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Guzmán-Lorite M, Rosu F, Marina ML, García MC, Gabelica V. miRNA and DNA analysis by negative ion electron transfer dissociation and infrared multiple-photon dissociation mass spectrometry. Anal Chim Acta 2024; 1299:342431. [PMID: 38499418 DOI: 10.1016/j.aca.2024.342431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND The use of simple and hybrid fragmentation techniques for the identification of molecules in tandem mass spectrometry provides different and complementary information on the structure of molecules. Nevertheless, these techniques have not been as widely explored for oligonucleotides as for peptides or proteins. The analysis of microRNAs (miRNAs) warrants special attention, given their regulatory role and their relationship with several diseases. The application of different fragmentation techniques will be very interesting for their identification. RESULTS Four synthetic miRNAs and a DNA sequence were fragmented in an ESI-FT-ICR mass spectrometer using both simple and hybrid fragmentation techniques: CID, nETD followed by CID, IRMPD, and, for the first time, nETD in combination with IRMPD. The main fragmentation channel was base loss. The use of nETD-IRMPD resulted in d/z, a/w, and c/y ions at higher intensities. Moreover, nETD-IRMPD provided high sequence coverage and low internal fragmentation. Native MS analysis revealed that only miR159 and the DNA sequence formed stable dimers under physiological ionic strength. The use of organic co-solvents or additives resulted in a lower sequence coverage due to lesser overall ionization efficiency. NOVELTY This work demonstrates that the combination of nETD and IRMPD for miRNA fragmentation constitutes a suitable alternative to common fragmentation methods. This strategy resulted in efficient fragmentation of [miRNA]5- using low irradiation times and fewer internal fragments while ensuring a high sequence coverage. Moreover, given that such low charge states predominate upon spraying in physiological-like conditions, native MS can be applied for obtaining structural information at the same time.
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Affiliation(s)
- Miriam Guzmán-Lorite
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain
| | - Frédéric Rosu
- Université de Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600, Pessac, France
| | - María Luisa Marina
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain; Universidad de Alcalá, Instituto de Investigación Química "Andrés M. Del Río", Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain
| | - María Concepción García
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain; Universidad de Alcalá, Instituto de Investigación Química "Andrés M. Del Río", Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain.
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600, Pessac, France; Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600, Pessac, France
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Brundridge NM, Fritz JM, Dickerhoff J, Yang D, McLuckey SA. Negative Electron Transfer Collision-Induced Dissociation of G-Quadruplexes: Uncovering the Guanine Radical Anion Loss Pathway. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:756-766. [PMID: 38456425 PMCID: PMC11022967 DOI: 10.1021/jasms.3c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
G-quadruplex (G4) DNA can form highly stable secondary structures in the presence of metal cations, and research has shown its potential as a transcriptional regulator for oncogenes in the human genome. In order to explore the interactions of DNA with metal cations using mass spectrometry, employing complementary fragmentation methods can enhance structural information. This study explores the use of ion-ion reactions for sequential negative electron transfer collision-induced dissociation (nET-CID) as a complement to traditional ion-trap CID (IT-CID). The resulting nET-CID data for G4 anions with and without metal cations show an increase in fragment ion type diversity and yield of structurally informative ions relative to IT-CID. The nET-CID yields greater sequence coverage by virtue of fragmentation at the 3'-side of thymine residues, which is lacking with IT-CID. Potassium adductions to backbone fragments in IT-CID and nET-CID spectra were nearly identical. Of note is a prominent fragment resulting from a loss of a 149 Da anion seen in nET-CID of large, G-rich sequences, proposed to be radical anion guanine loss. Neutral loss of neutral guanine (151 Da) and deprotonated nucleobase loss (150 Da) have been previously reported, but this is the first report of radical anion guanine loss (149 Da). Confirmation of the identity of the 149 Da anion results from the examination of the homonucleobase sequence 5'-GGGGGGGG-3'. Loss of a charged adenine radical anion at much lower relative abundance was also noted for the sequence 5'-AAAAAAAA-3'. DFT modeling indicates that the loss of a nucleobase as a radical anion from odd-electron nucleic acid anions is a thermodynamically favorable fragmentation pathway for G.
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Affiliation(s)
- Nicole M Brundridge
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jordan M Fritz
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W. Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Danzhou Yang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W. Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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Karasawa K, Duchoslav E, Burton L, Kawakami J, Baba T. Sequencing of Morpholino Antisense Oligonucleotides Using Electron Capture Dissociation Mass Spectrometry. Anal Chem 2023; 95:16352-16358. [PMID: 37871344 DOI: 10.1021/acs.analchem.3c03621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We report the first sequencing of morpholino antisense oligonucleotides (phosphorodiamidate morpholino oligomers, PMOs) using electron capture dissociation (ECD) mass spectrometry. In this research, we found dissociation of the backbone of 18- to 25-mer PMOs to produce d and z ions as the major ions, and 100% cleavage coverage (sequence coverage) was obtained with these ions. This is a critical contrast with beam-type collision-induced dissociation, which dominantly induces base loss, so it is difficult to obtain sequence information. The results showed that an electron beam energy (typically 15 eV) can be used universally for PMOs with different sequences, lengths, and charge states so that no detailed optimization is required for multiprecursor targeting liquid chromatography coupled with tandem mass spectrometry measurements. We also confirmed that the ECD reaction speed was compatible with the high-performance liquid chromatography time scale. Finally, we demonstrated a liquid chromatography electron capture dissociation tandem mass spectrometry workflow to survey the modification sites of the emulated PMO impurities.
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Affiliation(s)
- Kaoru Karasawa
- SCIEX, 4-7-35 Kitashinagawa, Shinagawa, Tokyo 140-0001, Japan
| | - Eva Duchoslav
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Lyle Burton
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Junji Kawakami
- Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe, Hyogo 658-8501, Japan
| | - Takashi Baba
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
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Brundridge NM, Dickerhoff J, Yang D, McLuckey SA. Gas-Phase Fragmentation as a Probe of G-Quadruplex Formation. Anal Chem 2023; 95:15057-15067. [PMID: 37774231 PMCID: PMC11022955 DOI: 10.1021/acs.analchem.3c03143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
G-quadruplex (G4) DNA is found in oncogene promoters and human telomeres and is an attractive anticancer target. Stable G4 structures form in guanine-rich sequences in the presence of metal cations and can stabilize further with specific ligand adduction. To explore the preservation and stability of this secondary structure with mass spectrometry, gas-phase collision-induced dissociation kinetics of G4-like and non-G4-like ion structures were determined in a linear quadrupole ion trap. This study focused on a sequence from the promoter of the MYC oncogene, MycG4, and a mutant non-G4-forming sequence, MycNonG4. At relatively high ion activation energies, the backbone fragmentation patterns of the MycG4 and MycNonG4 are similar, while potassium ion-stabilized G4-folded [MycG4 + 2K-7H]5- and counterpart [MycG4-5H]5- ions are essentially indistinguishable, indicating that high-energy fragmentation is not sensitive to the G4 structure. At low energies, the backbone fragmentation patterns of MycG4 and MycNonG4 are significantly different. For MycG4, fragmentation over time differed significantly between the potassium-bound and free structures, reflecting the preservation of the G4 structure in the gas phase. Kinetic measurements revealed the [MycG4 + 2K-7H]5- ions to fragment two to three times more slowly than the [MycG4-5H]5-. Results for the control MycNonG4 indicated that the phenomena noted for [MycG4 + 2K-7H]5- ions are specific to G4-folding. Therefore, our data show that gentle activation conditions can lead to fragmentation behavior that is sensitive to G-quadruplex structure, revealing differences in kinetic stabilities of isomeric structures as well as the regions of the sequence that are directly involved in forming these structures.
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Affiliation(s)
- Nicole M Brundridge
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Danzhou Yang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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Dias DM, Coombes SR, Benstead D, Whittaker DTE, Ray A, Xu J. Advances in the Specificity of Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy Based Structural Characterisation Methods for Synthetic Oligonucleotides. J Pharm Sci 2023; 112:2524-2531. [PMID: 37105438 DOI: 10.1016/j.xphs.2023.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
Identity testing is a critical part in the development of a therapeutic synthetic oligonucleotide. Tandem Mass Spectrometry (MS/MS) is commonly used for the analysis of oligonucleotides to obtain structural and sequence information, however there are challenges resulting from chemical modifications introduced to improve their pharmacokinetics and stability. For these structurally complex oligonucleotides, Nuclear Magnetic Resonance (NMR) Spectroscopy has found limited use for characterisation and identity testing, as only partial NMR resonance assignment for oligonucleotides is achieved without isotopic labelling methodologies. Regardless of the choice of method used for oligonucleotide analysis, the specificity is of critical importance. In this work, in-source dissociation mass spectrometry and proton (1H) and carbon (13C) NMR at high temperature were used to analyse danvatirsen, a 16 nucleotide phosphorothioate antisense oligonucleotide, and its closely related switch sequences. Both approaches have shown specificity to distinguish danvatirsen from these similar sequences.
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Affiliation(s)
- David M Dias
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - Steven R Coombes
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - David Benstead
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK
| | - David T E Whittaker
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Andrew Ray
- New Modalities Parenteral Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UK.
| | - Jingshu Xu
- Cellzome, Meyerhofstraße, Heidelberg, Germany
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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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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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8
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Schürch S. Characterization of nucleic acids by tandem mass spectrometry - The second decade (2004-2013): From DNA to RNA and modified sequences. MASS SPECTROMETRY REVIEWS 2016; 35:483-523. [PMID: 25288464 DOI: 10.1002/mas.21442] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 05/04/2014] [Accepted: 05/04/2014] [Indexed: 06/03/2023]
Abstract
Nucleic acids play key roles in the storage and processing of genetic information, as well as in the regulation of cellular processes. Consequently, they represent attractive targets for drugs against gene-related diseases. On the other hand, synthetic oligonucleotide analogues have found application as chemotherapeutic agents targeting cellular DNA and RNA. The development of effective nucleic acid-based chemotherapeutic strategies requires adequate analytical techniques capable of providing detailed information about the nucleotide sequences, the presence of structural modifications, the formation of higher-order structures, as well as the interaction of nucleic acids with other cellular components and chemotherapeutic agents. Due to the impressive technical and methodological developments of the past years, tandem mass spectrometry has evolved to one of the most powerful tools supporting research related to nucleic acids. This review covers the literature of the past decade devoted to the tandem mass spectrometric investigation of nucleic acids, with the main focus on the fundamental mechanistic aspects governing the gas-phase dissociation of DNA, RNA, modified oligonucleotide analogues, and their adducts with metal ions. Additionally, recent findings on the elucidation of nucleic acid higher-order structures by tandem mass spectrometry are reviewed. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:483-523, 2016.
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Affiliation(s)
- Stefan Schürch
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland
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Brodbelt JS. Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem Soc Rev 2014; 43:2757-83. [PMID: 24481009 PMCID: PMC3966968 DOI: 10.1039/c3cs60444f] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.
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Fragmentation Reactions of Nucleic Acid Ions in the Gas Phase. PHYSICAL CHEMISTRY IN ACTION 2014. [DOI: 10.1007/978-3-642-54842-0_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Martens SM, Marta RA, Martens JK, McMahon TB. Consecutive fragmentation mechanisms of protonated ferulic acid probed by infrared multiple photon dissociation spectroscopy and electronic structure calculations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1697-1706. [PMID: 22864827 DOI: 10.1007/s13361-012-0438-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 06/21/2012] [Accepted: 06/23/2012] [Indexed: 06/01/2023]
Abstract
Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm(-1). The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.
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