1
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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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2
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Zhou Y, Du W, Chen Y, Li L, Xiao X, Xu Y, Yang W, Hu X, Wang B, Zhang J, Jiang Q, Wang Y. Pathogen detection via inductively coupled plasma mass spectrometry analysis with nanoparticles. Talanta 2024; 277:126325. [PMID: 38833906 DOI: 10.1016/j.talanta.2024.126325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/24/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024]
Abstract
Infections caused by viruses and bacteria pose a significant threat to global public health, emphasizing the critical importance of timely and precise detection methods. Inductively coupled plasma mass spectrometry (ICP-MS), a contemporary approach for pathogen detection, offers distinct advantages such as high sensitivity, a wide linear range, and multi-index capabilities. This review elucidates the underexplored application of ICP-MS in conjunction with functional nanoparticles (NPs) for the identification of viruses and bacteria. The review commences with an elucidation of the underlying principles, procedures, target pathogens, and NP requirements for this innovative approach. Subsequently, a thorough analysis of the advantages and limitations associated with these techniques is provided. Furthermore, the review delves into a comprehensive examination of the challenges encountered when utilizing NPs and ICP-MS for pathogen detection, culminating in a forward-looking assessment of the potential pathways for advancement in this domain. Thus, this review contributes novel perspectives to the field of pathogen detection in biomedicine by showcasing the promising synergy of ICP-MS and NPs.
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Affiliation(s)
- Yujie Zhou
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Wenli Du
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Yuzuo Chen
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lei Li
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Xuanyu Xiao
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Yuanyuan Xu
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Wenjuan Yang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xuefeng Hu
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Baoning Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Jieyu Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China.
| | - Qing Jiang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
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Frańska M, Stȩżycka O, Jankowski W, Hoffmann M. Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1474-1479. [PMID: 35796751 PMCID: PMC9354248 DOI: 10.1021/jasms.2c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gas-phase decompositions of magnesium complexes with adenosine-5'-triphosphate (ATP) and adenosine-5'-diphosphate (ADP) were studied by using electrospray ionization-collision-induced dissociation-tandem mass spectrometry, in the negative ion mode. The loss of internal ribose residue was observed and was found to occur directly from the [ADP-3H+Mg]- ion. The occurrence of this process indicates the presence of a strong phosphate-Mg-adenine interaction. The performed quantum mechanics calculations confirmed the occurrence of this interaction in the [ADP-3H+Mg]- ion, namely the presence of Mg-N7 bond and hydrogen bond between the phosphate oxygen atom and amino group. Although the finding concerns the gas phase, it indicates that phosphate-Mg-adenine interaction may be also of importance for biological processes. The loss of an internal ribose residue was also observed for calcium and zinc complexes with ATP/ADP as well as for magnesium complexes with guanosine-5'-triphosphate (GTP) or guanosine-5'-diphosphate (GDP). Therefore, it is reasonable to conclude that the presence of the phosphate-metal-nucleobase interaction is a feature of gas phase [NDP-3H+metal]- ion (NDP, nucleoside-5'-diphosphate) and may also be important for biological processes.
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Affiliation(s)
- Magdalena Frańska
- Institute
of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Olga Stȩżycka
- Institute
of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Wojciech Jankowski
- Faculty of
Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego
8, 61-614 Poznań, Poland
| | - Marcin Hoffmann
- Faculty of
Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego
8, 61-614 Poznań, Poland
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4
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Li X, Liao L, Jiang B, Yuan R, Xiang Y. Invader assay-induced catalytic assembly of multi-DNAzyme junctions for sensitive detection of single nucleotide polymorphisms. Anal Chim Acta 2022; 1224:340225. [DOI: 10.1016/j.aca.2022.340225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/21/2022] [Accepted: 07/31/2022] [Indexed: 01/07/2023]
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Tyunina EY, Barannikov VP, Dunaeva VV, Krasnov AV. Enthalpies of Sublimation and Solvation of Alanine-Containing Dipeptides. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s003602442204032x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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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: 1] [Impact Index Per Article: 0.5] [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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7
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Takeuchi S, Yamamoto M, Matsumoto S, Kenjo E, Karashima M, Ikeda Y. Pinpoint modification strategy for stabilization of single guide RNA. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1192:123149. [PMID: 35139474 DOI: 10.1016/j.jchromb.2022.123149] [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: 12/26/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/23/2022]
Abstract
The clustered regularly interspaced short palindromic repeats-CRISPR associated protein9 (CRISPR-Cas9) system, which includes a single guide RNA (sgRNA) and a Cas9 protein, is an emerging and promising gene editing technology that produces specific changes, including insertions, deletions, or substitutions, in desired targets. This approach can be applied in novel therapeutic areas for multiple cancers and genetic diseases, including Parkinson's disease, sickle cell disease, and muscular dystrophy. However, there are many limitations to its potential application to therapeutics. CRISPR-Cas9 activity without side effects, delivery of CRISPR-Cas9 to the target cell within the desired tissue including liver, lungs, brain and muscle and the expression of Cas9 endonuclease in the target cell are key factors in achieving therapeutic efficacy. Generally, single-stranded RNA is immediately degraded in cells and biological fluids such as serum, as chemically unmodified single-stranded RNA shows extremely poor stability against nuclease degradation. To overcome this limitation, sgRNA is chemically modified to obtain a highly stable sgRNA for efficient gene editing in cells and in vivo. Here, we identified the cleavage site of sgRNA for pinpoint modification in biological tissues using mass spectrometry and improved stability of pinpoint modified sgRNA in these fluids. Although improved efficiency provided by modified sgRNA has already been reported, we identified the cleavage site by mass spectrometry and revealed that the stability increased with the pinpoint modification strategy for the first time in this study. In future studies, the efficiency of pinpoint modification strategy for the potential application of sgRNA by systematic routes, including intravenous and subcutaneous administration will be assessed.
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Affiliation(s)
- Shoko Takeuchi
- Analytical Development, Pharmaceutical Sciences, Takeda Pharmaceutical Company Limited, Japan.
| | - Mitsuo Yamamoto
- Analytical Development, Pharmaceutical Sciences, Takeda Pharmaceutical Company Limited, Japan
| | - Satoru Matsumoto
- Drug Product Development, Pharmaceutical Sciences, Takeda Pharmaceutical Company Limited, Japan
| | - Eriya Kenjo
- TCiRA Discovery, Takeda Pharmaceutical Company Limited, Japan
| | - Masatoshi Karashima
- Analytical Development, Pharmaceutical Sciences, Takeda Pharmaceutical Company Limited, Japan
| | - Yukihiro Ikeda
- Analytical Development, Pharmaceutical Sciences, Takeda Pharmaceutical Company Limited, Japan
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8
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Starke I, Fürstenberg S. Investigation of the binding site of ruthenium complexes to short single-stranded oligodeoxynucleotides using electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9231. [PMID: 34866265 DOI: 10.1002/rcm.9231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/18/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
RATIONALE In order to elucidate the nature of the interaction between metal complexes and DNA, use was made of short telomere single-stranded oligodeoxynucleotide (ODN) strand 5'-T1 T2 A3 G4 G5 G6 -3' (1) and strands 5'-T1 C2 A3 G4 G5 G6 -3' (2), 5'-T1 T2 A3 C4 G5 G6 -3' (3) and 5'-T1 C2 C3 C4 C5 G6 -3' (4) for the verification of the binding site with four different ruthenium complexes as possible anticancer drug candidates. METHODS The ability to form adducts between ruthenium complexes with short single-stranded 6-mers was investigated through the use of electrospray ionization mass spectrometry (ESI-MS). Full scan ESI mass spectra and collision-induced dissociation (CID) mass spectra were recorded on a high-resolution quadrupole time-of-flight mass spectrometer. The elemental compositions of the adducts and the most important product ions were calculated by exact mass measurements. RESULTS ESI-MS measurements showed that the mono-ruthenated ODNs were the main products produced under the conditions for the four ruthenium complexes and each of the ODNs. The CID results revealed that thymine and guanine are the preferred binding sites depending on the different compositions in the ODNs. However, for the ODN of the type: 5'-T1 C2 C3 C4 C5 G6 -3' the coordination site on cytosine was observed as well. The different ruthenium complexes interacted in the same way. CONCLUSIONS This study showed that the characterization of new ruthenium complexes with short single-stranded telomeric DNA (TTAGGG) and further different ODNs is possible with positive ESI-MS/MS measurement. The identification of thymine and cytosine besides guanine as possible binding sites suggests that the interaction site is highly affected by the ODN's structure.
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Affiliation(s)
- Ines Starke
- Institute of Chemistry, University of Potsdam, Potsdam, Germany
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9
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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: 31] [Impact Index Per Article: 10.3] [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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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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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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12
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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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13
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Huang C, Ma Z, Lin J, Gong X, Zhang F, Wu X, Wang F, Zheng W, Zhao Y, Wu K. Tandem Mass Spectrometry Reveals Preferential Ruthenation of Thymines in Human Telomeric G-Quadruplex DNA by an Organometallic Ruthenium Anticancer Complex. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chao Huang
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Ziqi Ma
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Jiafan Lin
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Xianxian Gong
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Fengfeng Zhang
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Xiaoqin Wu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Wei Zheng
- Peking University Health Science Center, Beijing 100191, People’s Republic of China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Kui Wu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
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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: 127] [Impact Index Per Article: 31.8] [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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15
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Li C, Attanayake K, Valentine SJ, Li P. Facile Improvement of Negative Ion Mode Electrospray Ionization Using Capillary Vibrating Sharp-Edge Spray Ionization. Anal Chem 2020; 92:2492-2502. [PMID: 31940176 PMCID: PMC7318871 DOI: 10.1021/acs.analchem.9b03983] [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: 12/11/2022]
Abstract
Electrospray ionization (ESI) is often affected by corona discharge when spraying 100% aqueous solutions as the voltage that induces discharge can be well below the onset voltage of ESI. As a result, it is especially challenging to perform native mass spectrometry in negative ion mode where 100% aqueous solution is preferred. Here we report a simple instrumentation method to improve the performance of ESI in negative ion mode based on capillary vibrating sharp-edge spray ionization. By attaching a fused silica capillary emitter to a vibrating glass slide, improved signal quality is achieved for various analytes in aqueous solutions over applying ESI alone. Compared to commercial ESI sources using nebulization gas to reduce discharge, 10-100-fold enhancement in signal intensity and 3-10-fold improvement in S/N are achieved for various kinds of molecules including DNA, peptides, proteins, and oligosaccharides. Finally, the new method demonstrates utility for native mass spectrometry analysis of proteins and G-quadruplex DNA. The present method is expected to have great potential to be adopted by the scientific community because of its improved analytical performance, simplicity, and low cost.
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Affiliation(s)
- Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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16
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Ma YF, Yuan F, Yu Y, Zhou YL, Zhang XX. Synthesis of a pH-Responsive Functional Covalent Organic Framework via Facile and Rapid One-Step Postsynthetic Modification and Its Application in Highly Efficient N1-Methyladenosine Extraction. Anal Chem 2019; 92:1424-1430. [DOI: 10.1021/acs.analchem.9b04600] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yu-Fang Ma
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yue Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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17
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Appy L, Chardet C, Peyrottes S, Roy B. Synthetic Strategies for Dinucleotides Synthesis. Molecules 2019; 24:molecules24234334. [PMID: 31783537 PMCID: PMC6930578 DOI: 10.3390/molecules24234334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Dinucleoside 5′,5′-polyphosphates (DNPs) are endogenous substances that play important intra- and extracellular roles in various biological processes, such as cell proliferation, regulation of enzymes, neurotransmission, platelet disaggregation and modulation of vascular tone. Various methodologies have been developed over the past fifty years to access these compounds, involving enzymatic processes or chemical procedures based either on P(III) or P(V) chemistry. Both solution-phase and solid-support strategies have been developed and are reported here. Recently, green chemistry approaches have emerged, offering attracting alternatives. This review outlines the main synthetic pathways for the preparation of dinucleoside 5′,5′-polyphosphates, focusing on pharmacologically relevant compounds, and highlighting recent advances.
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19
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Cheng Y, Zeng W, Cheng Y, Zhang J, Zou T, Wu K, Wang F. Selective binding of an organoruthenium complex to G-rich human telomeric sequence by tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:2152-2158. [PMID: 30252980 DOI: 10.1002/rcm.8292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Human telomeric DNA is reported to be a potential target for anticancer organometallic ruthenium(II) complexes, however, the interaction sites were not clearly discriminated and identified. METHODS In the current study, tandem mass spectrometry (MS/MS) using collision-induced dissociation (CID) was firstly introduced to identify the interaction sites of an organometallic ruthenium(II) complex [(η6 -biphenyl)Ru(en)Cl][PF6 ] (1; en = ethylenediamine) with 5'-T1 T2 A3 G4 G5 G6 -3' (I), the repeating unit of human telomeric DNA, in both positive- and negative-ion mode at a low reaction molar ratio (1/I = 0.2) which was applied to preserve the site selectivity. RESULTS Mass spectrometric results showed that mono-ruthenated I was the main product under the conditions. In positive-ion mode, MS/MS results indicated that ruthenium complex 1 binds to T2 or G6 in strand I. However, in negative-ion mode, no efficient information was obtained for exact identification of ruthenation sites which may be attributed to losses of fragment ions due to charge neutralization by the coordination of the positively charged ruthenium complex to the short MS/MS fragments. CONCLUSIONS This is the first report of using top-down MS to characterize the interactions of organometallic ruthenium(II) complexes and human telomeric DNA. Thymine can be thermodynamically competitive with guanine for binding to ruthenium complexes even at low reaction molar ratio, which inspired us to explore in greater depth the significance of thymine binding.
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Affiliation(s)
- Yiyu Cheng
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, 430081, PR China
| | - Wenjuan Zeng
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
- University of Chinese Academy Sciences, Beijing, 100049, PR China
| | - Yang Cheng
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, 430081, PR China
| | - Jishuai Zhang
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, 430081, PR China
| | - Tao Zou
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, 430081, PR China
| | - Kui Wu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, 430081, PR China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
- University of Chinese Academy Sciences, Beijing, 100049, PR China
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Jiménez-Meneses P, Bañuls MJ, Puchades R, Maquieira Á. Fluor-thiol Photocoupling Reaction for Developing High Performance Nucleic Acid (NA) Microarrays. Anal Chem 2018; 90:11224-11231. [DOI: 10.1021/acs.analchem.8b00265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Pilar Jiménez-Meneses
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - María-José Bañuls
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Rosa Puchades
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ángel Maquieira
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
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21
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Analysis of mononucleotides by tandem mass spectrometry: investigation of fragmentation pathways for phosphate- and ribose-modified nucleotide analogues. Sci Rep 2017; 7:8931. [PMID: 28827558 PMCID: PMC5567097 DOI: 10.1038/s41598-017-09416-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/24/2017] [Indexed: 12/23/2022] Open
Abstract
Synthetic nucleotide and nucleic acid analogues are useful research tools and modern therapeutics. Hence, methods for the rapid and unambiguous identification of mononucleotides derived from organic syntheses or biological materials are of broad interest. Here, we analysed over 150 mononucleotides (mostly nucleoside 5′-mono-, 5′-di-, and 5′-triphosphates) and their structurally related nucleobase-, phosphate-, and ribose-modified analogues by electrospray tandem mass spectrometry (ESI/MS/MS), identifying characteristic fragmentation ions that may be helpful in structure determination. While positive-ion mode yielded fragments derived mainly from nucleobases, negative-ion mode provided insight into the structures of phosphoryl and phosphoribosyl moieties, enabling the determination of structural features such as the number of phosphate groups and the presence of ribose or phosphate substitutions. Based on these data, we proposed fragmentation pathways that were confirmed by experiments with [18O]-isotopologues. We demonstrated the utility of ESI(−)/MS/MS in the analysis of structurally related compounds by analysing isomeric and isobaric nucleotides and applying ESI(−)/MS/MS to rapid identification of nucleotide synthesis products. We formulated general rules regarding nucleotide structure–fragmentation pattern relationships and indicating characteristic fragmentation ions for the interpretation of ESI(−)/MS/MS spectra of nucleotides and their analogues. The ESI(−)/MS/MS spectra of all nucleotides are available in an on-line database, msTide, at www.msTide-db.com.
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Yang W, Ma H, Yang Q, Wang J, Liu Y, Yang Q, Wu J, Song C, Chang J. The first example of palladium-catalyzed cascade amidine arylation–intramolecular ester amidation for the synthesis of hypoxanthines: application to the synthesis of 8-azanebularine analogues. Org Biomol Chem 2017; 15:379-386. [DOI: 10.1039/c6ob02121b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A synthetic route toward 8-azanebularines has been developed by involving a cycloaddition and a cascade amidine arylation–intramolecular ester amidation reaction.
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Affiliation(s)
- Wu Yang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Haoran Ma
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Qian Yang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Jingwen Wang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Yuan Liu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Qinghua Yang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Jie Wu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Chuanjun Song
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
| | - Junbiao Chang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Henan Province 450001
- China
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23
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Esparza C, Borisov R, Varlamov A, Zaikin V. Composite glycerol/graphite/aromatic acid matrices for thin-layer chromatography/matrix-assisted laser desorption/ionization mass spectrometry of heterocyclic compounds. J Chromatogr A 2016; 1470:118-122. [DOI: 10.1016/j.chroma.2016.09.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 11/30/2022]
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Schürch S. Characterization of nucleic acids by tandem mass spectrometry - The second decade (2004-2013): From DNA to RNA and modified sequences. MASS SPECTROMETRY REVIEWS 2016; 35:483-523. [PMID: 25288464 DOI: 10.1002/mas.21442] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 05/04/2014] [Accepted: 05/04/2014] [Indexed: 06/03/2023]
Abstract
Nucleic acids play key roles in the storage and processing of genetic information, as well as in the regulation of cellular processes. Consequently, they represent attractive targets for drugs against gene-related diseases. On the other hand, synthetic oligonucleotide analogues have found application as chemotherapeutic agents targeting cellular DNA and RNA. The development of effective nucleic acid-based chemotherapeutic strategies requires adequate analytical techniques capable of providing detailed information about the nucleotide sequences, the presence of structural modifications, the formation of higher-order structures, as well as the interaction of nucleic acids with other cellular components and chemotherapeutic agents. Due to the impressive technical and methodological developments of the past years, tandem mass spectrometry has evolved to one of the most powerful tools supporting research related to nucleic acids. This review covers the literature of the past decade devoted to the tandem mass spectrometric investigation of nucleic acids, with the main focus on the fundamental mechanistic aspects governing the gas-phase dissociation of DNA, RNA, modified oligonucleotide analogues, and their adducts with metal ions. Additionally, recent findings on the elucidation of nucleic acid higher-order structures by tandem mass spectrometry are reviewed. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:483-523, 2016.
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Affiliation(s)
- Stefan Schürch
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland
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25
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Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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26
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Gaston KW, Limbach PA. The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry. RNA Biol 2015; 11:1568-85. [PMID: 25616408 PMCID: PMC4615682 DOI: 10.4161/15476286.2014.992280] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.
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Affiliation(s)
- Kirk W Gaston
- a Rieveschl Laboratories for Mass Spectrometry; Department of Chemistry ; University of Cincinnati ; Cincinnati , OH USA
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27
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Yu C, Chang X, Liu J, Ding L, Peng J, Fang Y. Creation of reduced graphene oxide based field effect transistors and their utilization in the detection and discrimination of nucleoside triphosphates. ACS APPLIED MATERIALS & INTERFACES 2015; 7:10718-10726. [PMID: 25946520 DOI: 10.1021/acsami.5b00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two low-cost, micropatterned, solution-gated field effect transistors (modified FET and unmodified FET) based on reduced graphene oxide (RGO) were developed and used for detection and discrimination of nucleoside triphosphates (NTPs). The modified FET was realized by simple deposition of a positively charged bis-pyrenyl derivative, py-diIM-py, onto the conducting RGO strips of the unmodified FET. The electrical properties and sensing behaviors of the as-prepared devices were studied comprehensively. Electrical transfer property tests revealed that both of the two FETs exhibit V-shaped ambipolar field effect behavior from p-type region to n-type region. Sensing performance studies demonstrated that modification of the native FET with py-diIM-py improves its sensing ability to NTPs-GTP and ATP in particular. The detection limit of GTP and ATP was as low as 400 nM, which is the lowest value for graphene-based electronic sensors reported so far. Furthermore, based on the cross-reactive responses of the two devices to NTPs, NTPs can be conveniently distinguished via combining use of the two devices. The enhancement of the modifier (py-diIM-py) to the sensing performance of the FET is tentatively attributed to its possible mediation role in sticking onto RGO strips and accumulating analytes by electrostatic association with the relevant species. Because they are sensitive and fast in response, simple and low-cost in preparation, and possibly useful in sensor-array fabrication, the developed sensors show great potential in real-life application.
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Affiliation(s)
- Chunmeng Yu
- †Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Xingmao Chang
- ‡Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Materials Science and Engineering, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Jing Liu
- †Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Liping Ding
- †Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Junxia Peng
- †Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Yu Fang
- †Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, People's Republic of China
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Quantitation of endogenous nucleoside triphosphates and nucleosides in human cells by liquid chromatography tandem mass spectrometry. Anal Bioanal Chem 2015; 407:3693-704. [PMID: 25749797 DOI: 10.1007/s00216-015-8588-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/06/2015] [Accepted: 02/20/2015] [Indexed: 10/23/2022]
Abstract
Nucleosides and nucleoside triphosphates are the building blocks of nucleic acids and important bioactive metabolites, existing in all living cells. In the present study, two liquid chromatography tandem mass spectrometry methods were developed to quantify both groups of compounds from the same sample with a shared extraction procedure. After a simple protein precipitation with methanol, the nucleosides were separated with reversed phase chromatography on an Atlantis T3 column while for the separation of the nucleoside triphosphates, an anion exchange column (BioBasic AX) was used. No addition of ion pair reagent was required. A 5500 QTrap was used as analyzer, operating as triple quadrupole. The analytical method for the nucleoside triphosphates has been validated according to the guidelines of the US Food and Drug Administration. The lower limit of quantification values were determined as 10 pg on column (0.5 ng/mL in the injection solution) for deoxyadenosine triphosphate and deoxyguanosine triphosphate, 20 pg (1 ng/mL) for deoxycytidine triphosphate and thymidine triphosphate, 100 pg (5 ng/mL) for cytidine triphosphate and guanosine triphosphate, and 500 pg (25 ng/mL) for adenosine triphosphate und uridine triphosphate respectively. This methodology has been applied to the quantitation of nucleosides and nucleoside triphosphates in primary human CD4 T lymphocytes and macrophages. As expected, the concentrations for ribonucleosides and ribonucleoside triphophates were considerably higher than those obtained for the deoxy derivatives. Upon T cell receptor activation, the levels of all analytes, with the notable exceptions of deoxyadenosine triphosphate and deoxyguanosine triphosphate, were found to be elevated in CD4 T cells.
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Wang X, Chen X, Sun S, Zhang F, Zhu J. Salt-enabled visual detection of DNA. Chem Commun (Camb) 2014; 50:15744-7. [PMID: 25370740 DOI: 10.1039/c4cc06536k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein a label-free, salt-enabled visual detection strategy for DNA, based on the alteration of surface adhesion properties of salt solution, which can translate to the change in the size of the salt residue upon drying, with self-assembled DNA nanostructures. This environmentally friendly array assay protocol enables the achievement of a detection sensitivity comparable to classic colorimetric methods, single-base mismatch differentiation selectivity, multiple-target detection capability, RNA target detection, and a ligase chain reaction-rolling circle amplification implementation format.
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Affiliation(s)
- Xilong Wang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093, China.
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Gavina JMA, Yao C, Feng YL. Recent developments in DNA adduct analysis by mass spectrometry: a tool for exposure biomonitoring and identification of hazard for environmental pollutants. Talanta 2014; 130:475-94. [PMID: 25159438 DOI: 10.1016/j.talanta.2014.06.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 02/08/2023]
Abstract
DNA adducts represent an important category of biomarkers for detection and exposure surveillance of potential carcinogenic and genotoxic chemicals in the environment. Sensitive and specific analytical methods are required to detect and differentiate low levels of adducts from native DNA from in vivo exposure. In addition to biomonitoring of environmental pollutants, analytical methods have been developed for structural identification of adducts which provides fundamental information for determining the toxic pathway of hazardous chemicals. In order to achieve the required sensitivity, mass spectrometry has been increasingly utilized to quantify adducts at low levels as well as to obtain structural information. Furthermore, separation techniques such as chromatography and capillary electrophoresis can be coupled to mass spectrometry to increase the selectivity. This review will provide an overview of advances in detection of adducted and modified DNA by mass spectrometry with a focus on the analysis of nucleosides since 2007. Instrument advances, sample and instrument considerations, and recent applications will be summarized in the context of hazard assessment. Finally, advances in biomonitoring applying mass spectrometry will be highlighted. Most importantly, the usefulness of DNA adducts measurement and detection will be comprehensively discussed as a tool for assessment of in vitro and in vivo exposure to environmental pollutants.
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Affiliation(s)
- Jennilee M A Gavina
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Chunhe Yao
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Yong-Lai Feng
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9.
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31
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Escorihuela J, Bañuls MJ, Grijalvo S, Eritja R, Puchades R, Maquieira Á. Direct Covalent Attachment of DNA Microarrays by Rapid Thiol–Ene “Click” Chemistry. Bioconjug Chem 2014; 25:618-27. [DOI: 10.1021/bc500033d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jorge Escorihuela
- Centro
de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento
de Química, Universitat Politècnica de València, Camino
de Vera s/n, 46022 Valencia, Spain
| | - María-José Bañuls
- Centro
de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento
de Química, Universitat Politècnica de València, Camino
de Vera s/n, 46022 Valencia, Spain
| | - Santiago Grijalvo
- Networking Center on Bioengineering, Biomaterials and Biomedicine (CIBER-BBN) and Institute for Advanced Chemistry of Catalonia (IQAC−CSIC), Chemical and Biomolecular Nanotechnology Department, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramón Eritja
- Networking Center on Bioengineering, Biomaterials and Biomedicine (CIBER-BBN) and Institute for Advanced Chemistry of Catalonia (IQAC−CSIC), Chemical and Biomolecular Nanotechnology Department, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Rosa Puchades
- Centro
de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento
de Química, Universitat Politècnica de València, Camino
de Vera s/n, 46022 Valencia, Spain
| | - Ángel Maquieira
- Centro
de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento
de Química, Universitat Politècnica de València, Camino
de Vera s/n, 46022 Valencia, Spain
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32
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Xu N, Chingin K, Chen H. Ionic strength of electrospray droplets affects charging of DNA oligonucleotides. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:103-107. [PMID: 24446269 DOI: 10.1002/jms.3311] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/12/2013] [Accepted: 11/14/2013] [Indexed: 06/03/2023]
Abstract
The fundamental aspects of charging in electrospray ionization (ESI) are hotly debated. In the present study, ESI charging of DNA oligonucleotides was explored in both positive (ESI+) and negative (ESI-) polarity using mass spectrometry detection. Single-stranded 12-mer CCCCAATTCCCC in buffer solution (aqueous NH4Ac, 100 mM) produced similar charge state distribution (CSD) in either ESI+ or ESI-. Similarity of CSD in ESI+ and ESI- was also observed for the double-stranded 12-mer CGCGAATTCGCG. By adding typical low-vapor reagents (e.g. m-nitro benzyl alcohol, m-NBA; sulfolane) into the same buffer solution (<0.5% w/v), both CCCCAATTCCCC and CGCGAATTCGCG revealed strong supercharging (SC) effect in ESI-, while very little or no SC effect was observed in ESI+. With either sulfolane or m-NBA, the CGCGAATTCGCG duplex dissociated into single strands in ESI-. No SC was observed in both ESI+ and ESI- for thermally denatured CGCGAATTCGCG duplex in NH4 Ac buffer without the reagents. These findings are difficult to reconcile with the earlier model, which attributes SC in aqueous buffer solution to the conformational changes of analytes. Our observations suggest that the ionic strength of ESI droplets strongly affects the CSD of biopolymers such as DNA oligonucleotides and that SC effect is related to the depletion of ionic strength during the ESI process.
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Affiliation(s)
- Ning Xu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, 330013, P.R. China
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33
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Glycoconjugate Vaccines Used for Prevention from Biological Agents: Tandem Mass Spectrometric Analysis. DETECTION OF CHEMICAL, BIOLOGICAL, RADIOLOGICAL AND NUCLEAR AGENTS FOR THE PREVENTION OF TERRORISM 2014. [DOI: 10.1007/978-94-017-9238-7_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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34
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Escorihuela J, Bañuls MJ, Puchades R, Maquieira Á. Site-specific immobilization of DNA on silicon surfaces by using the thiol–yne reaction. J Mater Chem B 2014; 2:8510-8517. [DOI: 10.1039/c4tb01108b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Covalent immobilization of ssDNA fragments onto silicon-based materials was performed using the thiol–yne reaction.
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Affiliation(s)
- Jorge Escorihuela
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
| | - María-José Bañuls
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
| | - Rosa Puchades
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
| | - Ángel Maquieira
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
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35
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Kullolli M, Knouf E, Arampatzidou M, Tewari M, Pitteri SJ. Intact microRNA analysis using high resolution mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:80-87. [PMID: 24174127 PMCID: PMC4153431 DOI: 10.1007/s13361-013-0759-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/19/2013] [Accepted: 09/19/2013] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) are small single-stranded non-coding RNAs that post-transcriptionally regulate gene expression, and play key roles in the regulation of a variety of cellular processes and in disease. New tools to analyze miRNAs will add understanding of the physiological origins and biological functions of this class of molecules. In this study, we investigate the utility of high resolution mass spectrometry for the analysis of miRNAs through proof-of-concept experiments. We demonstrate the ability of mass spectrometry to resolve and separate miRNAs and corresponding 3' variants in mixtures. The mass accuracy of the monoisotopic deprotonated peaks from various miRNAs is in the low ppm range. We compare fragmentation of miRNA by collision-induced dissociation (CID) and by higher-energy collisional dissociation (HCD) which yields similar sequence coverage from both methods but additional fragmentation by HCD versus CID. We measure the linear dynamic range, limit of detection, and limit of quantitation of miRNA loaded onto a C18 column. Lastly, we explore the use of data-dependent acquisition of MS/MS spectra of miRNA during online LC-MS and demonstrate that multiple charge states can be fragmented, yielding nearly full sequence coverage of miRNA on a chromatographic time scale. We conclude that high resolution mass spectrometry allows the separation and measurement of miRNAs in mixtures and a standard LC-MS setup can be adapted for online analysis of these molecules.
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Affiliation(s)
- Majlinda Kullolli
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
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36
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Grishin ID. MALDI TOF mass spectrometry for the investigation of the structure of ruthenium carborane complexes. JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1134/s1061934813130078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Brahim B, Alves S, Cole RB, Tabet JC. Charge enhancement of single-stranded DNA in negative electrospray ionization using the supercharging reagent meta-nitrobenzyl alcohol. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1988-1996. [PMID: 24030289 DOI: 10.1007/s13361-013-0732-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 07/26/2013] [Accepted: 08/07/2013] [Indexed: 06/02/2023]
Abstract
Charge enhancement of single-stranded oligonucleotide ions in negative ESI mode is investigated. The employed reagent, meta-nitrobenzyl alcohol (m-NBA), was found to improve total signal intensity (Itot), increase the highest observed charge states (zhigh), and raise the average charge states (zavg) of all tested oligonucleotides analyzed in negative ESI. To quantify these increases, signal enhancement ratios (SER1%) and charge enhancement coefficients (CEC1%) were introduced. The SER1%, (defined as the quotient of total oligonucleotide ion abundances with 1% m-NBA divided by total oligonucleotide abundance without m-NBA) was found to be greater than unity for every oligonucleotide tested. The CEC1% values (defined as the average charge state in the presence of 1% m-NBA minus the average charge state in the absence of m-NBA) were found to be uniformly positive. Upon close inspection, the degree of charge enhancement for longer oligonucleotides was found to be dependent upon thymine density (i.e., the number and the location of phospho-thymidine units). A correlation between the charge enhancement induced by the presence of m-NBA and the apparent gas-phase acidity (largely determined by the sequence of thymine units but also by the presence of protons on other nucleobases) of multiply deprotonated oligonucleotide species, was thus established. Ammonium cations appeared to be directly involved in the m-NBA supercharging mechanism, and their role seems to be consistent with previously postulated ESI mechanisms describing desorption/ionization of single-stranded DNA into the gas phase.
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Affiliation(s)
- Bessem Brahim
- Institut Parisien de Chimie Moléculaire, Equipe de Chimie Structurale Organique et Biologique, Université Pierre et Marie Curie, CNRS UMR 7201, 75252, Paris cedex 05, France
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38
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Affiliation(s)
- Yonghui Liu
- Department of Polymer Science and Engineering, School
of Chemistry and Chemical Engineering, State Key Laboratory of Coordination
Chemistry, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093, China
| | - Huaxin Yao
- Department of Polymer Science and Engineering, School
of Chemistry and Chemical Engineering, State Key Laboratory of Coordination
Chemistry, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093, China
| | - Jin Zhu
- Department of Polymer Science and Engineering, School
of Chemistry and Chemical Engineering, State Key Laboratory of Coordination
Chemistry, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093, China
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39
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Silvestri C, Brodbelt JS. Tandem mass spectrometry for characterization of covalent adducts of DNA with anticancer therapeutics. MASS SPECTROMETRY REVIEWS 2013; 32:247-66. [PMID: 23150278 PMCID: PMC3578003 DOI: 10.1002/mas.21363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 05/17/2023]
Abstract
The chemotherapeutic activities of many anticancer and antibacterial drugs arise from their interactions with nucleic acid substrates. Some of these ligands interact with DNA in a way that causes conformational changes or damage to the nucleic acid targets, ultimately altering recognition by key DNA-specific enzymes, interfering with DNA transcription or prohibiting replication, and terminating cell growth and proliferation. The design and synthesis of ligands that bind to nucleic acids remains a dynamic field in medicinal chemistry and pharmaceutical research. The quest for more selective and efficacious DNA-interactive anticancer chemotherapeutics has likewise catalyzed the need for sensitive analytical methods that can provide structural information about the nature of the resulting DNA adducts and provide insight into the mechanistic pathways of the DNA/drug interactions and the impact on the cellular processes in biological systems. This review focuses on the array of tandem mass spectrometric strategies developed and applied for characterization of covalent adducts formed between DNA and anticancer ligands.
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Affiliation(s)
- Catherine Silvestri
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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40
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Wu K, Hu W, Luo Q, Li X, Xiong S, Sadler PJ, Wang F. Competitive binding sites of a ruthenium arene anticancer complex on oligonucleotides studied by mass spectrometry: ladder-sequencing versus top-down. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:410-420. [PMID: 23404464 DOI: 10.1007/s13361-012-0539-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 10/30/2012] [Accepted: 11/15/2012] [Indexed: 06/01/2023]
Abstract
We report identification of the binding sites for an organometallic ruthenium anticancer complex [(η (6)-biphenyl)Ru(en)Cl][PF6] (1; en = ethylenediamine) on the 15-mer single-stranded oligodeoxynucleotides (ODNs), 5'-CTCTCTX7G8Y9CTTCTC-3' [X = Y = T (I); X = C and Y = A (II); X = A and Y = T (III); X = T and Y = A (IV)] by electrospray ionization mass spectrometry (ESI-MS) in conjunction with enzymatic digestion or tandem mass spectrometry (top-down MS). ESI-MS combined with enzymatic digestion (termed MS-based ladder-sequencing), is effective for identification of the thermodynamically-favored G-binding sites, but not applicable to determine the thermodynamically unstable T-binding sites because the T-bound adducts dissociate during enzymatic digestion. In contrast, top-down MS is efficient for localization of the T binding sites, but not suitable for mapping ruthenated G bases, due to the facile fragmentation of G bases from ODN backbones prior to the dissociation of the phosphodiester bonds. The combination of the two MS approaches reveals that G8 in each ODN is the preferred binding site for 1, and that the T binding sites of 1 are either T7 or T11 on I and IV, and either T6 or T11 on II and III, respectively. These findings not only demonstrate for the first time that T-bases in single-stranded oligonucleotides are kinetically competitive with guanine for such organoruthenium complexes, but also illustrate the relative merits of the combination of ladder-sequencing and top-down MS approaches to elucidate the interactions of metal anticancer complexes with DNA.
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Affiliation(s)
- Kui Wu
- Beijing National Laboratory for Molecular Sciences, Beijing Centre for Mass Spectrometry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People's Republic of China
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41
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Wetzel C, Limbach PA. The global identification of tRNA isoacceptors by targeted tandem mass spectrometry. Analyst 2013; 138:6063-72. [DOI: 10.1039/c3an01224g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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42
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Sun J, Yan Y, Sun S, Shu X, Zhu C, Zhu J. DNA binding and reactivity assays based on in-frame protein expression. Chem Sci 2013. [DOI: 10.1039/c2sc21464d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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43
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Capaldi D, Ackley K, Brooks D, Carmody J, Draper K, Kambhampati R, Kretschmer M, Levin D, McArdle J, Noll B, Raghavachari R, Roymoulik I, Sharma BP(B, Thürmer R, Wincott F. Quality Aspects of Oligonucleotide Drug Development: Specifications for Active Pharmaceutical Ingredients. ACTA ACUST UNITED AC 2012. [DOI: 10.1177/0092861512445311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Losito I, Angelico R, Introna B, Ceglie A, Palmisano F. Cytosine to uracil conversion through hydrolytic deamination of cytidine monophosphate hydroxy-alkylated on the amino group: a liquid chromatography--electrospray ionization--mass spectrometry investigation. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1384-1393. [PMID: 23019171 DOI: 10.1002/jms.3078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A novel pathway for cytosine to uracil conversion performed in a micellar environment, leading to the generation of uridine monophosphate (UMP), was evidenced during the alkylation reaction of cytidine monophosphate (CMP) by dodecyl epoxide. Liquid chromatography-electrospray ionization - ion trap - mass spectrometry was used to separate and identify the reaction products and to follow their formation over time. The detection of hydroxy-amino-dodecane, concurrently with free UMP, in the reaction mixture suggested that, among the various alkyl-derivatives formed, CMP alkylated on the amino group of cytosine could undergo tautomerization to an imine and hydrolytic deamination, generating UMP. Interestingly, no evidence for this peculiar conversion pathway was obtained when guanosine monophosphate (GMP), the complementary ribonucleotide of CMP, was also present in the reaction mixture, due to the fact that NH(2)-alkylated CMP was not formed in this case. The last finding emphasized the role played by CMP-GMP molecular interactions, mediated by a micellar environment, in hindering the alkylation reaction at the level of the cytosine amino group.
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Affiliation(s)
- I Losito
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy.
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45
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Faria M, Halquist MS, Kindt E, Li W, Karnes HT, O'Brien PJ. Liquid chromatography-tandem mass spectrometry method for quantification of thymidine kinase activity in human serum by monitoring the conversion of 3'-deoxy-3'-fluorothymidine to 3'-deoxy-3'-fluorothymidine monophosphate. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 907:13-20. [PMID: 22995377 DOI: 10.1016/j.jchromb.2012.08.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 08/16/2012] [Accepted: 08/19/2012] [Indexed: 10/28/2022]
Abstract
Thymidine kinase 1 (TK1) is an enzyme involved in DNA synthesis whose activity in serum is indicative of tumor proliferation and the severity of blood malignancies. 3'-deoxy-3'-fluorothymidine (FLT), a specific exogenous substrate for TK1, is phosphorylated by TK1 in the presence of a phosphorylating buffer, therefore the conversion of FLT to 3'-deoxy-3'-fluorothymidine monophosphate (FLT-MP) can be measured to assess serum TK1 activity. Here we describe a liquid chromatography-MS/MS (LC-MS/MS) method for quantification of FLT and FLT-MP from serum using protein precipitation and column switching followed by detection on an Applied Biosystems SCIEX API 4000 QTrap mass spectrometer. The method was linear over the range of 0.5-500 ng/mL for FLT and 2.5-2000 ng/mL for FLT-MP with a mean correlation coefficient of 0.9964 and 0.9935 for FLT and FLT-MP, respectively. The lower limit of quantification was 0.5 ng/mL for FLT and 2.5 ng/mL for FLT-MP. Intra-assay accuracy and inter-assay accuracy was within ±12% for both FLT and FLT-MP. Intra-assay precision was 2.8% to 7.7% for FLT and 3.3% to 5.8% for FLT-MP. Inter-assay precision was 4.6% to 14.9% for FLT and 4.9% to 14.6% for FLT-MP. Serum TK1 activity was measured in serum from hepatocellular carcinoma patients and age-matched controls under standardized conditions. Elevated TK1 activity was detected in 26.3% of hepatocellular carcinoma samples compared to controls. This method provides a robust alternative to radiometric and immunochemical assays of serum TK1 activity.
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Affiliation(s)
- Morse Faria
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA 23298, USA
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46
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Shu X, Lu J, Lv H, Zhang X, Yan Y, Sun J, Zhu J. Ultrafast kinetic DNA hybridization assay based on the visualization of threshold turbidity. Anal Chem 2012; 84:3500-6. [PMID: 22458673 DOI: 10.1021/ac300824a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report herein the development of an ultrafast kinetic DNA hybridization assay system based on the visualization of threshold turbidity associated with the assembly of polystyrene nanospheres. Initial testing of our diagnostic protocol on a sequence associated with the anthrax lethal factor indicates that a visually identifiable, turbidity-definitive, and kinetic threshold state could be reached at a time as short as 1 min. The assay scheme allows for both target concentration quantification and differentiation of single base mismatches through registry of the threshold turbidity onset time. The positively charged environment on nanospheres not only contributes to expedited signal generation but also imparts cooperative DNA binding properties. The kinetic visual protocol complements conventionally used thermodynamic strategies and provides an entry point for the circumvention of assay issues associated with ill-defined thermodynamic end points.
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Affiliation(s)
- Xin Shu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, China
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47
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Liu Y, Wang R, Ding L, Sha R, Seeman NC, Canary JW. Templated synthesis of nylon nucleic acids and characterization by nuclease digestion. Chem Sci 2012; 3:1930-1937. [PMID: 23125913 PMCID: PMC3486707 DOI: 10.1039/c2sc20129a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis: Coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2'-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Risheng Wang
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Liang Ding
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Roujie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
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48
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Zhao C, Yin R, Yin J, Zhang D, Wang H. Capillary monolithic bioreactor of immobilized snake venom phosphodiesterase for mass spectrometry based oligodeoxynucleotide sequencing. Anal Chem 2011; 84:1157-64. [PMID: 22208283 DOI: 10.1021/ac2029387] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A capillary monolithic bioreactor of snake venom phosphodiesterase (SVP) was constructed to generate different single-nucleotide mass ladders of oligodeoxynucleotides for mass spectrometry (MS)-based sequencing by immobilization. The immobilization of SVP in the porous silica monolith significantly enhances its stability for prolonged and repeated applications. The constructed capillary bioreactor has the advantages of handling (sub)microliter DNA samples and having good permeability. Benefiting from its good permeability, DNA solutions can be directly injected into the sequential digestion bioreactor simply by hand pushing or a low-pressure microinjection pump. Moreover, the immobilization of SVP facilitates the elimination or repression of the metal adducts of oligodeoxynucleotides, improving the analytical performance of MS sequencing. By the application of capillary bioreactor of immobilized SVP, the sequence-specific modification of single-stranded oligodeoxynucleotide induced by a ubiquitous pollutant acrolein (Acr) was identified, demonstrating its promising applications in identification of sequence-specific damage, which may further our understanding of DNA damage caused mutagenesis.
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Affiliation(s)
- Chao Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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49
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Beverly MB. Applications of mass spectrometry to the study of siRNA. MASS SPECTROMETRY REVIEWS 2011; 30:979-998. [PMID: 20201110 DOI: 10.1002/mas.20260] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 08/13/2009] [Accepted: 08/13/2009] [Indexed: 05/28/2023]
Abstract
RNA interference (RNAi) has quickly become a well-established laboratory tool for regulating gene expression and is currently being explored for its therapeutic potential. The design and use of double-stranded RNA oligonucleotides as therapeutics to trigger the RNAi mechanism and a greater effort to understand the RNAi pathway itself is driving the development of analytical techniques that can characterize these oligonucleotides. Electrospray (ESI) and MALDI have been used routinely to analyze oligonucleotides and their ability to provide mass and sequence information has made them ideal for this application. Reviewed here is the work done to date on the use of ESI and MALDI for the study of RNAi oligonucleotides as well as the strategies and issues associated with siRNA analysis by mass spectrometry. While there is not a large body of literature on the specific application of mass spectrometry to RNAi, the work done in this area is a good demonstration of the range of experiments that can be conducted and the value that ESI and MALDI can provide to the RNAi field.
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Affiliation(s)
- Michael B Beverly
- RNA Therapeutics Department, Merck and Co., Inc., Boulder, CO 80301, USA.
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Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. MASS SPECTROMETRY REVIEWS 2011; 30:1203-24. [PMID: 21557290 PMCID: PMC7168406 DOI: 10.1002/mas.20320] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 05/25/2023]
Abstract
Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan.
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