainly generates a noncomplementary d/w ion series. Furthermore, we found that NET-CID did not show preferential dissociations at the DNA residue sites and thus generated higher sequence coverage for the studied oligonucleotide. Information from NET-CID of different charge states is not fully redundant such that the examination of multiple charge states can lead to more extensive sequence confirmation. This work demonstrates that the NET-CID is a valuable tool to provide high sequence coverage for chemically modified oligonucleotides, and such detailed characterization can serve as an important assay to control the quality of therapeutic oligonucleotides that are produced under the good manufacture practice (GMP) regulations.
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Affiliation(s)
- Yang Gao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, United States
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Abstract
We present a simple and secure system for encrypting and decrypting information using DNA self-assembly. Binary data is encoded in the geometry of DNA nanostructures with two distinct conformations. Removing or leaving out a single component reduces these structures to an encrypted solution of ssDNA, whereas adding back this missing “decryption key” causes the spontaneous formation of the message through self-assembly, enabling rapid read out via gel electrophoresis. Applications include authentication, secure messaging, and barcoding.
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Affiliation(s)
- Ken Halvorsen
- Immune Disease Institute/Program in Cellular and Molecular Medicine, Harvard Medical School and Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Wesley P. Wong
- Immune Disease Institute/Program in Cellular and Molecular Medicine, Harvard Medical School and Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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10
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Izumi Y, Takimura S, Yamaguchi S, Iida J, Bamba T, Fukusaki E. Application of electrospray ionization ion trap/time-of-flight mass spectrometry for chemically-synthesized small RNAs. J Biosci Bioeng 2012; 113:412-9. [DOI: 10.1016/j.jbiosc.2011.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/06/2011] [Accepted: 11/08/2011] [Indexed: 12/13/2022]
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11
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Comprehensive hydrophilic interaction and ion-pair reversed-phase liquid chromatography for analysis of di- to deca-oligonucleotides. J Chromatogr A 2011; 1255:237-43. [PMID: 22204934 DOI: 10.1016/j.chroma.2011.11.062] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/24/2011] [Accepted: 11/29/2011] [Indexed: 11/22/2022]
Abstract
A comprehensive two-dimensional HPLC approach with a high degree of orthogonality was developed for analysis of di- to deca-oligonucleotides (ONs). Hydrophilic interaction liquid chromatography (HILIC) was used in the first dimension, and ion-pair reversed-phase liquid chromatography (IP-RPLC) was employed in the second dimension. The two dimensions were connected via a ten-port valve interface equipped with octadecyl silica (ODS) traps to immobilize and focus the ONs eluting from the first dimension prior to IP-RPLC separation. An aqueous make-up flow was used for effective trapping. The comprehensive two-dimensional HPLC system was optimized with a mixture consisting of 27 oligonucleotide standards. An overall chromatographic peak capacity of 500 was obtained. The use of the volatile buffer triethylamine acetate in the second dimension allowed straightforward coupling to electrospray ionization mass spectrometry (ESI-MS) and detection of each ON in the negative ionization mode.
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12
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Beverly MB. Applications of mass spectrometry to the study of siRNA. MASS SPECTROMETRY REVIEWS 2011; 30:979-998. [PMID: 20201110 DOI: 10.1002/mas.20260] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 08/13/2009] [Accepted: 08/13/2009] [Indexed: 05/28/2023]
Abstract
RNA interference (RNAi) has quickly become a well-established laboratory tool for regulating gene expression and is currently being explored for its therapeutic potential. The design and use of double-stranded RNA oligonucleotides as therapeutics to trigger the RNAi mechanism and a greater effort to understand the RNAi pathway itself is driving the development of analytical techniques that can characterize these oligonucleotides. Electrospray (ESI) and MALDI have been used routinely to analyze oligonucleotides and their ability to provide mass and sequence information has made them ideal for this application. Reviewed here is the work done to date on the use of ESI and MALDI for the study of RNAi oligonucleotides as well as the strategies and issues associated with siRNA analysis by mass spectrometry. While there is not a large body of literature on the specific application of mass spectrometry to RNAi, the work done in this area is a good demonstration of the range of experiments that can be conducted and the value that ESI and MALDI can provide to the RNAi field.
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Affiliation(s)
- Michael B Beverly
- RNA Therapeutics Department, Merck and Co., Inc., Boulder, CO 80301, USA.
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Turner JJ, Hoos JS, Vonhoff S, Klussmann S. Methods for L-ribooligonucleotide sequence determination using LCMS. Nucleic Acids Res 2011; 39:e147. [PMID: 21948795 PMCID: PMC3241672 DOI: 10.1093/nar/gkr776] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The ability to verify the sequence of a nucleic acid-based therapeutic is an essential step in the drug development process. The challenge associated with sequence identification increases with the length and nuclease resistance of the nucleic acid molecule, the latter being an important attribute of therapeutic oligonucleotides. We describe methods for the sequence determination of Spiegelmers, which are enantiomers of naturally occurring RNA with high resistance to enzymatic degradation. Spiegelmer sequencing is effected by affixing a label or hapten to the 5′-end of the oligonucleotide and chemically degrading the molecule in a controlled fashion to generate fragments that are then resolved and identified using liquid chromatography-mass spectrometry. The Spiegelmer sequence is then derived from these fragments. Examples are shown for two different Spiegelmers (NOX-E36 and NOX-A12), and the specificity of the method is shown using a NOX-E36 mismatch control.
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Affiliation(s)
- John J Turner
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, D-10589 Berlin, Germany.
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McGinnis AC, Chen B, Bartlett MG. Chromatographic methods for the determination of therapeutic oligonucleotides. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 883-884:76-94. [PMID: 21945211 DOI: 10.1016/j.jchromb.2011.09.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/31/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
Both DNA and RNA are being explored for their therapeutic potential against a wide range of diseases. As these new drugs emerge, new demands arise for the analysis and quantitation of these biomolecules. Pharmacokinetic and pharmacodynamic analysis requirements for drug approval place enormous challenges on the methods for analyzing these therapeutics. This review will focus on bioanalytical methods for DNA antisense and aptamers as well as small-interfering RNA (siRNA) therapeutics. Chromatography methods employing ultraviolet (UV), fluorescence and mass spectrometric (MS) detection along with matrix-assisted laser desorption/ionization (MALDI) will be covered. Sample preparation from biological matrices will be reviewed as well as metabolite analysis and identification. All of these techniques are important contributions toward oligonucleotide therapeutic development. They will also be important in microRNA (miRNA) biomarker discovery and RNomics in general, as more non-coding RNAs are inevitably discovered.
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Affiliation(s)
- A Cary McGinnis
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
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Taucher M, Ganisl B, Breuker K. Identification, localization, and relative quantitation of pseudouridine in RNA by tandem mass spectrometry of hydrolysis products. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 304:91-97. [PMID: 21960742 PMCID: PMC3180913 DOI: 10.1016/j.ijms.2010.05.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The constitutional isomers uridine (U) and pseudouridine (Ψ) cannot be distinguished from each other by simple mass measurements of RNA or its fragments because the conversion of U into Ψ is a "mass-silent" post-transcriptional modification. Here we propose a new mass spectrometry based method for identification, localization, and relative quantitation of Ψ in RNA consisting of ∼20 nucleotides that does not require chemical labeling. Our approach takes advantage of the different fragmentation behavior of uridine (N-glycosidic bond) and pseudouridine (C-glycosidic bond) residues in RNA upon collisionally activated dissociation.
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Affiliation(s)
| | | | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Nyakas A, Stucki SR, Schürch S. Tandem mass spectrometry of modified and platinated oligoribonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:875-887. [PMID: 21472522 DOI: 10.1007/s13361-011-0106-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 02/04/2011] [Accepted: 02/09/2011] [Indexed: 05/30/2023]
Abstract
Therapeutic approaches for treatment of various diseases aim at the interruption of transcription or translation. Modified oligonucleotides, such as 2'-O-methyl- and methylphosphonate-derivatives, exhibit high resistance against cellular nucleases, thus rendering application for, e.g., antigene or antisense purposes possible. Other approaches are based on administration of cross-linking agents, such as cis-diamminedichloroplatinum(II) (cisplatin, DDP), which is still the most widely used anticancer drug worldwide. Due to the formation of 1,2-intrastrand cross links at adjacent guanines, replication of the double-strand is disturbed, thus resulting in significant cytotoxicity. Evidence for the gas-phase dissociation mechanism of platinated RNA is given, based on nano-electrospray ionization high-resolution multistage tandem mass spectrometry (MS(n)). Confirmation was found by investigating the fragmentation pattern of platinated and unplatinated 2'-methoxy oligoribonucleotide hexamers and their corresponding methylphosphonate derivatives. Platinated 2'-methoxy oligoribonucleotides exhibit a similar gas-phase dissociation behavior as the corresponding DNA and RNA sequences, with the 3'-C-O bond adjacent to the vicinal guanines being cleaved preferentially, leading to w(x)-ion formation. By examination of the corresponding platinated methylphosphonate derivatives of the 2'-methoxy oligoribonucleotides, the key role of the negatively charged phosphate oxygen atoms in direct proximity to the guanines was proven. The significant alteration of fragmentation due to platination is demonstrated by comparison of the fragment ion patterns of unplatinated and platinated 2'-O-methyl- and 2'-O-methyl methylphosphonate oligoribonucleotides, and the results obtained by H/D exchange experiments.
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Affiliation(s)
- Adrien Nyakas
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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17
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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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18
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Smith M. Characterisation of a modified oligonucleotide together with its synthetic impurities using accurate mass measurements. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:511-525. [PMID: 21259360 DOI: 10.1002/rcm.4886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Oligonucleotide-based drugs are beginning to establish themselves within the pharmaceutical industry as important agents in the treatment of various disease states with the potential of exhibiting high specificity with gene targeted therapies. Recent studies regarding RNA interference has stimulated interest in this field. There are now an increasing number of oligonucleotide-based pharmaceutical products in various stages of clinical development for the treatment of life-threatening diseases. As a result, the production of synthetic oligonucleotides has become increasingly important, with both antisense and RNAi-related oligonucleotides under development as therapeutic agents. One potential drug candidate currently under development at GlaxoSmithKline, is a 2'-O-methyl phosphorothioate in which the non-bridging oxygens of the phosphate diester are replaced with sulphur. Oligonucleotides are polymeric sequences made from an array of nucleotides (RNA, DNA and their respective analogs) usually ranging from 20-100 nucleotides. The polar nature, low thermal stability, complexity and large molecular weights of oligonucleotides have posed a challenge for the analysis of oligonucleotides by mass spectrometry. This paper demonstrates the use of negative ion electrospray with a combination of high resolution and high mass accuracy for the characterisation of oligonucleotides with the intention of supporting an evidence of structure document for a regulatory submission. This is a new area within the mass spectrometry field and as such there is limited software amongst the instrument companies for the data processing for the analysis of these compounds. Therefore, many of the examples in the literature only use mass spectrometry to generate average molecular weights by deconvoluting the multiple charged states observed to give an average molecular weight; under-utilizing the capability of high-resolution instruments.
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Affiliation(s)
- Marco Smith
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK.
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Shelke SA, Sigurdsson ST. Site-Directed Nitroxide Spin Labeling of Biopolymers. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2011. [DOI: 10.1007/430_2011_62] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Ivleva VB, Yu YQ, Gilar M. Ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) and UPLC/MS(E) analysis of RNA oligonucleotides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2631-2640. [PMID: 20740540 DOI: 10.1002/rcm.4683] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fast and efficient ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) analysis of short interfering RNA oligonucleotides was used for identity confirmation of the target sequence-related impurities. Multiple truncated oligonucleotides and metabolites were identified based on the accurate mass, and their presumed sequence was confirmed by MS/MS and MS(E) (alternating low and elevated collision energy scanning modes) methods. Based on the resulting fragmentation of native and chemically modified oligonucleotides, it was found that the MS(E) technique is as efficient as the traditional MS/MS method, yet MS(E) is more general, faster, and capable of producing higher signal intensities of fragment ions. Fragmentation patterns of modified oligonucleotides were investigated using RNA 2'-ribose substitutions, phosphorothioate RNA, and LNA modifications. The developed sequence confirmation method that uses the MS(E) approach was applied to the analysis of in vitro hydrolyzed RNA oligonucleotide. The target RNA and metabolites, including the structural isomers, were resolved by UPLC, and their identity was confirmed by MS(E). Simultaneous RNA truncations from both termini were observed. The UPLC quadrupole time-of-flight (QTOF) MS/MS and MS(E) methods were shown to be an effective tool for the analysis and sequence confirmation of complex oligonucleotide mixtures.
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Affiliation(s)
- Vera B Ivleva
- Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
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Kretschmer M, Lavine G, McArdle J, Kuchimanchi S, Murugaiah V, Manoharan M. An automated algorithm for sequence confirmation of chemically modified oligonucleotides by tandem mass spectrometry. Anal Biochem 2010; 405:213-23. [PMID: 20599656 DOI: 10.1016/j.ab.2010.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/11/2010] [Accepted: 06/11/2010] [Indexed: 02/01/2023]
Abstract
We have developed a tandem mass spectrometry (MS/MS) data analysis program for confirmation of sequence of chemically modified oligonucleotides. The method is based on the analysis of deconvoluted MS/MS data for fragment ions from three charge states and comparison of these data against a set of computer-generated masses from expected fragmentation patterns. The algorithm compares the experimental masses not only against the fragment set predicted for the expected sequence but also against a wider test set covering all next-neighbor position switches of the original sequence and all pairwise swaps of nucleosides, which in synthesis would result in molecules with masses within a preset mass tolerance. The algorithm is capable of identifying incorrect sequences that would not be distinguished by identity testing with electrospray ionization mass spectrometry. The method has been tested with permutations of the two 21-mer single strands of a chemically modified short interfering RNA containing 2'-O-methyl and phosphorothioate linkages. For both strands, challenge sequences were synthesized and tested with the premise that they were the original sequences. The algorithm correctly reported the locations of next-neighbor position switches and nucleoside swaps. The results confirm the approach as useful for MS/MS-based identity test methods for synthetic oligonucleotides.
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Taucher M, Rieder U, Breuker K. Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:278-85. [PMID: 19932627 DOI: 10.1016/j.jasms.2009.10.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 09/28/2009] [Accepted: 10/14/2009] [Indexed: 05/25/2023]
Abstract
In recent years, new classes of nonprotein-coding ribonucleic acids (ncRNAs) with important cellular functions have been discovered. Of particular interest for biomolecular research and pharmaceutical developments are small ncRNAs that are involved in gene regulation, such as small interfering RNAs (21-28 nt), pre-microRNAs (70-80 nt), or riboswitches (34-200 nt). De novo sequencing of RNA by top-down mass spectrometry has so far been limited to RNA consisting of up to approximately 20 nt. We report here complete sequence coverage for 34 nt RNA (10.9 kDa), along with 30 out of 32 possible complementary ion pairs from collisionally activated dissociation (CAD) experiments. The key to minimizing undesired base loss and internal fragmentation is to minimize the internal energy of fragment ions from primary backbone cleavage. This can be achieved by collisional cooling of primary fragment ions and selection of precursor ions of relatively low negative net charge (about -0.2/nt).
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Affiliation(s)
- Monika Taucher
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
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Huang TY, Kharlamova A, McLuckey SA. Ion trap collision-induced dissociation of locked nucleic acids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:144-153. [PMID: 19854063 DOI: 10.1016/j.jasms.2009.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Revised: 09/25/2009] [Accepted: 09/25/2009] [Indexed: 05/28/2023]
Abstract
Gas-phase dissociation of model locked nucleic acid (LNA) oligonucleotides and functional LNA-DNA chimeras have been investigated as a function of precursor ion charge state using ion trap collision-induced dissociation (CID). For the model LNA 5 and 8 mer, containing all four LNA monomers in the sequence, cleavage of all backbone bonds, generating a/w-, b/x-, c/y-, and d/z-ions, was observed with no significant preference at lower charge states. Base loss ions, except loss of thymine, from the cleavage of N-glycosidic bonds were also present. In general, complete sequence coverage was achieved in all charge states. For the two LNA-DNA chimeras, however, dramatic differences in the relative contributions of the competing dissociation channels were observed among different precursor ion charge states. At lower charge states, sequence information limited to the a-Base/w-fragment ions from cleavage of the 3'C-O bond of DNA nucleotides, except thymidine (dT), was acquired from CID of both the LNA gapmer and mixmer ions. On the other hand, extensive fragmentation from various dissociation channels was observed from post-ion/ion ion trap CID of the higher charge state ions of both LNA-DNA chimeras. This report demonstrates that tandem mass spectrometry is effective in the sequence characterization of LNA oligonucleotides and LNA-DNA chimeric therapeutics.
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Affiliation(s)
- Teng-yi Huang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-1393, USA
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