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Sattler C, Ceylan B, Hoffmann L, Juric A, Kraus J, Marandi S, Shahnazari A, Rühl M. Sequence confirmation of synthetic DNA exceeding 100 nucleotides using restriction enzyme mediated digestion combined with high-resolution tandem mass spectrometry. J Pharm Biomed Anal 2024; 245:116180. [PMID: 38703748 DOI: 10.1016/j.jpba.2024.116180] [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: 12/21/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024]
Abstract
Oligonucleotides have emerged as important therapeutic options for inherited diseases. In recent years, RNA therapeutics, especially mRNA, have been pushed to the market. Analytical methods for these molecules have been published extensively in the last few years. Notably, mass spectrometry has proven as a state-of-the-art quality control method. For RNA based therapeutics, numerous methods are available, while DNA therapeutics lack of suitable MS-based methods when it comes to molecules exceeding approximately 60 nucleotides. We present a method which combines the use of common restriction enzymes and short enzyme-directing oligonucleotides to generate DNA digestion products with the advantages of high-resolution tandem mass spectrometry. The instrumentation includes ion pair reverse phase chromatography coupled to a time-of-flight mass spectrometer with a collision induced dissociation (CID) for sequence analysis. Utilizing this approach, we increased the sequence coverage from 23.3% for a direct CID-MS/MS experiment of a 100 nucleotide DNA molecule to 100% sequence coverage using the restriction enzyme mediated approach presented in this work. This approach is suitable for research and development and quality control purposes in a regulated environment, which makes it a versatile tool for drug development.
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Affiliation(s)
| | - Burak Ceylan
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Luisa Hoffmann
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Andela Juric
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Julia Kraus
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Shima Marandi
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Aref Shahnazari
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Michael Rühl
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany.
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2
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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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Abdullah AM, Sommers C, Rodriguez JD, Zhang D, Kozak D, Hawes J, Sapru M, Yang K. Decoding Complexity in Synthetic Oligonucleotides: Unraveling Coeluting Isobaric Impurity Ions by High Resolution Mass Spectrometry. Anal Chem 2024; 96:904-909. [PMID: 38158374 PMCID: PMC10794994 DOI: 10.1021/acs.analchem.3c05016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Analyzing coeluting impurities with similar masses in synthetic oligonucleotides by liquid chromatography-mass spectrometry (LC-MS) poses challenges due to inadequate separation in either dimension. Herein, we present a direct method employing fully resolved isotopic envelopes, enabled by high resolution mass spectrometry (HRMS), to identify and quantify isobaric impurity ions resulting from the deletion or addition of a uracil (U) or cytosine (C) nucleotide from or to the full-length sequence. These impurities may each encompass multiple sequence variants arising from various deletion or addition sites. The method utilizes a full or targeted MS analysis to measure accurate isotopic distributions that are chemical formula dependent but nucleotide sequence independent. This characteristic enables the quantification of isobaric impurity ions involving sequence variants, a capability typically unavailable in sequence-dependent MS/MS methods. Notably, this approach does not rely on standard curves to determine isobaric impurity compositions in test samples; instead, it utilizes the individual isotopic distributions measured for each impurity standard. Moreover, in cases where specific impurity standards are unavailable, the measured isotopic distributions can be adequately replaced with the theoretical distributions (calculated based on chemical formulas of standards) adjusted using experiment-specific correction factors. In summary, this streamlined approach overcomes the limitations of LC-MS analysis for coeluting isobaric impurity ions, offering a promising solution for the in-depth profiling of complex impurity mixtures in synthetic oligonucleotide therapeutics.
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Affiliation(s)
- A. M. Abdullah
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| | - Cynthia Sommers
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| | - Jason D. Rodriguez
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| | - Deyi Zhang
- Division
of Therapeutic Performance I, Office of Research and Standards, Office
of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Darby Kozak
- Division
of Therapeutic Performance I, Office of Research and Standards, Office
of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Jessica Hawes
- Division
of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, United States
| | - Mohan Sapru
- Division
of New Drug Product III, Office of New Drug Product, Office of Pharmaceutical
Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Kui Yang
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
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Hannauer F, Black R, Ray AD, Stulz E, Langley GJ, Holman SW. Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9596. [PMID: 37580500 PMCID: PMC10909466 DOI: 10.1002/rcm.9596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 08/16/2023]
Abstract
The fragmentation of oligonucleotides by mass spectrometry allows for the determination of their sequences. It is necessary to understand how oligonucleotides dissociate in the gas phase, which allows interpretation of data to obtain sequence information. Since 2014, a range of fragmentation mechanisms, including a novel internal rearrangement, have been proposed using different ion dissociation techniques. The recent publications have focused on the fragmentation of modified oligonucleotides such as locked nucleic acids, modified nucleobases (methylated, spacer, nebularine and aminopurine) and modification to the carbon 2'-position on the sugar ring; these modified oligonucleotides are of great interest as therapeutics. Comparisons of different dissociation techniques have been reported, including novel approaches such as plasma electron detachment dissociation and radical transfer dissociation. This review covers the period 2014-2022 and details the new knowledge gained with respect to oligonucleotide dissociation using tandem mass spectrometry (without priori sample digestion) during that time, with a specific focus on synthetic single-stranded oligonucleotides.
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Affiliation(s)
- Fabien Hannauer
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Rachelle Black
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Andrew D. Ray
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Eugen Stulz
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - G. John Langley
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Stephen W. Holman
- Chemical Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
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Sun RX, Zuo MQ, Zhang JS, Dong MQ. Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37463304 DOI: 10.1021/jasms.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1- to 5-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.
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Affiliation(s)
- Rui-Xiang Sun
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Ji-Shuai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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Li F, Chen S, Studzińska S, Lämmerhofer M. Polybutylene terephthalate-based stationary phase for ion-pair-free reversed-phase liquid chromatography of small interfering RNA. Part 2: Use for selective comprehensive two-dimensional liquid chromatography. J Chromatogr A 2023; 1701:464069. [PMID: 37216850 DOI: 10.1016/j.chroma.2023.464069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/06/2023] [Accepted: 05/13/2023] [Indexed: 05/24/2023]
Abstract
With the increasing numbers of nucleic acid-based pharmaceuticals like antisense oligonucleotides (ASO), small interfering ribonucleic acid (siRNA) entering the market, research facilities, pharmaceutical industries and also regulatory authorities have been looking for efficient analytical methods for these synthetic oligonucleotides (ON). Besides of conventional one-dimensional (1D) reversed-phase liquid chromatography with or without ion-pairing (IP-RP-LC, RP-LC), hydrophilic liquid chromatography (HILIC) and mixed-mode chromatography (MMC), two-dimensional (2D) approaches combining two orthogonal chromatographic techniques also become more relevant due to the high structural complexity of oligonucleotides. Recently, we tested a polybutylene terephthalate(PBT)-based stationary phase under ion-pairing free RP mode for the liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS) analysis of siRNA (Patisiran). In this study, retention profile and chromatographic orthogonality, respectively, were compared to other LC-modes like HILIC, IP-RPLC, another ion-pair free cholesterol-bonded RPLC and MMC considering their normalized retention times. Finally, because of higher orthogonality, the ion-pairing free PBT-bonded RPLC as first dimension (1D) was hyphenated with HILIC in the second dimension (2D) in a selective comprehensive 2D-LC setup leading to an enhanced resolution for peak purity evaluation of the main ON entities.
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Affiliation(s)
- Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Shenkai Chen
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Sylwia Studzińska
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 7 Gagarin Str., PL-87-100 Toruń, Poland
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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Investigation of the Influence of Charge State and Collision Energy on Oligonucleotide Fragmentation by Tandem Mass Spectrometry. Molecules 2023; 28:molecules28031169. [PMID: 36770836 PMCID: PMC9921629 DOI: 10.3390/molecules28031169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Due to the increasing pharmaceutical interest of oligonucleotides, for example in antisense therapy and vaccines, their analytical characterization is of fundamental importance due to their complex structure. For this purpose, mass spectrometry is a viable tool for structural studies of nucleic acids. Structural information regarding the primary sequence of a nucleic acid can reliably be gained via tandem mass spectrometry (MSMS) fragmentation. In this work, we present the characteristic fragmentation behavior of short-chain oligonucleotides (15-35 nucleotides) with respect to the collision-induced dissociation (CID) voltage used. The relationship and influence of the length of the oligonucleotide and its charge state is also discussed. The results presented here can be helpful for estimating the required fragmentation energies of short-chain oligonucleotides and their sequencing.
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