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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 DOI: 10.1021/acs.analchem.3c04351] [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: 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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Yuen BPN, Wong KS, So YM, Kwok WH, Cheung HW, Wan TSM, Ho ENM, Wong WT. Gene Doping Control Analysis of Human Erythropoietin Transgene in Equine Plasma by PCR-Liquid Chromatography High-Resolution Tandem Mass Spectrometry. Anal Chem 2024; 96:5307-5314. [PMID: 38504497 DOI: 10.1021/acs.analchem.4c00247] [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: 03/21/2024]
Abstract
Gene doping involves the misuse of genetic materials to alter an athlete's performance, which is banned at all times in both human and equine sports. Quantitative polymerase chain reaction (qPCR) assays have been used to control the misuse of transgenes in equine sports. Our laboratory recently developed and implemented duplex as well as multiplex qPCR assays for transgenes detection. To further advance gene doping control, we have developed for the first time a sensitive and definitive PCR-liquid chromatography high-resolution tandem mass spectrometry (PCR-LC-HRMS/MS) method for transgene detection with an estimated limit of detection of below 100 copies/mL for the human erythropoietin (hEPO) transgene in equine plasma. The method involved magnetic-glass-particle-based extraction of DNA from equine plasma prior to PCR amplification with 2'-deoxyuridine 5'-triphosphate (dUTP) followed by treatments with uracil DNA glycosylase and hot piperidine for selective cleavage to give small oligonucleotide fragments. The resulting DNA fragments were then analyzed by LC-HRMS/MS. The applicability of this method has been demonstrated by the successful detection of hEPO transgene in a blood sample collected from a gelding (castrated male horse) that had been administered the transgene. This novel approach not only serves as a complementary method for transgene detection but also paves the way for developing a generic PCR-LC-HRMS/MS method for the detection of multiple transgenes.
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Affiliation(s)
- Bruce Pui-Nam Yuen
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Kin-Sing Wong
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Yat-Ming So
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Wai Him Kwok
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Hiu Wing Cheung
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Terence See Ming Wan
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Emmie Ngai-Man Ho
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
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Peters-Clarke TM, Quan Q, Anderson BJ, McGee WM, Lohr E, Hebert AS, Westphall MS, Coon JJ. Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry. Mol Cell Proteomics 2024; 23:100742. [PMID: 38401707 PMCID: PMC11047293 DOI: 10.1016/j.mcpro.2024.100742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 02/26/2024] Open
Abstract
Therapeutic RNAs are routinely modified during their synthesis to ensure proper drug uptake, stability, and efficacy. Phosphorothioate (PS) RNA, molecules in which one or more backbone phosphates are modified with a sulfur atom in place of standard nonbridging oxygen, is one of the most common modifications because of ease of synthesis and pharmacokinetic benefits. Quality assessment of RNA synthesis, including modification incorporation, is essential for drug selectivity and performance, and the synthetic nature of the PS linkage incorporation often reveals impurities. Here, we present a comprehensive analysis of PS RNA via tandem mass spectrometry (MS). We show that activated ion-negative electron transfer dissociation MS/MS is especially useful in diagnosing PS incorporation, producing diagnostic a- and z-type ions at PS linkage sites, beyond the standard d- and w-type ions. Analysis using resonant and beam-type collision-based activation reveals that, overall, more intense sequence ions and base-loss ions result when a PS modification is present. Furthermore, we report increased detection of b- and x-type product ions at sites of PS incorporation, in addition to the standard c- and y-type ions. This work reveals that the gas-phase chemical stability afforded by sulfur alters RNA dissociation and necessitates inclusion of additional product ions for MS/MS of PS RNA.
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Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Qiuwen Quan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benton J Anderson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Emily Lohr
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexander S Hebert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.
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Lanzillotti MB, Brodbelt JS. A High-Throughput Workflow for Mass Spectrometry Analysis of Nucleic Acids by Nanoflow Desalting. Anal Chem 2024. [PMID: 38330443 DOI: 10.1021/acs.analchem.3c05428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Broad interest in nucleic acids, both their therapeutic capabilities and understanding the nuances of their structure and resulting function, has increased in recent years. Post-transcriptional modifications, in particular, have become an important analysis target, as these covalent modifications to the sugars, nitrogenous bases, and phosphate backbone impart differential functionality to synthetic and biological nucleic acids. Characterizing these post-transcriptional modifications can be difficult with traditional sequencing workflows; however, advancements in top-down mass spectrometry address these challenges. Online desalting platforms have enabled facile sample cleanup and reliable ionization of increasingly large (100 nt) oligonucleotides, and application of existing tandem mass spectrometry techniques has yielded information-rich spectra which can be used to interrogate primary sequences. To extend the capabilities of top-down MS and its analysis of nucleic acids, we have developed a nanoflow desalting platform for high-throughput and low sample-use desalting coupled with collision-induced dissociation (CID), 213 nm ultraviolet photodissociation (UVPD), and activated-ion electron photodetachment dissociation (a-EPD) to yield high-quality MS/MS spectra. Fragments identified using an m/z-domain isotope matching strategy yielded high sequence coverage (>70%) of a yeast phenylalanine tRNA.
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Affiliation(s)
- Michael B Lanzillotti
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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Wan J, Nytka M, Qian H, Lemr K, Tureček F. Do d(GCGAAGC) Cations Retain the Hairpin Structure in the Gas Phase? A Cyclic Ion Mobility Mass Spectrometry and Density Functional Theory Computational Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2323-2340. [PMID: 37696624 DOI: 10.1021/jasms.3c00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
d(GCGAAGC) is the smallest oligonucleotide with a well-defined hairpin structure in solution. We report a study of multiply protonated d(GCGAAGC) and its sequence-scrambled isomers, d(CGAAGCG), d(GCGAACG), and d(CGGAAGC), that were produced by electrospray ionization with the goal of investigating their gas-phase structures and dissociations. Cyclic ion mobility measurements revealed that dications of d(GCGAAGC) as well as the scrambled-sequence ions were mixtures of protomers and/or conformers that had collision cross sections (CCS) within a 439-481 Å2 range. Multiple ion conformers were obtained by electrospray under native conditions as well as from aqueous methanol. Arrival time distribution profiles were characteristic of individual isomeric heptanucleotides. Extensive Born-Oppenheimer molecular dynamics (BOMD) and density functional theory (DFT) calculations of d(GCGAAGC)2+ isomers indicated that hairpin structures were high-energy isomers of more compact distorted conformers. Protonation caused a break up of the C2···G6 pair that was associated with the formation of strong hydrogen bonds in zwitterionic phosphate anion-nucleobase cation motifs that predominated in low energy ions. Multiple components were also obtained for d(GCGAAGC)3+ trications under native and denaturing electrospray conditions. The calculated trication structures showed disruption of the G···C pairs in low energy zwitterions. A hairpin trication was calculated to be a high energy isomer. d(GCGAAGC)4+ tetracations were produced and separated by c-IMS as two major isomers. All low energy d(GCGAAGC)4+ ions obtained by DFT geometry optimizations were zwitterions in which all five purine bases were protonated, and the ion charge was balanced by a phosphate anion. Tetracations of the scrambled sequences were each formed as one dominant isomer. The CCS calculated with the MobCal-MPI method were found to closely match experimental values. Collision-induced dissociation (CID) spectra of multiply charged heptanucleotides showed nucleobase loss and backbone cleavages occurring chiefly at the terminal nucleosides. Electron-transfer-CID tandem mass spectra were used to investigate dissociations of different charge and spin states of charge-reduced heptanucleotide cation radicals.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Marianna Nytka
- Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 779 00 Olomouc, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Haocheng Qian
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Karel Lemr
- Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 779 00 Olomouc, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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Hannauer F, Black R, Ray AD, Stulz E, Langley GJ, Holman SW. Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9596. [PMID: 37580500 PMCID: PMC10909466 DOI: 10.1002/rcm.9596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 08/16/2023]
Abstract
The fragmentation of oligonucleotides by mass spectrometry allows for the determination of their sequences. It is necessary to understand how oligonucleotides dissociate in the gas phase, which allows interpretation of data to obtain sequence information. Since 2014, a range of fragmentation mechanisms, including a novel internal rearrangement, have been proposed using different ion dissociation techniques. The recent publications have focused on the fragmentation of modified oligonucleotides such as locked nucleic acids, modified nucleobases (methylated, spacer, nebularine and aminopurine) and modification to the carbon 2'-position on the sugar ring; these modified oligonucleotides are of great interest as therapeutics. Comparisons of different dissociation techniques have been reported, including novel approaches such as plasma electron detachment dissociation and radical transfer dissociation. This review covers the period 2014-2022 and details the new knowledge gained with respect to oligonucleotide dissociation using tandem mass spectrometry (without priori sample digestion) during that time, with a specific focus on synthetic single-stranded oligonucleotides.
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Affiliation(s)
- Fabien Hannauer
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Rachelle Black
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Andrew D. Ray
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Eugen Stulz
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - G. John Langley
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Stephen W. Holman
- Chemical Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
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Sun RX, Zuo MQ, Zhang JS, Dong MQ. Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37463304 DOI: 10.1021/jasms.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1- to 5-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.
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Affiliation(s)
- Rui-Xiang Sun
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Mei-Qing Zuo
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Ji-Shuai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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Kenderdine T, Fabris D. The multifaceted roles of mass spectrometric analysis in nucleic acids drug discovery and development. MASS SPECTROMETRY REVIEWS 2023; 42:1332-1357. [PMID: 34939674 PMCID: PMC9218015 DOI: 10.1002/mas.21766] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/23/2021] [Accepted: 11/22/2021] [Indexed: 06/07/2023]
Abstract
The deceptively simple concepts of mass determination and fragment analysis are the basis for the application of mass spectrometry (MS) to a boundless range of analytes, including fundamental components and polymeric forms of nucleic acids (NAs). This platform affords the intrinsic ability to observe first-hand the effects of NA-active drugs on the chemical structure, composition, and conformation of their targets, which might affect their ability to interact with cognate NAs, proteins, and other biomolecules present in a natural environment. The possibility of interfacing with high-performance separation techniques represents a multiplying factor that extends these capabilities to cover complex sample mixtures obtained from organisms that were exposed to NA-active drugs. This report provides a brief overview of these capabilities in the context of the analysis of the products of NA-drug activity and NA therapeutics. The selected examples offer proof-of-principle of the applicability of this platform to all phases of the journey undertaken by any successful NA drug from laboratory to bedside, and provide the rationale for its rapid expansion outside traditional laboratory settings in support to ever growing manufacturing operations.
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Affiliation(s)
| | - Dan Fabris
- Department of Chemistry, University of Connecticut
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10
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Gau BC, Dawdy AW, Wang HL, Bare B, Castaneda CH, Friese OV, Thompson MS, Lerch TF, Cirelli DJ, Rouse JC. Oligonucleotide mapping via mass spectrometry to enable comprehensive primary structure characterization of an mRNA vaccine against SARS-CoV-2. Sci Rep 2023; 13:9038. [PMID: 37270636 DOI: 10.1038/s41598-023-36193-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023] Open
Abstract
Oligonucleotide mapping via liquid chromatography with UV detection coupled to tandem mass spectrometry (LC-UV-MS/MS) was recently developed to support development of Comirnaty, the world's first commercial mRNA vaccine which immunizes against the SARS-CoV-2 virus. Analogous to peptide mapping of therapeutic protein modalities, oligonucleotide mapping described here provides direct primary structure characterization of mRNA, through enzymatic digestion, accurate mass determinations, and optimized collisionally-induced fragmentation. Sample preparation for oligonucleotide mapping is a rapid, one-pot, one-enzyme digestion. The digest is analyzed via LC-MS/MS with an extended gradient and resulting data analysis employs semi-automated software. In a single method, oligonucleotide mapping readouts include a highly reproducible and completely annotated UV chromatogram with 100% maximum sequence coverage, and a microheterogeneity assessment of 5' terminus capping and 3' terminus poly(A)-tail length. Oligonucleotide mapping was pivotal to ensure the quality, safety, and efficacy of mRNA vaccines by providing: confirmation of construct identity and primary structure and assessment of product comparability following manufacturing process changes. More broadly, this technique may be used to directly interrogate the primary structure of RNA molecules in general.
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Affiliation(s)
- Brian C Gau
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Chesterfield, MO, USA.
| | - Andrew W Dawdy
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Chesterfield, MO, USA.
| | - Hanliu Leah Wang
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Chesterfield, MO, USA
| | - Bradley Bare
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Chesterfield, MO, USA
| | - Carlos H Castaneda
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Chesterfield, MO, USA
| | - Olga V Friese
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Chesterfield, MO, USA
| | | | - Thomas F Lerch
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Chesterfield, MO, USA
| | - David J Cirelli
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Andover, MA, USA
| | - Jason C Rouse
- BioTherapeutics Pharmaceutical Sciences, Pfizer Inc, Andover, MA, USA
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11
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Schultz M, Parker SL, Fernando MT, Wellalage MM, Thomas DA. Diserinol Isophthalamide: A Novel Reagent for Complexation with Biomolecular Anions in Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:745-753. [PMID: 36975839 DOI: 10.1021/jasms.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transferring biomolecules from solution to vacuum facilitates a detailed analysis of molecular structure and dynamics by isolating molecules of interest from a complex environment. However, inherent in the ion desolvation process is the loss of solvent hydrogen bonding partners, which are critical for the stability of a condensed-phase structure. Thus, transfer of ions to vacuum can favor structural rearrangement, especially near solvent-accessible charge sites, which tend to adopt intramolecular hydrogen bonding motifs in the absence of solvent. Complexation of monoalkylammonium moieties (e.g., lysine side chains) with crown ethers such as 18-crown-6 can disfavor structural rearrangement of protonated sites, but no equivalent ligand has been investigated for deprotonated groups. Herein we describe diserinol isophthalamide (DIP), a novel reagent for the gas-phase complexation of anionic moieties within biomolecules. Complexation is observed to the C-terminus or side chains of the small model peptides GD, GE, GG, DF-OMe, VYV, YGGFL, and EYMPME in electrospray ionization mass spectrometry (ESI-MS) studies. In addition, complexation is observed with the phosphate and carboxylate moieities of phosphoserine and phosphotyrosine. DIP performs favorably in comparison to an existing anion recognition reagent, 1,1'-(1,2-phenylene)bis(3-phenylurea), that exhibits moderate carboxylate binding in organic solvent. This improved performance in ESI-MS experiments is attributed to reduced steric constraints to complexation with carboxylate groups of larger molecules. Overall, diserinol isophthalamide is an effective complexation reagent that can be applied in future work to study retention of solution-phase structure, investigate intrinsic molecular properties, and examine solvation effects.
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Affiliation(s)
- Madeline Schultz
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah L Parker
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Maleesha T Fernando
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Miyuru M Wellalage
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel A Thomas
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
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12
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Crittenden CM, Lanzillotti MB, Chen B. Top-Down Mass Spectrometry of Synthetic Single Guide Ribonucleic Acids Enabled by Facile Sample Clean-Up. Anal Chem 2023; 95:3180-3186. [PMID: 36606446 DOI: 10.1021/acs.analchem.2c03030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In recent years, CRISPR-Cas9 genome editing has become an important technology in biomedical research and has demonstrated tremendous therapeutic potential. With Cas9 endonuclease, the use of single guide ribonucleic acids (sgRNAs) allows for sequence-specific cutting on target double-stranded deoxyribonucleic acids. Therefore, the design and quality of sgRNAs can greatly affect the efficiency and specificity of genome editing. Mass spectrometry (MS) has been a powerful tool to detect molecular features and sequence a variety of biomolecules; however, as the sizes of oligonucleotides get larger, it becomes more challenging to desalt samples and achieve high-quality intact spectra with effective fragmentation. Here, we develop a simple but effective online column-based clean-up method (reversed-phase column in a size exclusion mode) that removes formulation salts and metal adducts from larger oligonucleotides upon entering the mass spectrometer in a consistent manner. Using the top-down approach without any nuclease digestion, we characterized and sequenced 100-nucleotide-long sgRNAs by higher-energy collision dissociation (HCD), collision-induced dissociation (CID), ultraviolet photodissociation (UVPD), and activated electron photodetachment (a-EPD). In a single 10 min liquid chromatography-tandem MS (LC-MS/MS) run, CID yielded the best sequence coverage, of 67%. When adding complementary UVPD and a-EPD runs, we achieved 80% overall sequence coverage and 100% cleavages for the variable sequence, the first 20 nucleotides from the 5' end. This LC-MS/MS platform provides a facile top-down workflow to analyze and sequence larger chemically modified oligonucleotides with no sample treatment.
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Affiliation(s)
- Christopher M Crittenden
- Small Molecule Analytical Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | | | - Bifan Chen
- Small Molecule Analytical Chemistry, Genentech Inc., South San Francisco, California 94080, United States
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13
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Wan J, Brož B, Liu Y, Huang SR, Marek A, Tureček F. The DNA Radical Code. Resolution of Identity in Dissociations of Trinucleotide Codon Cation Radicals in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:304-319. [PMID: 36596259 DOI: 10.1021/jasms.2c00322] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Sixty DNA trinucleotide cation radicals covering a large part of the genetic code alphabet were generated by electron transfer in the gas phase, and their chemistry was studied by collision-induced dissociation tandem mass spectrometry and theoretical calculations. The major dissociations involved loss of nucleobase molecules and radicals, backbone cleavage, and cross-ring fragmentations that depended on the nature and position of the nucleobases. Mass identity in dissociations of symmetrical trinucleotide cation radicals of the (XXX+2H)+• and (XYX+2H)+• type was resolved by specific 15N labeling. The specific features of trinucleotide cation radical dissociations involved the dominant formation of d2+ ions, hydrogen atom migrations accompanying the formation of (w2+H)+•, (w2+2H)+, and (d2+2H)+ sequence ions, and cross-ring cleavages in the 3'- and 5'-deoxyribose moieties that depended on the nucleobase type and its position in the ion. Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations were used to obtain structures and energies of several cation-radical protomers and conformers for (AAA+2H)+•, (CCC+2H)+•, (GGG+2H)+•, (ACA+2H)+•, and (CAA+2H)+• that were representative of the different types of backbone dissociations. The ion electronic structure, protonation and radical sites, and hydrogen bonding were used to propose reaction mechanisms for the dissociations.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Břetislav Brož
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Yue Liu
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Shu R Huang
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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14
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Palasser M, Breuker K. RNA Chemical Labeling with Site-Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin-Sensing Riboswitch Aptamer Domain. Chempluschem 2022; 87:e202200256. [PMID: 36220343 PMCID: PMC9828840 DOI: 10.1002/cplu.202200256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/14/2022] [Indexed: 01/12/2023]
Abstract
High-resolution mass spectrometry was used for the label-free, direct localization and relative quantification of CMC+ -modifications of a neomycin-sensing riboswitch aptamer domain in the absence and presence of the aminoglycoside ligands neomycin B, ribostamycin, and paromomycin. The chemical probing and MS data for the free riboswitch show high exposure to solvent of the uridine nucleobases U7, U8, U13, U14, U18 as part of the proposed internal and apical loops, but those of U10 and U21 as part of the proposed internal loop were found to be far less exposed than expected. Thus, our data are in better agreement with the proposed secondary structure of the riboswitch in complexes with aminoglycosides than with that of free RNA. For the riboswitch in complexes with neomycin B, ribostamycin, and paromomycin, we found highly similar CMC+ -modification patterns and excellent agreement with previous NMR studies. Differences between the chemical probing and MS data in the absence and presence of the aminoglycoside ligands were quantitative rather than qualitative (i. e., the same nucleobases were labeled, but to different extents) and can be rationalized by stabilization of both the proposed bulge and the apical loop by aminoglycoside binding. Our study shows that chemical probing and mass spectrometry can provide important structural information and complement other techniques such as NMR spectroscopy.
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Affiliation(s)
- Michael Palasser
- Institut of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Kathrin Breuker
- Institut of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
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15
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Detection technologies for RNA modifications. Exp Mol Med 2022; 54:1601-1616. [PMID: 36266445 PMCID: PMC9636272 DOI: 10.1038/s12276-022-00821-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
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16
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Wan J, Brož B, Liu Y, Huang SR, Marek A, Tureček F. Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15N-Labeling and Computational Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1936-1950. [PMID: 36040435 DOI: 10.1021/jasms.2c00194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions were studied by tandem mass spectrometry using 15N-labeling to resolve identity in the nucleobase loss and backbone cleavages. The monocations showed different distributions of nucleobase loss from the 5'-, middle, and 3'-positions depending on the nucleobase, favoring cytosine over guanine, adenine, and thymine in an ensemble-averaged 62:27:11:<1 ratio. The distribution for the loss of the 5'-, middle, and 3'-nucleobase was 49:18:33, favoring the 5'-nucleobase, but also depending on its nature. The formation of sequence w2+ ions was unambiguously established for all codon mono- and dications. Structures of low-Gibbs-energy protomers and conformers of dAAA+, dGGG+, dCCC+, dTTT+, dACA+, and dATC+ were established by Born-Oppenheimer molecular dynamics and density functional theory calculations. Monocations containing guanine favored classical structures protonated at guanine N7. Structures containing adenine and cytosine produced classical nucleobase-protonated isomers as well as zwitterions in which two protonated bases were combined with a phosphate anion. Protonation at thymine was disfavored. Low threshold energies for nucleobase loss allowed extensive proton migration to occur prior to dissociation. Loss of the nucleobase from monocations was assisted by neighboring group participation in nucleophilic addition or proton abstraction, as well as allosteric proton migrations remote from the reaction center. The optimized structures of diprotonated isomers for dAAA2+ and dACA2+ revealed combinations of classical and zwitterionic structures. The threshold and transition-state energies for nucleobase-ion loss from dications were low, resulting in facile dissociations involving cytosine, guanine, and adenine.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Břetislav Brož
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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17
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Potential Misidentification of Natural Isomers and Mass-Analogs of Modified Nucleosides by Liquid Chromatography-Triple Quadrupole Mass Spectrometry. Genes (Basel) 2022; 13:genes13050878. [PMID: 35627263 PMCID: PMC9140458 DOI: 10.3390/genes13050878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 01/25/2023] Open
Abstract
Triple quadrupole mass spectrometry coupled to liquid chromatography (LC-TQ-MS) can detect and quantify modified nucleosides present in various types of RNA, and is being used increasingly in epitranscriptomics. However, due to the low resolution of TQ-MS and the structural complexity of the many naturally modified nucleosides identified to date (>160), the discrimination of isomers and mass-analogs can be problematic and is often overlooked. This study analyzes 17 nucleoside standards by LC-TQ-MS with separation on three different analytical columns and discusses, with examples, three major causes of analyte misidentification: structural isomers, mass-analogs, and isotopic crosstalk. It is hoped that this overview and practical examples will help to strengthen the accuracy of the identification of modified nucleosides by LC-TQ-MS.
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18
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D'Ascenzo L, Popova AM, Abernathy S, Sheng K, Limbach PA, Williamson JR. Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry. Nat Commun 2022; 13:2424. [PMID: 35505047 PMCID: PMC9065004 DOI: 10.1038/s41467-022-30057-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/12/2022] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry is an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated into RNA therapeutics. To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. The main features of Pytheas are flexible handling of isotope labeling and RNA modifications, with false discovery rate statistical validation based on sequence decoys. We demonstrate bottom-up mass spectrometry characterization of diverse RNA sequences, with broad applications in the biology of stable RNAs, and quality control of RNA therapeutics and mRNA vaccines.
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Affiliation(s)
- Luigi D'Ascenzo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
| | - Anna M Popova
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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19
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Greis K, Kirschbaum C, Taccone MI, Götze M, Gewinner S, Schöllkopf W, Meijer G, von Helden G, Pagel K. Studying the Key Intermediate of RNA Autohydrolysis by Cryogenic Gas-Phase Infrared Spectroscopy. Angew Chem Int Ed Engl 2022; 61:e202115481. [PMID: 35231141 PMCID: PMC9314874 DOI: 10.1002/anie.202115481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 11/09/2022]
Abstract
Over the course of the COVID-19 pandemic, mRNA-based vaccines have gained tremendous importance. The development and analysis of modified RNA molecules benefit from advanced mass spectrometry and require sufficient understanding of fragmentation processes. Analogous to the degradation of RNA in solution by autohydrolysis, backbone cleavage of RNA strands was equally observed in the gas phase; however, the fragmentation mechanism remained elusive. In this work, autohydrolysis-like intermediates were generated from isolated RNA dinucleotides in the gas phase and investigated using cryogenic infrared spectroscopy in helium nanodroplets. Data from both experiment and density functional theory provide evidence for the formation of a five-membered cyclic phosphate intermediate and rule out linear or six-membered structures. Furthermore, the experiments show that another prominent condensed-phase reaction of RNA nucleotides can be induced in the gas phase: the tautomerization of cytosine. Both observed reactions are therefore highly universal and intrinsic properties of the investigated molecules.
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Affiliation(s)
- Kim Greis
- Institut für Chemie und BiochemieFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Carla Kirschbaum
- Institut für Chemie und BiochemieFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Martín I. Taccone
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Michael Götze
- Institut für Chemie und BiochemieFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Kevin Pagel
- Institut für Chemie und BiochemieFreie Universität BerlinArnimallee 2214195BerlinGermany
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
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20
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Greis K, Kirschbaum C, Taccone MI, Götze M, Gewinner S, Schöllkopf W, Meijer G, Helden G, Pagel K. Untersuchung des reaktiven Intermediats der RNA Autohydrolyse mittels kryogener Infrarotspektroskopie in der Gasphase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kim Greis
- Institut für Chemie und Biochemie Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Carla Kirschbaum
- Institut für Chemie und Biochemie Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Martín I. Taccone
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Michael Götze
- Institut für Chemie und Biochemie Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Gert Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Kevin Pagel
- Institut für Chemie und Biochemie Freie Universität Berlin Arnimallee 22 14195 Berlin Deutschland
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
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21
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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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22
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Santos IC, Lanzillotti M, Shilov I, Basanta-Sanchez M, Roushan A, Lawler R, Tang W, Bern M, Brodbelt JS. Ultraviolet Photodissociation and Activated Electron Photodetachment Mass Spectrometry for Top-Down Sequencing of Modified Oligoribonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:510-520. [PMID: 35157441 DOI: 10.1021/jasms.1c00340] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the increased development of new RNA-based therapeutics, the need for robust analytical methods for confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging because diagnostic fragmentation may be suppressed for modified nucleotides, thus hampering complete sequence coverage and the confident localization of modifications. Ultraviolet photodissociation (UVPD) has shown great potential for the characterization of nucleic acids due to extensive backbone fragmentation. Activated electron photodetachment dissociation (a-EPD) has also been used as an alternative to capitalize on the dominant charge-reduction pathway prevalent in UVPD, facilitate dissociation, and produce high abundances of fragment ions. Here, we compare higher-energy collisional activation (HCD), UVPD using 193 and 213 nm photons, and a-EPD for the top-down sequencing of modified nucleic acids, including methylated, phosphorothioate, and locked nucleic acid-modified DNA. The presence of these modifications alters the fragmentation pathways observed upon UVPD and a-EPD, and extensive backbone cleavage is observed that results in the production of fragment ions that retain the modifications and allow them to be pinpointed. LNA and 2'-O-methoxy phosphorothioate modifications caused a significant suppression of fragmentation for UVPD but not for a-EPD, whereas phosphorothioate bonds did not cause any significant suppression for either method. The incorporation of 2'-O-methyl modifications suppressed fragmentation of the antisense strand of patisiran, which resulted in some gaps in sequence coverage. However, UVPD provided the highest sequence coverage when compared to a-EPD.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Michael Lanzillotti
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ignat Shilov
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Maria Basanta-Sanchez
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Abhishek Roushan
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Rose Lawler
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Wilfred Tang
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Marshall Bern
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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23
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Zaikin VG, Borisov RS. Mass Spectrometry as a Crucial Analytical Basis for Omics Sciences. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [PMCID: PMC8693159 DOI: 10.1134/s1061934821140094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review is devoted to the consideration of mass spectrometric platforms as applied to omics sciences. The most significant attention is paid to omics related to life sciences (genomics, proteomics, meta-bolomics, lipidomics, glycomics, plantomics, etc.). Mass spectrometric approaches to solving the problems of petroleomics, polymeromics, foodomics, humeomics, and exosomics, related to inorganic sciences, are also discussed. The review comparatively presents the advantages of various principles of separation and mass spectral techniques, complementary derivatization, used to obtain large arrays of various structural and quantitative information in the mentioned omics sciences.
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Affiliation(s)
- V. G. Zaikin
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R. S. Borisov
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991 Moscow, Russia
- RUDN University, 117198 Moscow, Russia
- Core Facility Center “Arktika,” Northern (Arctic) Federal University, 163002 Arkhangelsk, Russia
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24
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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25
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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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26
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Ruzgys P, Böhringer S, Dokumaci AS, Hari Y, Schürch CM, Brühl F, Schürch S, Szidat S, Riether C, Šatkauskas S, Geiser T, Hradetzky D, Gazdhar A. Electrospray Mediated Localized and Targeted Chemotherapy in a Mouse Model of Lung Cancer. Front Pharmacol 2021; 12:643492. [PMID: 33959011 PMCID: PMC8093875 DOI: 10.3389/fphar.2021.643492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
Background: An advanced stage, centrally localized invasive tumor is a major cause of sudden death in lung cancer patients. Currently, chemotherapy, radiotherapy, laser ablation, or surgical resection if possible are the available state-of-the-art treatments but none of these guarantee remedy or long-term relief and are often associated with fatal complications. Allowing localized chemotherapy, by direct and confined drug delivery only at the tumor site, could be a promising option for preoperative down staging or palliative therapy. Here we report the localized and targeted application of intra tumor delivery of chemotherapeutics using a novel device based on the principle of electrospray. Methods: C57BL/6J mice were injected with Lewis lung carcinoma cells subcutaneously. After 15 days, the animals were anesthetized and the tumors were exposed by skin incision. Tumors were electrosprayed with 100 µg cisplatin on days 0 and 2, and tumor volumes were measured daily. Animals were sacrificed on day 7 after the first electrospray and tumors were analyzed by immunohistochemistry. Results: In this proof-of-concept study, we report that the tumor volume was reduced by 81.2% (22.46 ± 12.14 mm3) after two electrospray mediated Cisplatin deliveries, while the control tumor growth, at the same time point, increased by 200% (514.30 ± 104.50 mm3). Moreover, tunnel and Caspase-3 positive cells were increased after Cisplatin electrospray compared to other experimental groups of animals. Conclusion: Targeted drug delivery by electrospray is efficient in the subcutaneous mouse model of lung cancer and offers a promising opportunity for further development toward its clinical application.
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Affiliation(s)
- Paulius Ruzgys
- Department of Pulmonary Medicine, University Hospital Bern, Bern, Switzerland.,Department of Biomedical Research, University of Bern, Bern, Switzerland.,Biophysical Research Group, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania
| | - Stephan Böhringer
- Institute for Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Ayse Sila Dokumaci
- Magnetic Resonance Spectroscopy and Methodology, Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Yvonne Hari
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | | | - Frido Brühl
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Stefan Schürch
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Sönke Szidat
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Carsten Riether
- Department of Biomedical Research, University of Bern, Bern, Switzerland.,Department of Medical Oncology, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
| | - Saulius Šatkauskas
- Biophysical Research Group, Faculty of Natural Sciences, Vytautas Magnus University, Kaunas, Lithuania
| | - Thomas Geiser
- Department of Pulmonary Medicine, University Hospital Bern, Bern, Switzerland.,Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - David Hradetzky
- Institute for Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Amiq Gazdhar
- Department of Pulmonary Medicine, University Hospital Bern, Bern, Switzerland.,Department of Biomedical Research, University of Bern, Bern, Switzerland
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27
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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28
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Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
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Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
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29
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Mao K, Zhang G. The role of PARP1 in neurodegenerative diseases and aging. FEBS J 2021; 289:2013-2024. [DOI: 10.1111/febs.15716] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Kanmin Mao
- Key Laboratory of Environmental Health Ministry of Education Department of Toxicology School of Public Health Tongji Medical College Wuhan China
- Institute for Brain Research Collaborative Innovation Center for Brain Science Huazhong University of Science and Technology Wuhan China
| | - Guo Zhang
- Key Laboratory of Environmental Health Ministry of Education Department of Toxicology School of Public Health Tongji Medical College Wuhan China
- Institute for Brain Research Collaborative Innovation Center for Brain Science Huazhong University of Science and Technology Wuhan China
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30
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Santos IC, Brodbelt JS. Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020). J Sep Sci 2021; 44:340-372. [PMID: 32974962 PMCID: PMC8378248 DOI: 10.1002/jssc.202000833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
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31
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Ortiz D, Gasilova N, Sepulveda F, Patiny L, Dyson PJ, Menin L. Aom 2 S: A new web-based application for DNA/RNA tandem mass spectrometry data interpretation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8927. [PMID: 32812285 DOI: 10.1002/rcm.8927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/31/2020] [Accepted: 08/15/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The Analysis of Oligonucleotide Modifications from Mass Spectra (Aom2 S) was created to support the analysis of oligonucleotide mass spectra. This application complements the existing software tools by providing a comprehensive analysis of oligonucleotide fragments from high-resolution tandem mass spectrometry (HR-MS/MS) data in a flexible and user-friendly manner, directly accessible through a web browser without any need for installation. METHODS MS measurements of aminoC6-DNA and inosine-RNA were performed using an LTQ Orbitrap FT-MS instrument. The obtained data were analyzed by our newly developed open-source package Aom2 S accessible from the ms.epfl.ch web page or directly at https://mstools.epfl.ch/am2s/ to demonstrate the various functionalities of this tool, notably the possibility to identify different product ions from a nucleotide sequence with any fixed/variable modification by matching theoretical isotopic patterns to any experimental mass spectra with similarity scores ranking. RESULTS A detailed description of the Aom2 S tool with its user-friendly interface is exemplified using HR-MS/MS data of modified DNA and RNA oligonucleotides. Explanations of analysis parameters and tool workflow, as well as multiple options for viewing and exporting the results, are provided. Product ion assignment and modification localization can be achieved in seconds, and results can be exported as tables, matched mass spectra, and fragmentation maps. CONCLUSIONS A new open source tool (Aom2 S) for the analysis of HR-MS/MS data for modified DNA and RNA oligonucleotides is described. Aom2 S is fast, highly flexible, and versatile, allowing automatic precursor and product ion assignment in a comprehensive manner, including internal fragments and variable modification localization, with clear graphical representation of the results.
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Affiliation(s)
- Daniel Ortiz
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Natalia Gasilova
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Francisco Sepulveda
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luc Patiny
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Paul J Dyson
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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32
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Daems E, Dewaele D, Barylyuk K, De Wael K, Sobott F. Aptamer-ligand recognition studied by native ion mobility-mass spectrometry. Talanta 2020; 224:121917. [PMID: 33379118 DOI: 10.1016/j.talanta.2020.121917] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/31/2022]
Abstract
The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.
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Affiliation(s)
- Elise Daems
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Debbie Dewaele
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Konstantin Barylyuk
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Karolien De Wael
- AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Frank Sobott
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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33
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Kimura S, Obika S. Effect of oligonucleotide structural difference on matrix-assisted laser desorption/ionization in-source decay in comparison with collision-induced dissociation fragmentation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8819. [PMID: 32346915 DOI: 10.1002/rcm.8819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/26/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Mass spectrometry (MS) is an effective tool for the structural analysis of oligonucleotides. Currently, various modifications of oligonucleotides have been proposed to increase the efficacy and safety of oligonucleotide therapeutics. For MS-based structural characterization, the fragmentation behavior of modified oligonucleotides by MS must first be determined. METHODS The impact of the oligonucleotide structure on the in-source decay (ISD) of matrix-assisted laser desorption/ionization (MALDI) was examined using a new matrix and compared with collision-induced dissociation (CID) fragmentation behavior. RESULTS When a part of the oligonucleotide structure was replaced, an impact was observed at the 3' side of the replaced structure. Among the oligonucleotide components considered herein, nucleobases most significantly impacted both ISD and CID fragmentation patterns. CONCLUSIONS Compared with CID, ISD was less sensitive to structural differences. Because ISD fragmentation was less affected by various oligonucleotide modifications, MALDI is a useful and applicable method for the structural characterization or identification of various modified oligonucleotide therapeutics.
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Affiliation(s)
- Satoshi Kimura
- 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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34
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Hagelskamp F, Borland K, Ramos J, Hendrick AG, Fu D, Kellner S. Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro. Nucleic Acids Res 2020; 48:e41. [PMID: 32083657 PMCID: PMC7144906 DOI: 10.1093/nar/gkaa091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/23/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
RNAs are post-transcriptionally modified by dedicated writer or eraser enzymes that add or remove specific modifications, respectively. Mass spectrometry (MS) of RNA is a useful tool to study the modification state of an oligonucleotide (ON) in a sensitive manner. Here, we developed an ion-pairing reagent free chromatography for positive ion detection of ONs by low- and high-resolution MS, which does not interfere with other types of small compound analyses done on the same instrument. We apply ON-MS to determine the ONs from an RNase T1 digest of in vitro transcribed tRNA, which are purified after ribozyme-fusion transcription by automated size exclusion chromatography. The thus produced tRNAValAAC is substrate of the human tRNA ADAT2/3 enzyme and we confirm the deamination of adenosine to inosine and the formation of tRNAValIACin vitro by ON-MS. Furthermore, low resolution ON-MS is used to monitor the demethylation of ONs containing 1-methyladenosine by bacterial AlkB in vitro. The power of high-resolution ON-MS is demonstrated by the detection and mapping of modified ONs from native total tRNA digested with RNase T1. Overall, we present an oligonucleotide MS method which is broadly applicable to monitor in vitro RNA (de-)modification processes and native RNA.
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Affiliation(s)
- Felix Hagelskamp
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alan G Hendrick
- STORM Therapeutics, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT UK
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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35
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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36
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Peters-Clarke TM, Quan Q, Brademan DR, Hebert AS, Westphall MS, Coon JJ. Ribonucleic Acid Sequence Characterization by Negative Electron Transfer Dissociation Mass Spectrometry. Anal Chem 2020; 92:4436-4444. [PMID: 32091202 PMCID: PMC7161943 DOI: 10.1021/acs.analchem.9b05388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Modified oligonucleotides represent a promising avenue for drug development, with small interfering RNAs (siRNA) and microRNAs gaining traction in the therapeutic market. Mass spectrometry (MS)-based analysis offers many benefits for characterizing modified nucleic acids. Negative electron transfer dissociation (NETD) has proven valuable in sequencing oligonucleotide anions, particularly because it can retain modifications while generating sequence-informative fragments. We show that NETD can be successfully implemented on a widely available quadrupole-Orbitrap-linear ion trap mass spectrometer that uses a front-end glow discharge source to generate radical fluoranthene reagent cations. We characterize both unmodified and modified ribonucleic acids and present the first application of activated-ion negative electron transfer dissociation (AI-NETD) to nucleic acids. AI-NETD achieved 100% sequence coverage for both a 6-mer (5'-rGmUrArCmUrG-3') with 2'-O-methyl modifications and a 21-mer (5'-rCrArUrCrCrUrCrUrArGrArGrGrArUrArGrArArUrG-3'), the luciferase antisense siRNA. Both NETD and AI-NETD afforded complete sequence coverage of these molecules while maintaining a relatively low degree of undesired base-loss products and internal products relative to collision-based methods.
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Affiliation(s)
| | - Qiuwen Quan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dain R. Brademan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | | | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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37
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Calderisi G, Glasner H, Breuker K. Radical Transfer Dissociation for De Novo Characterization of Modified Ribonucleic Acids by Mass Spectrometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Giovanni Calderisi
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Heidelinde Glasner
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
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Calderisi G, Glasner H, Breuker K. Radical Transfer Dissociation for De Novo Characterization of Modified Ribonucleic Acids by Mass Spectrometry. Angew Chem Int Ed Engl 2020; 59:4309-4313. [PMID: 31867820 PMCID: PMC7065001 DOI: 10.1002/anie.201914275] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) can reliably detect and localize all mass-altering modifications of ribonucleic acids (RNA), but current MS approaches that allow for simultaneous de novo sequencing and modification analysis generally require specialized instrumentation. Here we report a novel RNA dissociation technique, radical transfer dissociation (RTD), that can be used for the comprehensive de novo characterization of ribonucleic acids and their posttranscriptional or synthetic modifications. We demonstrate full sequence coverage for RNA consisting of up to 39 nucleotides and show that RTD is especially useful for RNA with highly labile modifications such as 5-hydroxymethylcytidine and 5-formylcytidine.
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Affiliation(s)
- Giovanni Calderisi
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Heidelinde Glasner
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
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Liu Y, Tureček F. Photodissociative Cross-Linking of Diazirine-Tagged Peptides with DNA Dinucleotides in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1992-2006. [PMID: 30945107 DOI: 10.1007/s13361-019-02189-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Non-covalent complexes of DNA dinucleotides dAA, dAT, dGG, dGC, and dCG with diazirine-tagged Cys-Ala-Gln-Lys peptides were generated as singly charged ions in the gas phase. Laser photodissociation at 355 nm of the diazirine ring in the gas-phase complexes created carbene intermediates that underwent covalent cross-linking to the dinucleotides. The dinucleotides differed in the cross-linking yields, ranging from 27 to 36% for dAA and dAT up to 90-98% for dGG, dGC, and dCG. Collision-induced dissociation tandem mass spectrometry (CID-MS3) of the cross-linked conjugates revealed that fragmentation occurred chiefly in the dinucleotide moieties, resulting in a loss of a nucleobase and backbone cleavages. The CID-MS3 spectra further revealed that cross-links were primarily formed in the 3'-nucleotides for the dAT, dGC, and dCG combinations. Gas-phase and solution structures of dGG complexes with S-tagged CAQK were investigated by Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations. The low free-energy complexes had zwitterionic structures in which the peptide was protonated at the N-terminus and in the Lys residue whereas the carboxyl or dGG phosphate were deprotonated, corresponding to the respective (Cys+, Lys+, COO-)+ and (Cys+, Lys+, phosphate-)+ protomeric types. Both types preferred structures in which the peptide N-terminal cysteine carrying the S-photo-tag was aligned with the 3'-guanine moiety. BOMD trajectories at 310 K were analyzed for close contacts of the incipient peptide carbene with the positions in dGG that pointed to frequent contacts with the N-1, NH2, and N-7 atoms of 3'-guanine, in agreement with the cross-linking results. Carbene insertion to the guanine N-1-H and NH2 bonds was calculated by density functional and Møller-Plesset perturbational theory to be 350-380 kJ mol-1 exothermic. Based on calculations, we proposed a mechanism for the carbene reaction with guanine starting with an exothermic attack at N-7 to form a dipolar intermediate that can close an aziridine ring in another exothermic reaction, forming a stable covalent cross link. Graphical Abstract.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA.
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Fuchs E, Falschlunger C, Micura R, Breuker K. The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry. Nucleic Acids Res 2019; 47:7223-7234. [PMID: 31276590 PMCID: PMC6698743 DOI: 10.1093/nar/gkz574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/15/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022] Open
Abstract
The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodiester backbone moiety on its 5'-side that facilitates preferential phosphodiester backbone bond cleavage upon vibrational excitation by low-energy collisionally activated dissociation. Removal of the basic N3 site by deaza-modification of adenine was found to abrogate preferential phosphodiester backbone bond cleavage. No such effects were observed for N1 or N7 of adenine. Importantly, we found that the pH of the solution used for generation of the multiply protonated, gaseous RNA ions by electrospray ionization affects phosphodiester backbone bond cleavage next to adenine, which implies that the protonation patterns in solution are at least in part preserved during and after transfer into the gas phase. Our study suggests that interactions between protonated adenine and phosphodiester moieties of RNA may play a more important mechanistic role in biological processes than considered until now.
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Affiliation(s)
- Elisabeth Fuchs
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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41
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Pourshahian S, Gryaznov SM. Sequencing of Phosphoramidate Oligonucleotides by Acid Hydrolysis and Mass Spectrometry. Anal Chem 2019; 91:11154-11161. [PMID: 31386344 DOI: 10.1021/acs.analchem.9b01858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrolysis of N3'-P5' phosphoramidate and thiophosphoramidate oligonucleotides with 0.1% formic acid leads to the cleavage of the 3' N-P bond and generates two products, one of which contains a 5'-phosphate. Analysis of the hydrolytic products by liquid chromatography, coupled with mass spectrometry, reveals the mass ladder from both termini, which is used to determine the sequence. While acid hydrolysis does not result in depurination, internal fragments especially in the low mass range are detected. The method is applied to DNA and RNA analogues with and without modifications at the 2'-position. This approach enables rapid sequence confirmation of synthetic phosphoramidate oligonucleotides for quality control as well as denovo sequencing.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson , South San Francisco , California 94080 , United States
| | - Sergei M Gryaznov
- Janssen Pharmaceutical Companies of Johnson & Johnson , South San Francisco , California 94080 , United States
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42
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:11/7/a032359. [PMID: 31262947 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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Abstract
Mass spectrometry (MS) is an analytical tool complimentary for being sensitive, accurate, and versatile in its application, such as the identification of multistranded nucleic acid assemblies, including G-quadruplex. More specifically, electrospray ionization mass spectrometry (ESI-MS) has been successfully applied to probe various G-quadruplex formations and G-quadruplex-ligand interactions. The benefit of the ESI process is that the noncovalent interactions, which typically stabilize the multistranded motifs of G-quadruplex in solution, are preserved in the gas phase. Here we use ESI-MS to describe the structural characterization of G-quadruplex structures found in three G-rich sequences, as well as the ligand binding. Detailed structural information of G-quadruplexes and their ligand-bound complexes (such as the cation/ligand binding stoichiometry, and the number of strands and G-quartets) can be obtained from a single spectrum using this ESI-MS-based method.
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Affiliation(s)
- Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, People's Republic of China.
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Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
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Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
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Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
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Quantitative analysis of imetelstat in plasma with LC-MS/MS using solid-phase or hybridization extraction. Bioanalysis 2017; 9:1859-1872. [PMID: 29205051 DOI: 10.4155/bio-2017-0145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
AIM Imetelstat, a 13-mer oligonucleotide with a lipid tail is being evaluated for treating hematologic myeloid malignancies. This report describes the development of extraction and quantification methods for imetelstat. Methodology & results: Imetelstat was extracted using SPE (rat plasma) or by hybridization using a biotinylated capture probe (human plasma) and was quantified by LC-MS/MS. Calibration curves were established (0.1-50 μg/ml). Stability of imetelstat in plasma was demonstrated. Concentrations of imetelstat extracted using either of the methods and quantified with LC-MS/MS were comparable with a validated ELISA. CONCLUSION Two extraction methods (solid phase and hybridization) were developed for quantifying imetelstat in plasma using LC-MS/MS. The hybridization extraction in combination with LC-MS/MS is a novel extraction approach.
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47
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Hari Y, Leumann CJ, Schürch S. What Hinders Electron Transfer Dissociation (ETD) of DNA Cations? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2677-2685. [PMID: 28932996 DOI: 10.1007/s13361-017-1791-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a•/w or d/z• ion pairs. This reaction pathway contrasts with previous findings on the dissociation processes after electron capture by DNA cations, suggesting multiple, parallel dissociation channels. However, all these channels merely result in partial fragmentation of the precursor ion because the charge-reduced DNA radical cations are quite stable. Two hypotheses are put forward to explain the low dissociation yield of DNA radical cations: it is either attributed to non-covalent interactions between complementary fragments or to the stabilization of the unpaired electron in stacked nucleobases. MS3 experiments suggest that the charge-reduced species is the intact oligonucleotide. Moreover, introducing abasic sites significantly increases the dissociation yield of DNA cations. Consequently, the stabilization of the unpaired electron by π-π-stacking provides an appropriate rationale for the high intensity of DNA radical cations after electron transfer. Graphical Abstract.
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Affiliation(s)
- Yvonne Hari
- Department of Chemistry and Biochemistry, Freiestrasse 3, 3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, Freiestrasse 3, 3012, Bern, Switzerland
| | - Stefan Schürch
- Department of Chemistry and Biochemistry, Freiestrasse 3, 3012, Bern, Switzerland.
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Schneeberger E, Breuker K. Native Top-Down Mass Spectrometry of TAR RNA in Complexes with a Wild-Type tat Peptide for Binding Site Mapping. Angew Chem Int Ed Engl 2017; 56:1254-1258. [PMID: 28000363 PMCID: PMC5299493 DOI: 10.1002/anie.201610836] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Indexed: 12/18/2022]
Abstract
Ribonucleic acids (RNA) frequently associate with proteins in many biological processes to form more or less stable complex structures. The characterization of RNA-protein complex structures and binding interfaces by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, or strategies based on chemical crosslinking, however, can be quite challenging. Herein, we have explored the use of an alternative method, native top-down mass spectrometry (MS), for probing of complex stoichiometry and protein binding sites at the single-residue level of RNA. Our data show that the electrostatic interactions between HIV-1 TAR RNA and a peptide comprising the arginine-rich binding region of tat protein are sufficiently strong in the gas phase to survive phosphodiester backbone cleavage of RNA by collisionally activated dissociation (CAD), thus allowing its use for probing tat binding sites in TAR RNA by top-down MS. Moreover, the MS data reveal time-dependent 1:2 and 1:1 stoichiometries of the TAR-tat complexes and suggest structural rearrangements of TAR RNA induced by binding of tat peptide.
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Affiliation(s)
- Eva‐Maria Schneeberger
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80-826020InnsbruckAustria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80-826020InnsbruckAustria
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49
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Schneeberger E, Breuker K. Native Top‐Down Mass Spectrometry of TAR RNA in Complexes with a Wild‐Type tat Peptide for Binding Site Mapping. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Eva‐Maria Schneeberger
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) Universität Innsbruck Innrain 80-82 6020 Innsbruck Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) Universität Innsbruck Innrain 80-82 6020 Innsbruck Austria
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50
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tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence. Nat Commun 2016; 7:13302. [PMID: 27834374 PMCID: PMC5114619 DOI: 10.1038/ncomms13302] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 09/21/2016] [Indexed: 02/07/2023] Open
Abstract
Microbial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification. We report that changes in gene expression in hypoxia-induced non-replicating persistence in mycobacteria—which models tuberculous granulomas—are partly determined by a mechanism of tRNA reprogramming and codon-biased translation. Mycobacterium bovis BCG responded to each stage of hypoxia and aerobic resuscitation by uniquely reprogramming 40 modified ribonucleosides in tRNA, which correlate with selective translation of mRNAs from families of codon-biased persistence genes. For example, early hypoxia increases wobble cmo5U in tRNAThr(UGU), which parallels translation of transcripts enriched in its cognate codon, ACG, including the DosR master regulator of hypoxic bacteriostasis. Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria. Mycobacteria can adapt to the stress of human infection by entering a dormant state. Here the authors show that hypoxia-induced dormancy in M. bovis BCG involves the reprogramming of tRNA wobble modifications and copy numbers, coupled with biased use of synonymous codons in survival genes.
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