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Kelley M, Holmes CJ, Herbert C, Rayhan A, Joves J, Uhran M, Frigard R, Singh K, Limbach PA, Addepalli B, Benoit JB. Tyrosine transfer RNA levels and modifications during blood-feeding and vitellogenesis in the mosquito, Aedes aegypti. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569187. [PMID: 38076852 PMCID: PMC10705485 DOI: 10.1101/2023.11.29.569187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Mosquitoes such as Aedes aegypti must consume a blood meal for the nutrients necessary for egg production. Several transcriptome and proteome changes occur post blood meal that likely corresponds with codon usage alterations. Transfer RNA (tRNA) is the adapter molecule that reads messenger RNA (mRNA) codons to add the appropriate amino acid during protein synthesis. Chemical modifications to tRNA enhance codons' decoding, improving the accuracy and efficiency of protein synthesis. Here, we examined tRNA modifications and transcripts associated with the blood meal and subsequent periods of vitellogenesis in A. aegypti. More specifically, we assessed tRNA transcript abundance and modification levels in the fat body at critical times post blood-feeding. Based on a combination of alternative codon usage and identification of particular modifications, we identified that increased transcription of tyrosine tRNAs is likely critical during the synthesis of egg yolk proteins in the fat body following a blood meal. Altogether, changes in both the abundance and modification of tRNA are essential factors in the process of vitellogenin production after blood-feeding in mosquitoes.
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Affiliation(s)
- Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | | | - Cassandra Herbert
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45211
| | - Asif Rayhan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45211
| | - Judd Joves
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Melissa Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Ronja Frigard
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Khwahish Singh
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | | | | | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
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2
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Zhang N, Shi S, Jia TZ, Ziegler A, Yoo B, Yuan X, Li W, Zhang S. A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures. Nucleic Acids Res 2020; 47:e125. [PMID: 31504795 PMCID: PMC6847078 DOI: 10.1093/nar/gkz731] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/07/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022] Open
Abstract
A complete understanding of the structural and functional potential of RNA requires understanding of chemical modifications and non-canonical bases; this in turn requires advances in current sequencing methods to be able to sequence not only canonical ribonucleotides, but at the same time directly sequence these non-standard moieties. Here, we present the first direct and modification type-independent RNA sequencing method via introduction of a 2-dimensional hydrophobic end-labeling strategy into traditional mass spectrometry-based sequencing (2D HELS MS Seq) to allow de novo sequencing of RNA mixtures and enhance sample usage efficiency. Our method can directly read out the complete sequence, while identifying, locating, and quantifying base modifications accurately in both single and mixed RNA samples containing multiple different modifications at single-base resolution. Our method can also quantify stoichiometry/percentage of modified RNA versus its canonical counterpart RNA, simulating a real biological sample where modifications exist but may not be 100% at a particular site in the RNA. This method is a critical step towards fully sequencing real complex cellular RNA samples of any type and containing any modification type and can also be used in the quality control of modified therapeutic RNAs.
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Affiliation(s)
- Ning Zhang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA.,Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Shundi Shi
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, WA 98154, USA
| | - Ashley Ziegler
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College, City University of New York, New York, NY 10065, USA
| | - Xiaohong Yuan
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
| | - Wenjia Li
- Department of Computer Science, New York Institute of Technology, New York, NY 10023, USA
| | - Shenglong Zhang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
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3
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Thakur P, Estevez M, Lobue PA, Limbach PA, Addepalli B. Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases. Analyst 2020; 145:816-827. [PMID: 31825413 PMCID: PMC7002195 DOI: 10.1039/c9an02111f] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Locating ribonucleoside modifications within an RNA sequence requires digestion of the RNA into oligoribonucleotides of amenable size for subsequent analysis by LC-MS (liquid chromatography-mass spectrometry). This approach, widely referred to as RNA modification mapping, is facilitated through ribonucleases (RNases) such as T1 (guanosine-specific), U2 (purine-selective) and A (pyrimidine-specific) among others. Sequence coverage by these enzymes depends on positioning of the recognized nucleobase (such as guanine or purine or pyrimidine) in the sequence and its ribonucleotide composition. Using E. coli transfer RNA (tRNA) and ribosomal RNA (rRNA) as model samples, we demonstrate the ability of complementary nucleobase-specific ribonucleases cusativin (C-specific) and MC1 (U-specific) to generate digestion products that facilitate confident mapping of modifications in regions such as G-rich and pyrimidine-rich segments of RNA, and to distinguish C to U sequence differences. These enzymes also increase the number of oligonucleotide digestion products that are unique to a specific RNA sequence. Further, with these additional RNases, multiple modifications can be localized with high confidence in a single set of experiments with minimal dependence on the individual tRNA abundance in a mixture. The sequence overlaps observed with these complementary digestion products and that of RNase T1 improved sequence coverage to 75% or above. A similar level of sequence coverage was also observed for the 2904 nt long 23S rRNA indicating their utility has no dependence on RNA size. Wide-scale adoption of these additional modification mapping tools could help expedite the characterization of modified RNA sequences to understand their structural and functional role in various living systems.
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Affiliation(s)
- Priti Thakur
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
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4
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Isotope-dilution mass spectrometry for exact quantification of noncanonical DNA nucleosides. Nat Protoc 2019; 14:283-312. [PMID: 30559375 DOI: 10.1038/s41596-018-0094-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA contains not only canonical nucleotides but also a variety of modifications of the bases. In particular, cytosine and adenine are frequently modified. Determination of the exact quantity of these noncanonical bases can contribute to the characterization of the state of a biological system, e.g., determination of disease or developmental processes, and is therefore extremely important. Here, we present a workflow that includes detailed description of critical sample preparation steps and important aspects of mass spectrometry analysis and validation. In this protocol, extraction and digestion of DNA by an optimized spin-column and enzyme-based method are described. Isotopically labeled standards are added in the course of DNA digestion, which allows exact quantification by isotope dilution mass spectrometry. To overcome the major bottleneck of such analyses, we developed a short (~14-min-per-sample) ultra-HPLC (UHPLC) and triple quadrupole mass spectrometric (QQQ-MS) method. Easy calculation of the modification abundance in the genome is possible with the provided evaluation sheets. Compared to alternative methods, the quantification procedure presented here allows rapid, ultrasensitive (low femtomole range) and highly reproducible quantification of different nucleosides in parallel. Including sample preparation and evaluation, quantification of DNA modifications can be achieved in less than a week.
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5
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tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii. J Bacteriol 2019; 201:JB.00690-18. [PMID: 30745370 DOI: 10.1128/jb.00690-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codon-decoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm5s2U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNAPhe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies.IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.
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6
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Marín M, Fernández-Calero T, Ehrlich R. Protein folding and tRNA biology. Biophys Rev 2017; 9:573-588. [PMID: 28944442 PMCID: PMC5662057 DOI: 10.1007/s12551-017-0322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022] Open
Abstract
Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.
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Affiliation(s)
- Mónica Marín
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Tamara Fernández-Calero
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Ricardo Ehrlich
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
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7
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Abstract
We describe the comparative analysis of ribonucleic acid digests (CARD) approach for RNA modification analysis. This approach employs isotope labeling during RNase digestion, which allows the direct comparison of a tRNA of unknown modification status against a reference tRNA, whose sequence or modification status is known. The reference sample is labeled with 18O during RNase digestion while the candidate (unknown) sample is labeled with 16O. These RNase digestion products are combined and analyzed by mass spectrometry. Identical RNase digestion products will appear in the mass spectrum as characteristic doublets, separated by 2 Da due to the 16O/18O mass difference. Singlets arise in the mass spectrum when the sequence or modification status of a particular RNase digestion product from the reference is not matched in the candidate (unknown) sample. This CARD approach for RNA modification analysis simplifies the determination of differences between reference and candidate samples, providing a route for higher throughput screening of samples for modification profiles, including determination of tRNA methylation patterns.
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8
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Ross R, Cao X, Yu N, Limbach PA. Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. Methods 2016; 107:73-8. [PMID: 27033178 DOI: 10.1016/j.ymeth.2016.03.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 02/04/2023] Open
Abstract
Mass spectrometry is a powerful analytical tool for identifying and characterizing structural modifications to the four canonical bases in RNA, information that is lost when using techniques such as PCR for RNA analysis. Here we described an updated method for sequence mapping of modified nucleosides in transfer RNA. This modification mapping approach utilizes knowledge of the modified nucleosides present in the sample along with the genome-derived tRNA sequence to readily locate modifications site-specifically in the tRNA sequence. The experimental approach involves isolation of the tRNA of interest followed by separate enzymatic digestion to nucleosides and oligonucleotides. Both samples are analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) and the data sets are then combined to yield the modification profile of the tRNA. Data analysis is facilitated by the use of unmodified sequence exclusion lists and new developments in software that can automate MS/MS spectral annotation. The method is illustrated using tRNA-Asn isolated from Thermus thermophilus.
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Affiliation(s)
- Robert Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States
| | - Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States
| | - Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States.
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9
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Abstract
A common feature of ribonucleic acids (RNAs) is that they can undergo a variety of chemical modifications. As nearly all of these chemical modifications result in an increase in the mass of the canonical nucleoside, mass spectrometry has long been a powerful approach for identifying and characterizing modified RNAs. Over the past several years, significant advances have been made in method development and software for interpreting tandem mass spectra resulting in approaches that can yield qualitative and quantitative information on RNA modifications, often at the level of sequence specificity. We discuss these advances along with instrumentation developments that have increased our ability to extract such information from relatively complex biological samples. With the increasing interest in how these modifications impact the epitranscriptome, mass spectrometry will continue to play an important role in bioanalytical investigations revolving around RNA.
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Affiliation(s)
- Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172. and University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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10
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Cao X, Limbach PA. Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS. Anal Chem 2015; 87:8433-40. [PMID: 26176336 PMCID: PMC4542202 DOI: 10.1021/acs.analchem.5b01826] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
There
has been a renewed appreciation for the dynamic nature of
ribonucleic acid (RNA) modifications and for the impact of modified
RNAs on organism health resulting in an increased emphasis on developing
analytical methods capable of detecting modifications within specific
RNA sequence contexts. Here we demonstrate that a DNA-based exclusion
list enhances data dependent liquid chromatography tandem mass spectrometry
(LC-MS/MS) detection of post-transcriptionally modified nucleosides
within specific RNA sequences. This approach is possible because all
post-transcriptional modifications of RNA, except pseudouridine, result
in a mass increase in the canonical nucleoside undergoing chemical
modification. Thus, DNA-based sequences reflect the state of the RNA
prior to or in the absence of modification. The utility of this exclusion
list strategy is demonstrated through the RNA modification mapping
of total tRNAs from the bacteria Escherichia coli, Lactococcus lactis, and Streptomyces griseus. Creation of a DNA-based exclusion list is shown to consistently
enhance the number of detected modified ribonuclease (RNase) digestion
products by ∼20%. All modified RNase digestion products that
were detected during standard data dependent acquisition (DDA) LC-MS/MS
were also detected when the DNA-based exclusion list was used. Consequently,
the increase in detected modified RNase digestion products is attributed
to new experimental information only obtained when using the exclusion
list. This exclusion list strategy should be broadly applicable to
any class of RNA and improves the utility of mass spectrometry approaches
for discovery-based analyses of RNA modifications, such as are required
for studies of the epitranscriptome.
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Affiliation(s)
- Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
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11
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Shepherd J, Ibba M. Bacterial transfer RNAs. FEMS Microbiol Rev 2015; 39:280-300. [PMID: 25796611 DOI: 10.1093/femsre/fuv004] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/21/2015] [Indexed: 11/14/2022] Open
Abstract
Transfer RNA is an essential adapter molecule that is found across all three domains of life. The primary role of transfer RNA resides in its critical involvement in the accurate translation of messenger RNA codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. This review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer RNAs. Codon recognition at the ribosome as well as the ever-increasing number of alternative roles for transfer RNA outside of translation will be discussed in the specific context of bacterial cells.
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Affiliation(s)
- Jennifer Shepherd
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
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12
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Abstract
Recent findings have elucidated numerous novel biological functions for oligonucleotides. Current standard methods for the study of oligonucleotides (i.e., hybridization and PCR) are not fully equipped to deal with the experimental needs arising from these new discoveries. More importantly, as the intracellular capacity of oligonucleotides is being harnessed for biomedical applications, alternative bioanalytical techniques become indispensable in order to comply with ever-increasing regulatory requirements. Owing to its ability to detect oligonucleotides independent of their sequence, LC-MS is emerging as the analytical method of choice for oligonucleotides. In this article, the current applications of LC-MS in the analysis of oligonucleotides, with an emphasis on RNA therapeutics and biomarkers, will be examined. In addition, the theoretical framework of oligonucleotide ESI is carefully inspected with the purpose of identifying the contributing factors to MS signal intensity.
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13
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Dudley E, Bond L. Mass spectrometry analysis of nucleosides and nucleotides. MASS SPECTROMETRY REVIEWS 2014; 33:302-31. [PMID: 24285362 DOI: 10.1002/mas.21388] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.
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Affiliation(s)
- Ed Dudley
- Institute of Mass Spectrometry, College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
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14
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Wetzel C, Li S, Limbach PA. Metabolic de-isotoping for improved LC-MS characterization of modified RNAs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1114-1123. [PMID: 24760295 DOI: 10.1007/s13361-014-0889-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/15/2014] [Accepted: 03/17/2014] [Indexed: 06/03/2023]
Abstract
Mapping, sequencing, and quantifying individual noncoding ribonucleic acids (ncRNAs), including post-transcriptionally modified nucleosides, by mass spectrometry is a challenge that often requires rigorous sample preparation prior to analysis. Previously, we have described a simplified method for the comparative analysis of RNA digests (CARD) that is applicable to relatively complex mixtures of ncRNAs. In the CARD approach for transfer RNA (tRNA) analysis, two complete sets of digestion products from total tRNA are compared using the enzymatic incorporation of (16)O/(18)O isotopic labels. This approach allows one to rapidly screen total tRNAs from gene deletion mutants or comparatively sequence total tRNA from two related bacterial organisms. However, data analysis can be challenging because of convoluted mass spectra arising from the natural (13)C and (15) N isotopes present in the ribonuclease-digested tRNA samples. Here, we demonstrate that culturing in (12)C-enriched/(13)C-depleted media significantly reduces the isotope patterns that must be interpreted during the CARD experiment. Improvements in data quality yield a 35 % improvement in detection of tRNA digestion products that can be uniquely assigned to particular tRNAs. These mass spectral improvements lead to a significant reduction in data processing attributable to the ease of spectral identification of labeled digestion products and will enable improvements in the relative quantification of modified RNAs by the (16)O/(18)O differential labeling approach.
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Affiliation(s)
- Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221-0172, USA
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15
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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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16
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El Yacoubi B, Bailly M, de Crécy-Lagard V. Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs. Annu Rev Genet 2012; 46:69-95. [DOI: 10.1146/annurev-genet-110711-155641] [Citation(s) in RCA: 380] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Marc Bailly
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
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