1
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Rahman M, Marzullo BP, Lam PY, Barrow MP, Holman SW, Ray AD, O'Connor PB. Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS. Analyst 2024; 149:4687-4701. [PMID: 39101388 PMCID: PMC11382339 DOI: 10.1039/d4an00484a] [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: 08/06/2024]
Abstract
Antisense oligonucleotides (ASOs) are crucial for biological applications as they bind to complementary RNA sequences, modulating protein expression. ASOs undergo synthetic modifications like phosphorothioate (PS) backbone and locked nucleic acid (LNA) to enhance stability and specificity. Tandem mass spectrometry (MS) techniques were employed to study gapmer ASOs, which feature a DNA chain within RNA segments at both termini, revealing enhanced cleavages with ultraviolet photodissociation (UVPD) and complementary fragment ions from collision-induced dissociation (CID) and electron detachment dissociation (EDD). 2DMS, a data-independent analysis technique, allowed for comprehensive coverage and identification of shared fragments across multiple precursor ions. EDD fragmentation efficiency correlated with precursor ion charge states, with higher charges facilitating dissociation due to intramolecular repulsions. An electron energy of 22.8 eV enabled electron capture and radical-based cleavage. Accumulating multiple scans and generating average spectra improved signal intensity, aided by denoising algorithms. Data analysis utilised a custom Python script capable of handling modifications and generating unique mass lists.
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Affiliation(s)
- Mohammed Rahman
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Bryan P Marzullo
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Pui Yiu Lam
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, AstraZeneca, SK10 2NA, UK
| | - Andrew D Ray
- New Modalities & Parental Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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2
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Avila JD, Wang P. Mass Spectrometry as a Quantitative Tool for SpCas9 sgRNA Quality Control. Nucleic Acid Ther 2024. [PMID: 39178119 DOI: 10.1089/nat.2024.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2024] Open
Abstract
Mass spectrometry (MS) has long been used for quality control of oligonucleotide therapeutics, including single-guide RNAs (sgRNAs) for clustered regularly interspaced short palindromic repeats techniques. However, the application of MS is limited to qualitative assays in most cases. Here, we showed that electrospray-ionization quadrupole time-of-flight MS (ESI-QTOF-MS) assays can be quantitative for chemical species found in sgRNA samples. More specifically, using a 100-nt SpCas9 sgRNA as the example, we estimated that the limits of quantification for length variants in the range of N - 4 to N + 4 (i.e., 96-104 nucleotides) were equal to or lower than 1%. Our study highlighted the potential of ESI-QTOF in its application as a quality control method for sgRNA molecules.
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Affiliation(s)
| | - Puzhou Wang
- Synthego Corporation, Redwood City, California, USA
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3
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Lippens JL, Florenzi B, Da Silva KM, Liu Y, Neefs T, Sauwen N, De Vijlder T. SynONIM: A Comprehensive Database of Synthetic Oligonucleotide Modifications and Impurities to Aid in Their Characterization by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39009439 DOI: 10.1021/jasms.4c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Given the resurgence of oligonucleotides in the biotherapeutic space, there is a profound focus on their characterization by mass spectrometry. These therapeutic moieties commonly employ synthetic modifications to aid in increasing efficacy and stability; however, these modifications can also increase the complexity of mass spectrometry data analysis. Additionally, various stress conditions can affect both the observed level and type of impurities stemming from the variety of utilized modifications. Within the oligonucleotide analytical development community, a clear desire exists for a unified database of synthetic oligonucleotide modifications and impurities where information regarding structure, mass, and shorthand nomenclature can be contained. To address this, the authors have prepared an online database and webtool of synthetic oligonucleotide impurities and modifications, SynONIM, to centrally locate information key to the mass spectrometry community. SynONIM can be queried by elemental composition lost or gained, mass shift, shorthand notation, nucleotide location, and species origin.
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Affiliation(s)
| | | | | | - Youzhong Liu
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Thomas Neefs
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Nicolas Sauwen
- Open Analytics NV, Jupiterstraat 20, 2600 Antwerpen, Belgium
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4
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Biggiogera M, Cavallo M, Casali C. A brief history of the Feulgen reaction. Histochem Cell Biol 2024; 162:3-12. [PMID: 38609528 PMCID: PMC11227455 DOI: 10.1007/s00418-024-02279-9] [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] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
Abstract
One hundred years ago, Robert Feulgen published a landmark paper in which he described the first method to stain DNA in cells and tissues. Although a century has passed since the discovery by Feulgen and Rossenbeck, the chemical reaction still exerts an important influence in current histochemical studies. Its contribution in diverse fields, spanning from biomedicine to plant biology, has paved the way for the most significant studies that constitute our current knowledge. The possibility to specifically explore the DNA in cell nuclei while quantifying its content makes it a contemporary and timeless method. Indeed, many histocytochemical studies following the 1924 paper have led to a deep understanding of genome organization in general as well as several specific mechanisms (e.g. DNA duplication or tumour pathology) that, nowadays, constitute some of the most fundamental pillars in biological investigations. In this review, we discuss the chemistry and application of the Feulgen reaction to both light and electron microscopy.
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Affiliation(s)
- Marco Biggiogera
- Cell Biology and Neurobiology Laboratory, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A.Ferrata 9, 27100, Pavia, Italy.
| | - Margherita Cavallo
- Cell Biology and Neurobiology Laboratory, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A.Ferrata 9, 27100, Pavia, Italy
| | - Claudio Casali
- Cell Biology and Neurobiology Laboratory, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A.Ferrata 9, 27100, Pavia, Italy
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5
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Herbert C, Valesyan S, Kist J, Limbach PA. Analysis of RNA and Its Modifications. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:47-68. [PMID: 38594935 DOI: 10.1146/annurev-anchem-061622-125954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Ribonucleic acids (RNAs) are key biomolecules responsible for the transmission of genetic information, the synthesis of proteins, and modulation of many biochemical processes. They are also often the key components of viruses. Synthetic RNAs or oligoribonucleotides are becoming more widely used as therapeutics. In many cases, RNAs will be chemically modified, either naturally via enzymatic systems within a cell or intentionally during their synthesis. Analytical methods to detect, sequence, identify, and quantify RNA and its modifications have demands that far exceed requirements found in the DNA realm. Two complementary platforms have demonstrated their value and utility for the characterization of RNA and its modifications: mass spectrometry and next-generation sequencing. This review highlights recent advances in both platforms, examines their relative strengths and weaknesses, and explores some alternative approaches that lie at the horizon.
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Affiliation(s)
- Cassandra Herbert
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Satenik Valesyan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Jennifer Kist
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
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6
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Prostko P, Radziński P, Ciach M, Liu Y, Startek M, Lermyte F, De Vijlder T, Gambin A, Appeltans S, Valkenborg D. MIND4OLIGOS: Determining the Monoisotopic Mass of Oligonucleotides Observed in High-Resolution Mass Spectrometry. Anal Chem 2024; 96:9343-9352. [PMID: 38804718 PMCID: PMC11342294 DOI: 10.1021/acs.analchem.3c04351] [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: 09/26/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Oligonucleotide therapeutics have emerged as an important class of drugs offering targeted therapeutic strategies that complement traditional modalities, such as monoclonal antibodies and small molecules. Their unique ability to precisely modulate gene expression makes them vital for addressing previously undruggable targets. A critical aspect of developing these therapies is characterizing their molecular composition accurately. This includes determining the monoisotopic mass of oligonucleotides, which is essential for identifying impurities, degradants, and modifications that can affect the drug efficacy and safety. Mass spectrometry (MS) plays a pivotal role in this process, yet the accurate interpretation of complex mass spectra remains challenging, especially for large molecules, where the monoisotopic peak is often undetectable. To address this issue, we have adapted the MIND algorithm, originally developed for top-down proteomics, for use with oligonucleotide data. This adaptation allows for the prediction of monoisotopic mass from the more readily detectable, most-abundant peak mass, enhancing the ability to annotate complex spectra of oligonucleotides. Our comprehensive validation of this modified algorithm on both in silico and real-world oligonucleotide data sets has demonstrated its effectiveness and reliability. To facilitate wider adoption of this advanced analytical technique, we have encapsulated the enhanced MIND algorithm in a user-friendly Shiny application. This online platform simplifies the process of annotating complex oligonucleotide spectra, making advanced mass spectrometry analysis accessible to researchers and drug developers. The application is available at https://valkenborg-lab.shinyapps.io/mind4oligos/.
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Affiliation(s)
- Piotr Prostko
- Faculty
of Science, Data Science Institute, Interuniversity Institute for
Biostatistics and statistical Bioinformatics, Center for Statistics, Hasselt University, Agoralaan, Diepenbeek BE 3500, Belgium
| | - Piotr Radziński
- Institute
of Informatics, University of Warsaw, Banacha 2, Warszawa PL 02-097, Poland
| | - Michał Ciach
- Institute
of Informatics, University of Warsaw, Banacha 2, Warszawa PL 02-097, Poland
| | - Youzhong Liu
- Johnson
& Johnson Innovative Medicine, Therapeutics Development &
Supply, Turnhoutseweg
30, Beerse BE 2340, Belgium
| | - Michał Startek
- Institute
of Informatics, University of Warsaw, Banacha 2, Warszawa PL 02-097, Poland
- University
Medical Center of the Johannes Gutenberg University Mainz, Institute
of Immunology, Mainz, Rheinland-Pfalz 55131, Germany
| | - Frederik Lermyte
- Department
of Chemistry, Technical University of Darmstadt, Darmstadt, Hessen 64289, Germany
- Centre
for
Synthetic Biology, Technical University
of Darmstadt, Darmstadt, Hessen 64289, Germany
| | - Thomas De Vijlder
- Johnson
& Johnson Innovative Medicine, Therapeutics Development &
Supply, Turnhoutseweg
30, Beerse BE 2340, Belgium
| | - Anna Gambin
- Institute
of Informatics, University of Warsaw, Banacha 2, Warszawa PL 02-097, Poland
| | - Simon Appeltans
- Faculty
of Science, Data Science Institute, Interuniversity Institute for
Biostatistics and statistical Bioinformatics, Center for Statistics, Hasselt University, Agoralaan, Diepenbeek BE 3500, Belgium
| | - Dirk Valkenborg
- Faculty
of Science, Data Science Institute, Interuniversity Institute for
Biostatistics and statistical Bioinformatics, Center for Statistics, Hasselt University, Agoralaan, Diepenbeek BE 3500, Belgium
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7
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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [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: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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8
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Bui QD, Deschrijver T, Noten B, Verluyten W, Vervoort N, Eeltink S. Optimization of elution conditions and comparison of emerging biocompatible columns on the resolving power and detection sensitivity of oligonucleotides by ion-pairing reversed-phase liquid chromatography mass spectrometry. J Chromatogr A 2024; 1720:464793. [PMID: 38484639 DOI: 10.1016/j.chroma.2024.464793] [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: 01/18/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024]
Abstract
A generic performance comparison strategy has been developed to evaluate the impact of mobile-phase additives (ion-pairing agent / counter ion systems), distinct stationary phases on resulting resolving power, and MS detectability of oligonucleotides and their critical impurities in gradient IP-RPLC. Stationary-phase considerations included particle type (core-shell vs. fully porous particles), particle diameter, and pore size. Separations were carried out at 60°C to optimize mass transfer (C-term). The incorporation of an active column preheater mitigated thermal mismatches, leading to narrower peaks and overcoming peak splitting. Acetonitrile as organic modifier outweighed methanol in terms of peak-capacity generation and yielded a 30% lower back pressure. Performance screening experiments were conducted varying ion-pairing agents and counter ions, while adjusting gradient span achieved an equivalent effective retention window. Hexafluoromethylisopropanol yielded superior chromatographic resolution, whereas hexafluoroisopropanol yielded significantly higher MS detection sensitivity. The 1.7 µm core-shell particle columns with 100 Å pores provided maximum resolving power for small (15-35 mers) oligonucleotides. Sub-min analysis for 15-35 polyT ladders was achieved operating a 50 mm long column at the kinetic performance limits. High-resolution separations between a 21-mer modified RNA sequence oligonucleotides and its related (shortmer and phosphodiester) impurities and complementary strand were obtained using a coupled column set-up with a total length of 450 mm.
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Affiliation(s)
- Quang-Dong Bui
- Vrije Universiteit Brussel (VUB), Department of Chemical Engineering, Brussels, Belgium
| | - Tiny Deschrijver
- Janssen Pharmaceutica, Process Analytical Research - Chemical Process Research and Development, Beerse, Belgium
| | - Bart Noten
- Janssen Pharmaceutica, Process Analytical Research - Chemical Process Research and Development, Beerse, Belgium
| | - Willy Verluyten
- Janssen Pharmaceutica, Analytical Development, Beerse, Belgium
| | - Nico Vervoort
- Janssen Pharmaceutica, Process Analytical Research - Chemical Process Research and Development, Beerse, Belgium
| | - Sebastiaan Eeltink
- Vrije Universiteit Brussel (VUB), Department of Chemical Engineering, Brussels, Belgium.
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9
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Ozaki M, Kuwayama T, Shimotsuma M, Hirose T. Separation and purification of short-, medium-, and long-stranded RNAs by RP-HPLC using different mobile phases and C 18 columns with various pore sizes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1948-1956. [PMID: 38445900 DOI: 10.1039/d4ay00114a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Nucleic acids, which have been employed in medicines for various diseases, are attracting attention as a new pharmaceutical model. Depending on the target substances, nucleic acid medicines with various nucleic acid chain lengths (several tens of nucleotides [nt] to several thousands of nt) exist. The purification of synthesized nucleic acids is crucial as various impurities remain in the crude product after synthesis. Presently, reversed-phase high-performance liquid chromatography (RP-HPLC) represents an effective purification method for nucleic acids. However, the information regarding the HPLC conditions for separating and purifying nucleic acids of various chain lengths is insufficient. Thus, this technical note describes the separation and purification of short-, medium-, and long-stranded nucleic acids (several tens of nt to thousands of nt) by RP-HPLC with various mobile phases and octadecyl-based columns with various pore sizes, such as normal (9-12 nm), wide (30 nm), and super wide (>30 nm) pores.
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Affiliation(s)
- Makoto Ozaki
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tomomi Kuwayama
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Motoshi Shimotsuma
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tsunehisa Hirose
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
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10
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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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11
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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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12
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Gawlig C, Hanci G, Rühl M. Quantification of Oligonucleotides Using Tandem Mass Spectrometry with Isobaric Internal Standards. Int J Mol Sci 2023; 24:14691. [PMID: 37834137 PMCID: PMC10573027 DOI: 10.3390/ijms241914691] [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: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In recent years, oligonucleotides have become more important in research, drug approvals and medical therapies. Due to this growing interest in pharmaceutical applications, it is essential to develop reliable analytical methods for this substance class. In this work, we present a quantification method using liquid chromatography coupled with tandem mass spectrometry by applying an isobaric oligonucleotide standard. In addition to a proof of principle, we perform a method qualification to assess its readiness for validation according to ICH Q2 guidelines. In addition to good linearity, sensitivity, accuracy and recovery, the method showed no significant matrix effects. Furthermore, we demonstrated the application of the method by applying the quantification in a biological matrix, as well as an exemplary degradation of an oligonucleotide in bovine plasma.
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Affiliation(s)
| | | | - Michael Rühl
- BioSpring GmbH, Alt Fechenheim 34, 60386 Frankfurt am Main, Germany; (C.G.); (G.H.)
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13
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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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14
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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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15
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Chen ML, Mekhssian K, Dutt M, Plomley J, Keyhani A. Volumetric absorptive microsampling coupled with hybridization LC-MS/MS for quantitation of antisense oligonucleotides. Bioanalysis 2023; 15:1115-1128. [PMID: 37681562 DOI: 10.4155/bio-2023-0092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Abstract
Background: Volumetric absorptive microsampling has emerged as a less invasive alternative to venous sampling for small-molecule pharmacokinetic studies, but its application to novel therapeutics such as antisense oligonucleotides (ASOs) is not well-established. Results: A workflow was developed using Mitra microsampling coupled with hybridization LC-MS/MS for accurate determination of fomivirsen, a 21-mer ASO, in human blood. Quantitative recovery was achieved regardless of blood hematocrit level or microsample age by implementing impact-assisted extraction. A thorough method evaluation confirmed sensitivity, linearity, precision/accuracy, matrix effect, metabolite interference and four months of microsample stability. Conclusion: The combined impact-assisted extraction and hybridization LC-MS/MS workflow demonstrated the successful quantitation of fomivirsen, establishing the validity and applicability of the approach for ASO drug candidates.
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Affiliation(s)
- Ming-Luan Chen
- Altasciences, 575 Armand-Frappier Blvd., Laval, QC, H7V 4B3, Canada
| | - Kevork Mekhssian
- Altasciences, 575 Armand-Frappier Blvd., Laval, QC, H7V 4B3, Canada
| | - Muskaan Dutt
- Altasciences, 575 Armand-Frappier Blvd., Laval, QC, H7V 4B3, Canada
| | - Jeff Plomley
- Altasciences, 575 Armand-Frappier Blvd., Laval, QC, H7V 4B3, Canada
| | - Anahita Keyhani
- Altasciences, 575 Armand-Frappier Blvd., Laval, QC, H7V 4B3, Canada
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16
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Sorensen MJ, Paulines MJ, Maloney TD. Evaluating orthogonality between ion-pair reversed phase, anion exchange, and hydrophilic interaction liquid chromatography for the separation of synthetic oligonucleotides. J Chromatogr A 2023; 1705:464184. [PMID: 37419013 DOI: 10.1016/j.chroma.2023.464184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/09/2023]
Abstract
The orthogonality of separation between ion-pair reversed phase (IP-RP), anion exchange (AEX), and hydrophilic interaction liquid chromatography (HILIC) was evaluated for oligonucleotides. A polythymidine standard ladder was first used to evaluate the three methods and showed zero orthogonality, where retention and selectivity were based on oligonucleotide charge/size under all three conditions. Next, a model 23-mer synthetic oligonucleotide containing 4 phosphorothioate bonds with 2' fluoro and 2'-O-methyl ribose modifications typical of small interfering RNA was used for evaluating orthogonality. The resolution and orthogonality were evaluated between the three modes of chromatography in terms of selectivity differences for nine common impurities, including truncations (n-1, n-2), addition (n + 1), oxidation, and de-fluorination. We first evaluated different ion-pairing reagents that provided the best separation of the key impurities while suppressing diastereomer separation due to phosphorothioate linkages. Although different ion-pairing reagents affected resolution, very little orthogonality was observed. We then compared the retention times between IP-RP, HILIC, and AEX for each impurity of the model oligonucleotide and observed various selectivity changes. The results suggest that coupling HILIC with either AEX or IP-RP provide the highest degree of orthogonality due to the differences in retention for hydrophilic nucleobases and modifications under HILIC conditions. IP-RP provided the highest overall resolution for the impurity mixture, whereas more co-elution was observed with HILIC and AEX. The unique selectivity patterns offered by HILIC provides an interesting alternative to IP-RP or AEX, in addition to the potential for coupling with multidimensional separations. Future work should explore orthogonality for oligonucleotides with subtle sequence differences such as nucleobase modifications and base flip isomers, longer strands such as guide RNA and messenger RNA, and other biotherapeutic modalities such as peptides, antibodies, and antibody-drug-conjugates.
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Affiliation(s)
- Matthew J Sorensen
- Synthetic Molecule Design and Development, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Mellie June Paulines
- Synthetic Molecule Design and Development, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Todd D Maloney
- Synthetic Molecule Design and Development, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN 46285, United States.
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17
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Macias LA, Garcia SP, Back KM, Wu Y, Johnson GH, Kathiresan S, Bellinger AM, Rohde E, Freitas MA, Madsen JA. Spacer Fidelity Assessments of Guide RNA by Top-Down Mass Spectrometry. ACS CENTRAL SCIENCE 2023; 9:1437-1452. [PMID: 37521788 PMCID: PMC10375574 DOI: 10.1021/acscentsci.3c00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Indexed: 08/01/2023]
Abstract
The advancement of CRISPR-based gene editing tools into biotherapeutics offers the potential for cures to genetic disorders and for new treatment paradigms for even common diseases. Arguably, the most important component of a CRISPR-based medicine is the guide RNA, which is generally large (>100-mer) synthetic RNA composed of a "tracr" and "spacer" region, the latter of which dictates the on-target editing site as well as potential undesired off-target edits. Aiming to advance contemporary capabilities for gRNA characterization to ensure the spacer region is of high fidelity, top-down mass spectrometry was herein implemented to provide direct and quantitative assessments of highly modified gRNA. In addition to sequencing the spacer region and pinpointing modifications, top-down mass spectra were utilized to quantify single-base spacer substitution impurities down to <1% and to decipher highly dissimilar spacers. To accomplish these results in an automated fashion, we devised custom software capable of sequencing and quantifying impurities in gRNA spacers. Notably, we developed automated tools that enabled the quantification of single-base substitutions, including advanced isotopic pattern matching for C > U and U > C substitutions, and created a de novo sequencing strategy to facilitate the identification and quantification of gRNA impurities with highly dissimilar spacer regions.
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Affiliation(s)
- Luis A. Macias
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Sara P. Garcia
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Kayla M. Back
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Yue Wu
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - G. Hall Johnson
- MassMatrix,
Inc., 600 Teteridge Road, Columbus, Ohio 43214, United States
| | - Sekar Kathiresan
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Andrew M. Bellinger
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Ellen Rohde
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Michael A. Freitas
- MassMatrix,
Inc., 600 Teteridge Road, Columbus, Ohio 43214, United States
- The
Ohio State University, 281 West Lane Avenue, Columbus, Ohio 43210, United States
| | - James A. Madsen
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
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18
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Becette OB, Marino JP, Brinson RG. Structural Fingerprinting of Antisense Oligonucleotide Therapeutics by Solution NMR Spectroscopy. Pharm Res 2023; 40:1373-1382. [PMID: 36195820 DOI: 10.1007/s11095-022-03403-x] [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: 06/14/2022] [Accepted: 09/21/2022] [Indexed: 10/10/2022]
Abstract
PURPOSE Antisense oligonucleotide (ASO) therapeutics are an emerging class of biopharmaceuticals to treat and prevent diseases, particularly those involving "undruggable" protein targets. Impurities generated throughout the ASO drug manufacturing and formulation pipeline can be detrimental to drug safety and efficacy. Therefore, analytical techniques are needed to rigorously characterize these molecules for quality assurance purposes. METHODS We demonstrate 1D and 2D nuclear magnetic resonance (NMR) spectroscopy methods that can generate high-resolution structural "fingerprints" of ASOs. RESULTS AND CONCLUSIONS 1D 1H and 31P measurements are shown to provide rapid initial assessment of the ASO integrity. In particular, a well-resolved pair of 31P signals arising from the 5´-end of the phosphorodiamidate morpholino oligomer (PMO) are sensitive to complex formation and oligomerization state. 2D 1H-1H, 1H-13C, and 1H-15 N experiments, although less sensitive, are further shown to enable resonance assignment, which will allow the tracking of structural changes at high-resolution during the drug development and manufacturing processes. We further anticipate that the described NMR approaches will be broadly applicable to fully formulated ASO therapeutics, including modalities other than PMOs.
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Affiliation(s)
- Owen B Becette
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA.
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19
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Guan B, Yan W, Stolee JA. Trace analysis of dimethoxytrityl alcohol (DMT-OH) in oligonucleotide matrices using liquid chromatography coupled with tandem mass spectrometry. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1054-1061. [PMID: 36722996 DOI: 10.1039/d2ay02020c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A liquid chromatography (LC) method with ultraviolet (UV) and tandem mass spectrometry (MS/MS) detection was developed to quantify dimethoxytrityl alcohol (DMT-OH), a small molecule byproduct generated during the detritylation reaction in oligonucleotide synthesis. The pros and cons of quantification via multiple analytical methods including LC coupled with UV, selected ion monitoring (SIM), and multiple reaction monitoring (MRM) were evaluated. The MRM method was ultimately selected for further qualification and exhibited good linearity (R2 = 0.997 from 0.5 to 64 ng mL-1), accuracy (recoveries ranging 75-90% with ≤ 2% RSD), repeatability (<5% RSD), and sensitivity (LOQ of 1.6 ng mL-1). The MRM method was further applied to analyze DMT-OH in various oligonucleotide intermediates and drug substances. Similar MRM methods for six other small molecule impurities (aniline, benzamide, isobutyramide, 2-phenylacetamide, succinamide, and uny-CTP) as well as their application are also presented.
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Affiliation(s)
- Bing Guan
- Biogen Inc., Cambridge, Massachusetts, USA
| | - Wuming Yan
- Biogen Inc., Cambridge, Massachusetts, USA
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20
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Togawa H, Okubo T, Nonaka Y, Yamaguchi T, Obika S. Retention behavior of short double-stranded oligonucleotide and its potential impurities by anion-exchange chromatography under non-denaturing conditions. J Chromatogr A 2023; 1691:463808. [PMID: 36706652 DOI: 10.1016/j.chroma.2023.463808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
Small interfering RNA (siRNA), consisting of two complementary single-stranded RNAs with overhanging bases, is being adopted as a potent and specific inhibitor of target gene expression. However, non-duplexed single strands and undesired double strands composed of impurities (e.g., n-1 mer) could be produced in addition to the target double strand in the siRNA manufacturing process. Compared to the liquid chromatography analysis of single strands, the analysis of the duplexes under non-denaturing conditions is challenging, since restricted chromatographic conditions are required to maintain the Watson-Crick hydrogen bonds. This study reports the analysis of double-stranded oligomers having approximately 20 base pairs with some overhanging bases as non-denatured forms by anion-exchange chromatography (AEX). Optimization of the chromatographic conditions could potentially achieve the adequate separation of excess single strands from the double strand. Non-optimal duplexes, such as duplexes with long overhangs or bulge structures, were prepared by intentionally deleting terminal or middle nucleotide(s) of either the sense or the antisense strand, and these non-optimal duplexes were eluted at different retention times in most of the cases. Interestingly, under alkaline chromatographic conditions (pH 9.0), non-optimal duplexes containing a shortmer tended to exhibit a stronger retention than their parent duplexes, although they possessed a less negative charge. This study demonstrated some retention behavior of double strands with overhangs by AEX under non-denaturing conditions.
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Affiliation(s)
- Hiroyuki Togawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takashi Okubo
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Yumi Nonaka
- CERI Kurume, Chemicals Evaluation and Research Institute, Japan, 3-2-7 Miyanojin, Kurume, Fukuoka 839-0801, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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21
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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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22
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Goyon A, Nguyen D, Boulanouar S, Yehl P, Zhang K. Characterization of Impurities in Therapeutic RNAs at the Single Nucleotide Level. Anal Chem 2022; 94:16960-16966. [PMID: 36410036 DOI: 10.1021/acs.analchem.2c04681] [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: 11/22/2022]
Abstract
The chemistry of guide RNA (gRNA) affects the performance of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome editing technique. However, the literature is very scarce about the study of gRNA degradation and in particular at the single nucleotide level. In this work, we developed a workflow to characterize the impurities of large RNAs at the single nucleotide level and identified the residues prone to degradation. Our strategy involves (i) the reduction of RNA length, (ii) a chromatographic mode able to capture subtle changes in impurity polarity, and (iii) a streamlined data treatment. To illustrate the approach, stressed gRNA samples were analyzed by coupling an immobilized ribonuclease T1 cartridge to a hydrophilic interaction liquid chromatography (HILIC) column hyphenated with tandem mass spectrometry (MS/MS). Critical findings were made possible by the presented technology. In particular, the desulfurization of phosphorothioate (PS) linkages was the major degradation observed at the single nucleotide level while no change in purity profile could be observed when using conventional ion-pairing reversed-phase (IPRP) liquid chromatography. To our knowledge, this is the first time that several impurity types are screened for a large RNA molecule using an automated online digestion analysis approach.
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Affiliation(s)
- Alexandre Goyon
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Nguyen
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Sara Boulanouar
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Yehl
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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23
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Osawa T, Ren Q, Obika S. Development of Phosphoramidite Reagents for the Synthesis of Base-Labile Oligonucleotides Modified with a Linear Aminoalkyl and Amino-PEG Linker at the 3'-End. Molecules 2022; 27:molecules27238501. [PMID: 36500594 PMCID: PMC9736658 DOI: 10.3390/molecules27238501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotides with an amino linker at the 3'-end are useful for the preparation of conjugated oligonucleotides. However, chemically modified nucleosides, which are unstable under basic conditions, cannot be incorporated into oligonucleotides using the conventional method entailing the preparation of oligonucleotides bearing a 3'-amino linker. Therefore, we designed Fmoc-protected phosphoramidites for the synthesis of base-labile oligonucleotides modified with a 3'-amino linker. The resultant phosphoramidites were then successfully incorporated into oligonucleotides bearing a 3'-amino linker. Various basic solutions were investigated for protecting group removal. All the protecting groups were removed by treating the oligonucleotides with 40% aqueous methylamine at room temperature for 2 h. Thus, the deprotection time and temperature were significantly reduced compared to the conventional conditions (28% NH3 aq., 55 °C, 17 h). In addition, the oligonucleotide protecting groups could be removed using a mild base (e.g., 50 mM potassium carbonate methanol solution). Furthermore, base-labile oligonucleotides bearing an amino linker at the 3'-end were successfully synthesized using the developed phosphoramidite reagents, highlighting the utility of our strategy.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
| | - Qin Ren
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Japan
- Correspondence: ; Tel.: +81-6-6879-8200
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24
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Studzińska S, Li F, Szumski M, Buszewski B, Lämmerhofer M. Cholesterol Stationary Phase in the Separation and Identification of siRNA Impurities by Two-Dimensional Liquid Chromatography-Mass Spectrometry. Int J Mol Sci 2022; 23:ijms232314960. [PMID: 36499291 PMCID: PMC9738757 DOI: 10.3390/ijms232314960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The aim of this research was to develop a simple and efficient ion-pair reagent-free chromatographic method for the separation and qualitative determination of oligonucleotide impurities, exemplified by synthesis of raw products of the two single strands of patisiran siRNA. The stationary phases with mixed hydrophobic/hydrophilic properties (cholesterol and alkylamide) were firstly used for this purpose with reversed-phased high-performance liquid chromatography. Several different chromatographic parameters were tested for their impact on impurities separation: type, concentration, pH of salt, as well as organic solvent type in the mobile phase. The pH was the most influential factor on the separation and signal intensities in mass spectrometry detection. Finally, the optimized method included the application of cholesterol stationary phase, with mobile phase containing 20 mM ammonium formate (pH 6.5) and methanol. It allowed good separation and the identification of most impurities within 25 min. Since not all closely related impurities could be fully resolved from the main peak in this oligonucleotide impurity profiling, two-dimensional liquid chromatography was used for peak purity determination of the target oligonucleotides. The Ethylene Bridged Hybrid (BEH) Amide column in hydrophilic interaction liquid chromatography was applied in the second dimension, allowing additional separation of three closely related impurities.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., 87-100 Toruń, Poland
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +48-56-6114753
| | - Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michał Szumski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 4 Wilenska St., 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., 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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25
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Alharbi KS, Javed Shaikh MA, Afzal O, Alfawaz Altamimi AS, Hassan almalki W, Kazmi I, Al-Abbasi FA, Alzarea SI, Babu MR, Singh SK, Chellappan DK, Dua K, Gupta G. Oligonucleotides: A novel area of interest for drug delivery in neurodegenerative diseases. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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26
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Quantification of synthetic errors during chemical synthesis of DNA and its suppression by non-canonical nucleosides. Sci Rep 2022; 12:12095. [PMID: 35840646 PMCID: PMC9287346 DOI: 10.1038/s41598-022-16222-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022] Open
Abstract
Substitutions, insertions, and deletions derived from synthetic oligonucleotides are the hurdles for the synthesis of long DNA such as genomes. We quantified these synthetic errors by next-generation sequencing and revealed that the quality of the enzymatically amplified final combined product depends on the conditions of the preceding solid phase chemical synthesis, which generates the initial pre-amplified fragments. Among all possible substitutions, the G-to-A substitution was the most prominently observed substitution followed by G-to-T, C-to-T, T-to-C, and A-to-G substitutions. The observed error rate for G-to-A substitution was influenced by capping conditions, suggesting that the capping step played a major role in the generation of G-to-A substitution. Because substitutions observed in long DNA were derived from the generation of non-canonical nucleosides during chemical synthesis, non-canonical nucleosides resistant to side reactions could be used as error-proof nucleosides. As an example of such error-proof nucleosides, we evaluated 7-deaza-2´-deoxyguanosine and 8-aza-7-deaza-2´-deoxyguanosine and showed 50-fold decrease in the error rate of G-to-A substitution when phenoxyacetic anhydride was used as capping reagents. This result is the first example that improves the quality of synthesized sequences by using non-canonical nucleosides as error-proof nucleosides. Our results would contribute to the development of highly accurate template DNA synthesis technologies.
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27
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Morreel K, t’Kindt R, Debyser G, Jonckheere S, Sandra P. Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography–Mass Spectrometry-Based Oligonucleotide Profiling. LCGC EUROPE 2022. [DOI: 10.56530/lcgc.eu.jk3969w4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The production process of in vitro transcribed messenger RNA (IVT-mRNA)-based vaccines has matured in recent years, partly due to the fight against infectious diseases such as COVID-19. One key to success has been the use of modified, next to canonical, nucleotides and the efficient addition of a Cap-structure and poly A tail to the 5’ and 3’ end, respectively, of this massive biomolecule. These important features affect mRNA stability and impact translation efficiency, consequently boosting the optimization and implementation of liquid chromatography–mass spectrometry (LC–MS)-based oligonucleotide profiling methods for their characterization. This article will provide an overview of these LC–MS methods at a fundamental and application level. It will be shown how LC–MS is implemented in mRNA-based vaccine analysis to determine the capping efficiency and the poly A tail length, and how it allows, via RNA mapping, (i) to determine the mRNA sequence, (ii) to screen the fidelity of the manufactured modifications, and (iii) to identify and quantify unwanted modifications resulting from manufacturing or storage, and sequence variants resulting from mutation or transcription errors.
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28
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Vervaeke P, Borgos SE, Sanders NN, Combes F. Regulatory guidelines and preclinical tools to study the biodistribution of RNA therapeutics. Adv Drug Deliv Rev 2022; 184:114236. [PMID: 35351470 PMCID: PMC8957368 DOI: 10.1016/j.addr.2022.114236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/09/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
The success of the messenger RNA-based COVID-19 vaccines of Moderna and Pfizer/BioNTech marks the beginning of a new chapter in modern medicine. However, the rapid rise of mRNA therapeutics has resulted in a regulatory framework that is somewhat lagging. The current guidelines either do not apply, do not mention RNA therapeutics, or do not have widely accepted definitions. This review describes the guidelines for preclinical biodistribution studies of mRNA/siRNA therapeutics and highlights the relevant differences for mRNA vaccines. We also discuss the role of in vivo RNA imaging techniques and other assays to fulfill and/or complement the regulatory requirements. Specifically, quantitative whole-body autoradiography, microautoradiography, mass spectrometry-based assays, hybridization techniques (FISH, bDNA), PCR-based methods, in vivo fluorescence imaging, and in vivo bioluminescence imaging, are discussed. We conclude that this new and rapidly evolving class of medicines demands a multi-layered approach to fully understand its biodistribution and in vivo characteristics.
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Affiliation(s)
- P Vervaeke
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - S E Borgos
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway
| | - N N Sanders
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
| | - F Combes
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway.
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29
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Abdullah AM, Sommers C, Hawes J, Rodriguez JD, Yang K. Tandem mass spectrometric sequence characterization of synthetic thymidine-rich oligonucleotides. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4819. [PMID: 35347805 PMCID: PMC9287059 DOI: 10.1002/jms.4819] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 05/30/2023]
Abstract
Tandem mass spectrometry (MS/MS) can provide direct and accurate sequence characterization of synthetic oligonucleotide drugs, including modified oligonucleotides. Multiple factors can affect oligonucleotide MS/MS sequencing, including the intrinsic properties of oligonucleotides (i.e., nucleotide composition and structural modifications) and instrument parameters associated with the ion activation for fragmentation. In this study, MS/MS sequencing of a thymidine (T)-rich and phosphorothioate (PS)-modified DNA oligonucleotide was investigated using two fragmentation techniques: trap-type collision-induced dissociation ("CID") and beam-type CID also termed as higher-energy collisional dissociation ("HCD"), preceded by a hydrophilic interaction liquid chromatography (HILIC) separation. A low to moderate charge state (-4), which predominated under the optimized HILIC-MS conditions, was selected as the precursor ion for MS/MS analysis. Comparison of the two distinctive ion activation mechanisms on the same precursor demonstrated that HCD was superior to CID in promoting higher sequence coverage and analytical sensitivity in sequence elucidation of T-rich DNA oligonucleotides. Specifically, HCD provided more sequence-defining fragments with higher fragment intensities than CID. Furthermore, the direct comparison between unmodified and PS-modified DNA oligonucleotides demonstrated a loss of MS/MS fragmentation efficiency by PS modification in both CID and HCD approaches, and a resultant reduction in sequence coverage. The deficiency in PS DNA sequence coverage observed with single collision energy HCD, however, was partially recovered by applying HCD with multiple collision energies. Collectively, this work demonstrated that HCD is advantageous to MS/MS sequencing of T-rich PS-modified DNA oligonucleotides.
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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 ResearchU.S. Food and Drug AdministrationSaint LouisMissouriUSA
| | - Cynthia Sommers
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and ResearchU.S. Food and Drug AdministrationSaint LouisMissouriUSA
| | - Jessica Hawes
- Division of Systems Biology, National Center for Toxicological ResearchU.S. Food and Drug AdministrationJeffersonArkansasUSA
| | - Jason D. Rodriguez
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and ResearchU.S. Food and Drug AdministrationSaint LouisMissouriUSA
| | - Kui Yang
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and ResearchU.S. Food and Drug AdministrationSaint LouisMissouriUSA
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30
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Becette OB, Tran A, Jones JW, Marino JP, Brinson RG. Structural Fingerprinting of Short Interfering RNA Therapeutics by Solution Nuclear Magnetic Resonance Spectroscopy. Nucleic Acid Ther 2022; 32:267-279. [PMID: 35263184 PMCID: PMC9416564 DOI: 10.1089/nat.2021.0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nucleic acids are an increasingly popular platform for the development of biotherapeutics to treat a wide variety of illnesses, including diseases where traditional drug development efforts have failed. To date, there are 14 short oligonucleotide therapeutics and 2 messenger RNA (mRNA) vaccines approved by the U.S. Food and Drug Administration (FDA), which demonstrates the potential of nucleic acids as a platform for the development of safe and effective medicines and vaccines. Despite the increasing popularity of nucleic acid-based drugs, there has been a paucity of high-resolution structural techniques applied to rigorously characterize these molecules during drug development. Here, we present application of nuclear magnetic resonance (NMR) methods to structurally "fingerprint" short oligonucleotide therapeutics at natural isotope abundance under full formulation conditions. The NMR methods described herein leverage signals arising from the native structural features of nucleic acids, including imino, aromatic, and ribose resonances, in addition to non-native chemistries, such as 2'-fluoro (2'-F), 2'-O-methyl (2'-OMe), and phosphorothioate (PS) modifications, introduced during drug development. We demonstrate the utility of the NMR methods to structurally "fingerprint" a model short interfering RNA (siRNA) and a sample that simulated the drug product Givosiran. We anticipate broad applicability of the NMR methods to other nucleic acid-based therapeutics due to the generalized nature of the approach and ability to monitor many quality attributes simultaneously.
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Affiliation(s)
- Owen B Becette
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, USA
| | - Anh Tran
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Jace W Jones
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, USA
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, USA
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31
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Camperi J, Moshref M, Dai L, Lee HY. Physicochemical and Functional Characterization of Differential CRISPR-Cas9 Ribonucleoprotein Complexes. Anal Chem 2022; 94:1432-1440. [PMID: 34958212 DOI: 10.1021/acs.analchem.1c04795] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Advances in gene-editing technology enable efficient, targeted ex vivo engineering of different cell types, which offer a potential therapeutic platform for most challenging disease areas. CRISPR-Cas9 is a widely used gene-editing tool in therapeutic applications. The quality of gene-editing reagents (i.e., Cas9 nuclease, single guide (sg)RNA) is associated with the final cellular product quality as they can impact the gene-editing accuracy and efficiency. To assess the impact of the quality of Cas9 protein and sgRNA in the formation of a Cas9 ribonucleoprotein (RNP) complex, stability, and functional activities, we developed a size exclusion chromatography method that utilizes multiple detectors and an in vitro DNA cleavage assay using anion-exchange chromatography. Using these methods, we characterized the formation and stability of Cas9 RNP complexes associated with Cas9 and sgRNA characteristics as well as their functional activities. Multi-angle light scattering characterization showed different types and levels of aggregates in different source sgRNA materials, which contribute to form different Cas9 RNP complexes. The aggregations irreversibly dissociated at high temperatures. When the Cas9 RNP complexes derived from non-heated and heated sgRNAs were characterized, the data showed that specific RNP peaks were impacted. The Cas9 RNP complexes derived from the heated sgRNA retained their biological function and cleaved the double-strand target DNA at a higher rate. This work provides new tools to characterize the Cas9 RNP complex formation, stability, and functional activity and provides insights into sgRNA properties and handling procedures to better control the Cas9 RNP complex formation.
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Affiliation(s)
- Julien Camperi
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Maryam Moshref
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lu Dai
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ho Young Lee
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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32
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Kita R, Osawa T, Obika S. Conjugation of oligonucleotides with activated carbamate reagents prepared by the Ugi reaction for oligonucleotide library synthesis. RSC Chem Biol 2022; 3:728-738. [PMID: 35755192 PMCID: PMC9175101 DOI: 10.1039/d1cb00240f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
The DNA-encoded library (DEL) is a powerful tool for drug discovery. As a result, to obtain diverse DELs, many DNA-compatible chemical reactions have been developed over the past decade. Among the most commonly used reactions in medicinal chemistry, multicomponent reactions (MCRs) can lead to the generation of various compounds in a one-step reaction. In particular, the Ugi reaction can easily provide a peptoid library. Thus, we herein report a solution-phase DEL synthesis based on the Ugi reaction. Using 6-(4-nitrophenoxycarbonylamino)hexanoic acid and N-4-nitrophenoxycarbonylglycine as carboxylic acids, peptoids with activated carbamate moieties were obtained as the products of the Ugi reaction. These peptoids were then treated with oligonucleotides bearing a 5′- or 3′-terminal aminohexyl linker to give various oligonucleotide-tagged peptoids in good yields. Moreover, the obtained peptoids could be substituted by a Suzuki cross-coupling reaction and by hydrolysis of the carboxylate ester, followed by condensation with amines. These advances should therefore promote pharmaceutical and medicinal research using DELs. A solution-phase conjugation method based on the Ugi reaction is reported, which enables the synthesis of an oligonucleotide-tagged peptoid library.![]()
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Affiliation(s)
- Ryosuke Kita
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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33
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Klont F, Hopfgartner G. Mass spectrometry based approaches and strategies in bioanalysis for qualitative and quantitative analysis of pharmaceutically relevant molecules. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:64-68. [PMID: 34916025 DOI: 10.1016/j.ddtec.2021.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Mass spectrometry plays an essential role in qualitative and quantitative analysis of pharmaceutically relevant molecules. The present review summarizes some the most common applications of LC-MS for the characterization of therapeutic low-molecular-weight compounds, peptides and proteins, and oligonucleotides using low-resolution and high-resolution tandem mass spectrometry. In addition, the benefit of multistage MS, differential ion mobility, and data independent acquisition is emphasized. At last, the potential of coupling MS with novel interfaces for high-throughput analysis is discussed.
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Affiliation(s)
- Frank Klont
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211 Geneva, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211 Geneva, Switzerland.
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34
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Talap J, Zhao J, Shen M, Song Z, Zhou H, Kang Y, Sun L, Yu L, Zeng S, Cai S. Recent advances in therapeutic nucleic acids and their analytical methods. J Pharm Biomed Anal 2021; 206:114368. [PMID: 34571322 DOI: 10.1016/j.jpba.2021.114368] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022]
Abstract
Therapeutic nucleic acids are various chemically modified RNA or DNA with different functions, which mainly play roles at the gene level. Owing to its accurately targeting at pathogenic genes, nucleic acid based therapeutics have a wide range of application prospects. Recently, the improvement on chemical synthesis and delivery materials accelerated the development of therapeutic nucleic acids rapidly. Up to now, 17 nucleic acid based therapeutics approved by Food and Drug Administration (FDA) or European Medicines Agency (EMA). The development of therapeutics raised higher requirements for analytical methods, both in quality control and in clinical research. The first part of this review introduces different classes of therapeutic nucleic acids, including antisense oligonucleotide (ASO), RNA interference (RNAi) therapy, mRNA, aptamer and other classes which are under research. The second part reviews the therapeutic nucleic acids commercialized from 2019 to now. The third part discusses the analytical methods for nucleic acid based therapeutics, including liquid chromatography-based methods, capillary gel electrophoresis (CGE), hybridization enzyme-linked immunosorbent assay (ELISA) and other infrequently used methods. Finally, the advantages and shortcomings of these methods are summarized, and the future development of analysis methods are prospected.
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Affiliation(s)
- Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jing Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zihan Song
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
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35
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Zhou X, Kiesman WF, Yan W, Jiang H, Antia FD, Yang J, Fillon YA, Xiao L, Shi X. Development of Kilogram-Scale Convergent Liquid-Phase Synthesis of Oligonucleotides. J Org Chem 2021; 87:2087-2110. [PMID: 34807599 DOI: 10.1021/acs.joc.1c01756] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oligonucleotide drugs show promise to treat diseases afflicting millions of people. To address the need to manufacture large quantities of oligonucleotide therapeutics, the novel convergent liquid-phase synthesis has been developed for an 18-mer oligonucleotide drug candidate. Fragments containing tetra- and pentamers were synthesized and assembled into the 18-mer without column chromatography, which had a similar impurity profile to material made by standard solid-phase oligonucleotide synthesis. Two of the fragments have been synthesized at ∼3 kg/batch sizes and four additional tetra- and pentamer fragments were synthesized at >300-g scale, and a 34-mer was assembled from the fragments. Critical impurities are controlled in the fragment syntheses to provide oligonucleotides of purities suitable for clinical use after applying standard full-length product purification process. Impurity control in the assembly steps demonstrated the potential to eliminate chromatography of full-length oligonucleotides, which should enhance scalability and reduce the environmental impact of the process. The convergent assembly and telescoping of reactions made the long synthesis (>60 reactions) practical by reducing production time, material loss, and chances for impurity generation.
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Affiliation(s)
- Xuan Zhou
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - William F Kiesman
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Wuming Yan
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Hong Jiang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Firoz D Antia
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Jing Yang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Yannick A Fillon
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Li Xiao
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Xianglin Shi
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts 02142, United States
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36
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Agten A, Prostko P, Geubbelmans M, Liu Y, De Vijlder T, Valkenborg D. A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides. Metabolites 2021; 11:400. [PMID: 34207227 PMCID: PMC8234063 DOI: 10.3390/metabo11060400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/23/2022] Open
Abstract
Structural modifications of DNA and RNA molecules play a pivotal role in epigenetic and posttranscriptional regulation. To characterise these modifications, more and more MS and MS/MS- based tools for the analysis of nucleic acids are being developed. To identify an oligonucleotide in a mass spectrum, it is useful to compare the obtained isotope pattern of the molecule of interest to the one that is theoretically expected based on its elemental composition. However, this is not straightforward when the identity of the molecule under investigation is unknown. Here, we present a modelling approach for the prediction of the aggregated isotope distribution of an average DNA or RNA molecule when a particular (monoisotopic) mass is available. For this purpose, a theoretical database of all possible DNA/RNA oligonucleotides up to a mass of 25 kDa is created, and the aggregated isotope distribution for the entire database of oligonucleotides is generated using the BRAIN algorithm. Since this isotope information is compositional in nature, the modelling method is based on the additive log-ratio analysis of Aitchison. As a result, a univariate weighted polynomial regression model of order 10 is fitted to predict the first 20 isotope peaks for DNA and RNA molecules. The performance of the prediction model is assessed by using a mean squared error approach and a modified Pearson's χ2 goodness-of-fit measure on experimental data. Our analysis has indicated that the variability in spectral accuracy contributed more to the errors than the approximation of the theoretical isotope distribution by our proposed average DNA/RNA model. The prediction model is implemented as an online tool. An R function can be downloaded to incorporate the method in custom analysis workflows to process mass spectral data.
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Affiliation(s)
- Annelies Agten
- Data Science Institute, UHasselt—Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium; (A.A.); (P.P.); (M.G.)
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, BE 3590 Diepenbeek, Belgium
| | - Piotr Prostko
- Data Science Institute, UHasselt—Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium; (A.A.); (P.P.); (M.G.)
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, BE 3590 Diepenbeek, Belgium
| | - Melvin Geubbelmans
- Data Science Institute, UHasselt—Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium; (A.A.); (P.P.); (M.G.)
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, BE 3590 Diepenbeek, Belgium
| | - Youzhong Liu
- Chemical & Pharmaceutical Development & Supply, Janssen Research & Development, Turnhoutseweg 30, BE 2340 Beerse, Belgium; (Y.L.); (T.D.V.)
| | - Thomas De Vijlder
- Chemical & Pharmaceutical Development & Supply, Janssen Research & Development, Turnhoutseweg 30, BE 2340 Beerse, Belgium; (Y.L.); (T.D.V.)
| | - Dirk Valkenborg
- Data Science Institute, UHasselt—Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium; (A.A.); (P.P.); (M.G.)
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, BE 3590 Diepenbeek, Belgium
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37
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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: 36] [Impact Index Per Article: 9.0] [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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38
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Goyon A, Zhang K. Characterization of Antisense Oligonucleotide Impurities by Ion-Pairing Reversed-Phase and Anion Exchange Chromatography Coupled to Hydrophilic Interaction Liquid Chromatography/Mass Spectrometry Using a Versatile Two-Dimensional Liquid Chromatography Setup. Anal Chem 2020; 92:5944-5951. [DOI: 10.1021/acs.analchem.0c00114] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexandre Goyon
- Research and Early Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Research and Early Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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