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Hasan MM, Mimi MA, Mamun MA, Islam A, Waliullah ASM, Nabi MM, Tamannaa Z, Kahyo T, Setou M. Mass Spectrometry Imaging for Glycome in the Brain. Front Neuroanat 2021; 15:711955. [PMID: 34393728 PMCID: PMC8358800 DOI: 10.3389/fnana.2021.711955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Glycans are diverse structured biomolecules that play crucial roles in various biological processes. Glycosylation, an enzymatic system through which various glycans are bound to proteins and lipids, is the most common and functionally crucial post-translational modification process. It is known to be associated with brain development, signal transduction, molecular trafficking, neurodegenerative disorders, psychopathologies, and brain cancers. Glycans in glycoproteins and glycolipids expressed in brain cells are involved in neuronal development, biological processes, and central nervous system maintenance. The composition and expression of glycans are known to change during those physiological processes. Therefore, imaging of glycans and the glycoconjugates in the brain regions has become a “hot” topic nowadays. Imaging techniques using lectins, antibodies, and chemical reporters are traditionally used for glycan detection. However, those techniques offer limited glycome detection. Mass spectrometry imaging (MSI) is an evolving field that combines mass spectrometry with histology allowing spatial and label-free visualization of molecules in the brain. In the last decades, several studies have employed MSI for glycome imaging in brain tissues. The current state of MSI uses on-tissue enzymatic digestion or chemical reaction to facilitate successful glycome imaging. Here, we reviewed the available literature that applied MSI techniques for glycome visualization and characterization in the brain. We also described the general methodologies for glycome MSI and discussed its potential use in the three-dimensional MSI in the brain.
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Affiliation(s)
- Md Mahmudul Hasan
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mst Afsana Mimi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Al Mamun
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ariful Islam
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - A S M Waliullah
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Mahamodun Nabi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Zinat Tamannaa
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomoaki Kahyo
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu, Japan
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2
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Buhimschi AD, Gooden DM, Jing H, Fels DR, Hansen KS, Beyer WF, Dewhirst MW, Walder H, Gasparro FP. Psoralen Derivatives with Enhanced Potency. Photochem Photobiol 2020; 96:1014-1031. [PMID: 32221980 DOI: 10.1111/php.13263] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/28/2020] [Indexed: 12/22/2022]
Abstract
Psoralen is a furocoumarin natural product that intercalates within DNA and forms covalent adducts when activated by ultraviolet radiation. It is well known that this property contributes to psoralen's clinical efficacy in several disease contexts, which include vitiligo, psoriasis, graft-versus-host disease and cutaneous T-cell lymphoma. Given the therapeutic relevance of psoralen and its derivatives, we attempted to synthesize psoralens with even greater potency. In this study, we report a library of 73 novel psoralens, the largest collection of its kind. When screened for the ability to reduce cell proliferation, we identified two derivatives even more cytotoxic than 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), one of the most potent psoralens identified to date. Using MALDI-TOF MS, we studied the DNA adduct formation for a subset of novel psoralens and found that in most cases enhanced DNA binding correlated well with cytotoxicity. Generally, our most potent derivatives contain positively charged substituents, which we believe increase DNA affinity and enhance psoralen intercalation. Thus, we provide a rational approach to guide efforts toward further optimizing psoralens to fully capitalize on this drug class' therapeutic potential. Finally, the structure-activity insights we have gained shed light on several opportunities to study currently underappreciated aspects of psoralen's mechanism.
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Affiliation(s)
- Alexandru D Buhimschi
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL.,Photobiology Laboratory, Hamden Hall Country Day School, Hamden, CT
| | | | - Hongwu Jing
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, IL
| | - Diane R Fels
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC.,Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Katherine S Hansen
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC.,Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | | | - Mark W Dewhirst
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC.,Duke Cancer Institute, Duke University Medical Center, Durham, NC
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3
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Kimura S, Fujisaka A, Obika S. Nucleobase derivatives induce in-source decay of oligonucleotides as new matrix-assisted laser desorption/ionization matrices. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8620. [PMID: 31658399 DOI: 10.1002/rcm.8620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE For quality control of oligonucleotide therapeutics, accurate and efficient structural characterization using mass spectrometry techniques, such as liquid chromatography/mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), is essential. In MALDI MS analysis, matrix selection is critical and a new matrix could enable more efficient and rapid structural analysis. METHODS We hypothesized that nucleobase derivatives could act as matrices more efficiently than the currently used matrices for oligonucleotides because of structural similarity, which leads to close contact with the analyte. To evaluate their suitability as matrices, 16 nucleobase derivatives were selected and tested as matrix candidates for oligonucleotide analysis. RESULTS Six of the 16 nucleobase derivatives acted as matrices for oligonucleotides. Particularly, 6-thioguanine (TG) performed well and induced clear in-source decay fragmentation. When TG or 2-amino-6-chloropurine was used as the matrix, oligonucleotides were ionized, and mainly the w and d fragment ions were observed. CONCLUSIONS Herein we demonstrate that a 10-mer RNA or DNA sequence can be successfully characterized using TG as matrix and suggest the possibility of using nucleobase derivatives as novel matrices in oligonucleotide sequencing.
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Affiliation(s)
- Satoshi Kimura
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Aki Fujisaka
- Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-Kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
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4
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Studzińska S. Review on investigations of antisense oligonucleotides with the use of mass spectrometry. Talanta 2017; 176:329-343. [PMID: 28917758 DOI: 10.1016/j.talanta.2017.08.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022]
Abstract
Antisense oligonucleotides have been investigated as potential drugs for years. They inhibit target gene or protein expression. The present review summarizes their modifications, modes of action, and applications of liquid chromatography coupled with mass spectrometry for qualitative and quantitative analysis of these compounds. The most recent reports on a given topic were given prominence, while some early studies were reviewed in order to provide a theoretical background. The present review covers the issues of using ion-exchange chromatography, ion-pair reversed-phase high performance liquid chromatography and hydrophilic interaction chromatography for the separation of antisense oligonucleotides. The application of mass spectrometry was described with regard to the ionization type used for the determination of these potential therapeutics. Moreover, the current approaches and applications of mass spectrometry for quantitative analysis of antisense oligonucleotides and their metabolites as well as their impurities during in vitro and in vivo studies were discussed. Finally, certain conclusions and perspectives on the determination of therapeutic oligonucleotides in various samples were briefly described.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland.
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5
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Organic matrices, ionic liquids, and organic matrices@nanoparticles assisted laser desorption/ionization mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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6
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Gross JH. Matrix-Assisted Laser Desorption/Ionization. Mass Spectrom (Tokyo) 2017. [DOI: 10.1007/978-3-319-54398-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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7
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Ling L, Xiao C, Jiang L, Wang S, Li Y, Chen X, Guo X. A cool and high salt-tolerant ionic liquid matrix for preferential ionization of phosphopeptides by negative ion MALDI-MS. NEW J CHEM 2017. [DOI: 10.1039/c7nj01706e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
An optimized ILM G3THAP/PA matrix significantly improved the detection of phosphopeptides by negative ion MALDI-MS compared with using 3-AQ/CHCA/ADP and DHB/PA matrices.
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Affiliation(s)
- Ling Ling
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
- Changchun 130021
- P. R. China
| | - Liyan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University
- Changchun 130012
- P. R. China
| | - Sheng Wang
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Ying Li
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
- Changchun 130021
- P. R. China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
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8
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AlMasoud N, Correa E, Trivedi DK, Goodacre R. Fractional Factorial Design of MALDI-TOF-MS Sample Preparations for the Optimized Detection of Phospholipids and Acylglycerols. Anal Chem 2016; 88:6301-8. [DOI: 10.1021/acs.analchem.6b00512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Najla AlMasoud
- School
of Chemistry and Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| | - Elon Correa
- School
of Chemistry and Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| | - Drupad K. Trivedi
- School
of Chemistry and Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| | - Royston Goodacre
- School
of Chemistry and Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
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9
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Ahn SH, Park KM, Moon JH, Lee SH, Kim MS. Preparation of Homogeneous Solid Samples for Reproducible and Quantitative MALDI. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10704] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sung Hee Ahn
- Department of Chemistry; Seoul National University; Seoul 151-747 Korea
| | - Kyung Man Park
- Department of Chemistry; Seoul National University; Seoul 151-747 Korea
| | - Jeong Hee Moon
- Functional Genomics Research Center, KRIBB; Daejeon 305-806 Korea
| | - Seong Hoon Lee
- Department of Chemistry; Seoul National University; Seoul 151-747 Korea
| | - Myung Soo Kim
- Seoul National University Research Institute for Basic Sciences; Seoul 151-747 Korea
- Center for Nanoparticle Research, Institute for Basic Science (IBS); Seoul 151-742 Korea
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10
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Chen F, Gülbakan B, Weidmann S, Fagerer SR, Ibáñez AJ, Zenobi R. Applying mass spectrometry to study non-covalent biomolecule complexes. MASS SPECTROMETRY REVIEWS 2016; 35:48-70. [PMID: 25945814 DOI: 10.1002/mas.21462] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/09/2014] [Indexed: 05/10/2023]
Abstract
Non-covalent interactions are essential for the structural organization of biomacromolecules and play an important role in molecular recognition processes, such as the interactions between proteins, glycans, lipids, DNA, and RNA. Mass spectrometry (MS) is a powerful tool for studying of non-covalent interactions, due to the low sample consumption, high sensitivity, and label-free nature. Nowadays, native-ESI MS is heavily used in studies of non-covalent interactions and to understand the architecture of biomolecular complexes. However, MALDI-MS is also becoming increasingly useful. It is challenging to detect the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are two methodological approaches to do so. In the first approach, different experimental and instrumental parameters are fine-tuned in order to find conditions under which the complex is stable, such as applying non-acidic matrices and collecting first-shot spectra. In the second approach, the interacting species are "artificially" stabilized by chemical crosslinking. Both approaches are capable of studying non-covalently bound biomolecules even in quite challenging systems, such as membrane protein complexes. Herein, we review and compare native-ESI and MALDI MS for the study of non-covalent interactions.
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Affiliation(s)
- Fan Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Basri Gülbakan
- Institute of Child Health, Division of Pediatric Basic Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Simon Weidmann
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Stephan R Fagerer
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Alfredo J Ibáñez
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
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11
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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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12
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Yasuda A, Ishimaru T, Nishihara S, Sakai M, Kawasaki H, Arakawa R, Shigeri Y. A thiophene-containing compound as a matrix for matrix-assisted laser desorption/ ionization mass spectrometry and the electrical conductivity of matrix crystals. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:29-37. [PMID: 23841223 DOI: 10.1255/ejms.1215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The electrical conductivity of the matrix crystal might be a new factor to enhance matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) sensitivity. In MALDI-MS, several compounds are used as a standard matrix. Utilization of such compounds is based on an a posteriori approach, but there is no theoretical guidance for selecting a matrix. In an attempt to further understand performance in MALDI-MS, we utilized peptide detection for random screening of a chemical library (12,383 compounds) for compounds with matrix functions in MALDI-MS. A lot of thiophene compounds were found to be a matrix, in which 2-[5-(2,4-dichlorobenzoyl)-2-thienyl] acetic acid (DCBTA) provided an important clue to measure the electrical conductivity of the matrix crystal, because the structure of DCBTA is analogous to conductive polymers and organic solar cells. Most of the crystals of standard matrices, such as alpha-cyano-4-hydroxycinnamic acid (CHCA), 3,5-dimethoxy-4-hydroxycinnamic acid [sinapinic acid, (SA)], and DCBTA showed electrical conductivity, whereas the conductivity of crystal was not observed in 2,5-dihydroxybenzoic acid (2,5-DHB). On the other hand, super-DHB using 2-hydroxy-5-methoxybenzoic acid [5-methoxysalicylic acid, (MSA)] as an additive to 2,5-DHB, improved the electrical conductivity of the crystal, that followed the enhancement of peak intensity in MS spectrum. These observations might indicate that the electrical conductivity of matrix crystals is a key consideration in obtaining efficient MALDI performance.
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Affiliation(s)
- Akikazu Yasuda
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Midorigaoka, Ikeda, Osaka 563-8577, Japan
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13
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Giessing AMB, Kirpekar F. Mass spectrometry in the biology of RNA and its modifications. J Proteomics 2012; 75:3434-49. [PMID: 22348820 DOI: 10.1016/j.jprot.2012.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/20/2012] [Accepted: 01/26/2012] [Indexed: 01/31/2023]
Abstract
Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Anders M B Giessing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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14
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Improved detection of phosphopeptides by negative ion matrix-assisted laser desorption/ionization mass spectrometry using a proton sponge co-matrix. Anal Chim Acta 2012; 711:77-82. [DOI: 10.1016/j.aca.2011.10.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/01/2011] [Accepted: 10/27/2011] [Indexed: 01/25/2023]
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15
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Shanta SR, Kim TY, Hong JH, Lee JH, Shin CY, Kim KH, Kim YH, Kim SK, Kim KP. A new combination MALDI matrix for small molecule analysis: application to imaging mass spectrometry for drugs and metabolites. Analyst 2012; 137:5757-62. [DOI: 10.1039/c2an35782h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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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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17
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McGinnis AC, Chen B, Bartlett MG. Chromatographic methods for the determination of therapeutic oligonucleotides. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 883-884:76-94. [PMID: 21945211 DOI: 10.1016/j.jchromb.2011.09.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/31/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
Both DNA and RNA are being explored for their therapeutic potential against a wide range of diseases. As these new drugs emerge, new demands arise for the analysis and quantitation of these biomolecules. Pharmacokinetic and pharmacodynamic analysis requirements for drug approval place enormous challenges on the methods for analyzing these therapeutics. This review will focus on bioanalytical methods for DNA antisense and aptamers as well as small-interfering RNA (siRNA) therapeutics. Chromatography methods employing ultraviolet (UV), fluorescence and mass spectrometric (MS) detection along with matrix-assisted laser desorption/ionization (MALDI) will be covered. Sample preparation from biological matrices will be reviewed as well as metabolite analysis and identification. All of these techniques are important contributions toward oligonucleotide therapeutic development. They will also be important in microRNA (miRNA) biomarker discovery and RNomics in general, as more non-coding RNAs are inevitably discovered.
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Affiliation(s)
- A Cary McGinnis
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
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18
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Olson MT, Epstein JA, Sackett DL, Yergey AL. Production of reliable MALDI spectra with quality threshold clustering of replicates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:969-975. [PMID: 21953038 DOI: 10.1007/s13361-011-0097-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/21/2011] [Accepted: 01/22/2011] [Indexed: 05/31/2023]
Abstract
We present the first application of the quality threshold (QT) clustering algorithm to mass spectrometry (MS) data. The unique abilities of QT clustering to yield precision nodes that are commensurate with the mass measurement precision of the instrument are exploited to generate a consensus spectrum out of multiple replicate spectra. The spectral dot product and confidence intervals are used as a tool for evaluating the similarity and reproducibility between the consensus and replicates. The method is equally applicable to high and low resolution measurements. This paper demonstrates applications to linear spectra from a matrix assisted laser desorption ionization (MALDI) time of flight (TOF) instrument as well as peptide fragmentation data obtained from a TOF/TOF after unimolecular decomposition. The advantages of clustering to mitigate the inherent precision the shortcomings of MALDI data are discussed.
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Affiliation(s)
- Matthew T Olson
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
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19
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Kailasa SK, Wu HF. Semiconductor cadmium sulphide nanoparticles as matrices for peptides and as co-matrices for the analysis of large proteins in matrix-assisted laser desorption/ionization reflectron and linear time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:271-280. [PMID: 21192022 DOI: 10.1002/rcm.4834] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The use of semiconductor cadmium sulphide nanoparticles (CdS NPs) capped with 4-aminothiophenol (ATP) and 11-mercaptoundecanoic acid (MUA) is described for the first time as matrices and as co-matrices for the analysis of peptides and proteins in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). UV-visible spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were applied for the characterization of functionalized CdS NPs. The synthesized CdS-ATP and CdS-MUA NPs exhibit uniform size distribution with diameter of 15-25 nm and 20-30 nm, respectively. The -NH(2) (ATP) and -COOH (MUA) groups modified on the surfaces of CdS NPs provide ionizable moieties for efficient transfer of protons during the desorption/ionization of analytes. The functionalized CdS NPs have desirable properties for the analysis of peptides in reflectron MALDI-TOF-MS with suppressed background noise and increased mass resolution (4-13-fold) in linear MALDI-TOF-MS. The application of CdS-MUA NPs and SA as the co-matrices in MALDI-MS is demonstrated for the analysis of hydrophobic proteins from soybean.
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Affiliation(s)
- Suresh Kumar Kailasa
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
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20
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Gross JH. Matrix-Assisted Laser Desorption/Ionization. Mass Spectrom (Tokyo) 2011. [DOI: 10.1007/978-3-642-10711-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Kuramochi H, Kobayashi T, Suzuki T, Ichimura T. Excited-State Dynamics of 6-Aza-2-thiothymine and 2-Thiothymine: Highly Efficient Intersystem Crossing and Singlet Oxygen Photosensitization. J Phys Chem B 2010; 114:8782-9. [DOI: 10.1021/jp102067t] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hikaru Kuramochi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Takashi Kobayashi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Suzuki
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Teijiro Ichimura
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
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22
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Stübiger G, Belgacem O, Rehulka P, Bicker W, Binder BR, Bochkov V. Analysis of Oxidized Phospholipids by MALDI Mass Spectrometry Using 6-Aza-2-thiothymine Together with Matrix Additives and Disposable Target Surfaces. Anal Chem 2010; 82:5502-10. [DOI: 10.1021/ac100280p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gerald Stübiger
- Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria, Shimadzu Biotech, Wharfside, Trafford Wharf Road, Manchester M17 1GP, England, Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic, and Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Omar Belgacem
- Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria, Shimadzu Biotech, Wharfside, Trafford Wharf Road, Manchester M17 1GP, England, Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic, and Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Pavel Rehulka
- Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria, Shimadzu Biotech, Wharfside, Trafford Wharf Road, Manchester M17 1GP, England, Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic, and Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Wolfgang Bicker
- Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria, Shimadzu Biotech, Wharfside, Trafford Wharf Road, Manchester M17 1GP, England, Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic, and Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Bernd R. Binder
- Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria, Shimadzu Biotech, Wharfside, Trafford Wharf Road, Manchester M17 1GP, England, Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic, and Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Valery Bochkov
- Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria, Shimadzu Biotech, Wharfside, Trafford Wharf Road, Manchester M17 1GP, England, Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic, and Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria
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23
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Ruthenium versus platinum: interactions of anticancer metallodrugs with duplex oligonucleotides characterised by electrospray ionisation mass spectrometry. J Biol Inorg Chem 2010; 15:677-88. [PMID: 20213306 DOI: 10.1007/s00775-010-0635-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 02/03/2010] [Indexed: 01/22/2023]
Abstract
The binding of the ruthenium-based anticancer drug candidates KP1019, NAMI-A and RAPTA-T towards different double-stranded oligonucleotides was probed by electrospray ionisation mass spectrometry and compared with that of the widely used platinum-based chemotherapeutics cisplatin, carboplatin and oxaliplatin. It was found that the extent of adduct formation decreased in the following order: cisplatin > oxaliplatin > NAMI-A > RAPTA-T > carboplatin > KP1019. In addition to the characterisation of the adducts formed with the DNA models, the binding sites of the metallodrugs on the oligonucleotides were elucidated employing top-down tandem mass spectrometry and were found to be similar for all the metallodrugs studied, irrespective of the sequence of the oligonucleotide. A strong preference for guanine residues was established.
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24
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Fabris D. A role for the MS analysis of nucleic acids in the post-genomics age. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1-13. [PMID: 19897384 DOI: 10.1016/j.jasms.2009.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 09/04/2009] [Accepted: 09/04/2009] [Indexed: 05/28/2023]
Abstract
The advances of mass spectrometry in the analysis of nucleic acids have tracked very closely the exciting developments of instrumentation and ancillary technologies, which have taken place over the years. However, their diffusion in the broader life sciences community has been and will be linked to the ever evolving focus of biomedical research and its changing demands. Before the completion of the Human Genome Project, great emphasis was placed on sequencing technologies that could help accomplish this project of exceptional scale. After the publication of the human genome, the emphasis switched toward techniques dedicated to the exploration of sequences not coding for actual protein products, which amount to the vast majority of transcribed elements. The broad range of capabilities offered by mass spectrometry is rapidly advancing this platform to the forefront of the technologies employed for the structure-function investigation of these noncoding elements. Increasing focus on the characterization of functional assemblies and their specific interactions has prompted a re-evaluation of what has been traditionally construed as nucleic acid analysis by mass spectrometry. Inspired by the accelerating expansion of the broader field of nucleic acid research, new applications to fundamental biological studies and drug discovery will help redefine the evolving role of MS-analysis of nucleic acids in the post-genomics age.
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Affiliation(s)
- Daniele Fabris
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21228, USA.
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25
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Bahr U, Aygün H, Karas M. Detection and relative quantification of siRNA double strands by MALDI mass spectrometry. Anal Chem 2008; 80:6280-5. [PMID: 18616347 DOI: 10.1021/ac800605z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While MALDI-MS is widely accepted for quality control of synthetic oligonucleotides, this method has been regarded as not applicable for a control of the purity and correct annealing of double strands. The results presented here show that the double-strand intensities measured by MALDI-MS maintain and reflect the solution conditions. Using a single-stranded RNA as internal standard, the double-strand intensity can be determined by measuring the intensity ratio of the single strands to the standard under "native" conditions and after denaturation with formic acid. For siRNAs with fully matched 20-21 base pairs, relative intensities of the double strands are between 94 and 97.2%. The stability determined by MALDI-MS for different RNA duplexes correlates well with calculated T m values and the content of G-C pairs. Furthermore, the quantification method enables one to determine an excess of one single strand and the contribution of duplex formation by truncated strands. The results show that MALDI-MS is a fast and reliable method for quality control of synthetic siRNA.
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Affiliation(s)
- Ute Bahr
- Cluster of Excellence Macromolecular Complexes, Institute of Pharmaceutical Chemistry, University of Frankfurt, 60438 Frankfurt, Germany.
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26
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Abstract
Branched nucleic acids (bNAs) have been of particular interest since the discovery of RNA forks and lariats as intermediates of nuclear mRNA splicing, as well as multicopy, single-stranded DNA (msDNA). Such molecules contain the inherent trait of vicinal 2',5'- and 3',5'-phosphodiester linkages. bNAs have many potential applications in nucleic acid biochemistry, particularly as tools for studying the substrate specificity of lariat debranching enzymes, and as biological probes for the investigation of branch recognition during pre-mRNA splicing. The protocols described herein allow for the facile solid-phase synthesis of branched DNA and/or RNA oligonucleotides of varying chain length, containing symmetrical or asymmetrical sequences immediate to an RNA branch point. The synthetic methodology utilizes widely adopted phosphoramidite chemistry. Methods for efficient purification of bNAs via anion-exchange HPLC and PAGE are also illustrated.
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Chou CW, Limbach PA. Analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. ACTA ACUST UNITED AC 2008; Chapter 10:Unit 10.1. [PMID: 18428820 DOI: 10.1002/0471142700.nc1001s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
MALDI-MS is one of the most useful techniques available for determining biomolecule mass. It offers high mass accuracy, good sensitivity, simplicity, and speed. Because singly charged ions of oligonucleotides are typically observed, MALDI-MS spectra are easy to interpret. This unit presents protocols for sample preparation and purification, matrix preparation, and matrix/analyte sample preparation. It provides an introduction to the instrumentation and its calibration, and a discussion of some of the useful applications of MALDI-MS analysis in the study of oligonucleotides. This technique is typically used for 120-mer or smaller oligonucleotides.
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Affiliation(s)
- C W Chou
- Louisiana State University, Baton Rouge, Louisiana, USA
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28
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Chen WY, Chen YC. MALDI MS analysis of oligonucleotides: desalting by functional magnetite beads using microwave-assisted extraction. Anal Chem 2007; 79:8061-6. [PMID: 17902633 DOI: 10.1021/ac0709450] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The presence of alkali cation adductions of oligonucleotides commonly deteriorates matrix-assisted laser desorption/ionization (MALDI) mass spectra. Thus, desalting is required for oligonucleotide samples prior to MALDI MS analysis in order to prevent the mass spectra from developing poor quality. In this paper, we demonstrate a new approach to extract traces of oligonucleotides from aqueous solutions containing high concentrations of salts using microwave-assisted extraction. The C18-presenting magnetite beads, capable of absorbing microwave irradiation, are used as affinity probes for oligonucleotides with the addition of triethylammonium acetate as the counterions. This new microwave-assisted extraction approach using magnetite beads as the trapping agents and as microwave-absorbers has been demonstrated to be very effective in the selective binding of oligonucleotides from aqueous solutions. The extraction of oligonucleotides from solutions onto the C18-presenting magnetite beads takes only 30 s to enrich oligonucleotides in sufficient quantities for MALDI MS analysis. After using this desalting approach, alkali cation adductions of oligonucleotides are dramatically reduced in the MALDI mass spectra. The presence of saturated NaCl (approximately 6 M) in the oligonucleotide sample is tolerated without degrading the mass spectra. The detection limit for d(A)6 is approximately 2.8 fmol.
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Affiliation(s)
- Wei-Yu Chen
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan
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29
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Sauer S. The essence of DNA sample preparation for MALDI mass spectrometry. ACTA ACUST UNITED AC 2007; 70:311-8. [DOI: 10.1016/j.jbbm.2006.10.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Accepted: 10/16/2006] [Indexed: 01/20/2023]
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30
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Paranjape JM, Xu D, Kushner DM, Okicki J, Lindner DJ, Cramer H, Silverman RH, Leaman DW. Human telomerase RNA degradation by 2'-5'-linked oligoadenylate antisense chimeras in a cell-free system, cultured tumor cells, and murine xenograft models. Oligonucleotides 2006; 16:225-38. [PMID: 16978086 DOI: 10.1089/oli.2006.16.225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ribonuclease L (RNase L) is a latent single-stranded RNA-directed endoribonuclease that is activated on binding to short 2'-5'-linked oligoadenylates (2-5A), a feature that has led to its use in antisense therapeutic strategies. By attaching a 2-5A moiety to the 5' terminus of standard antisense oligonucleotides, it is possible to activate RNase L and guide it to specific RNAs for degradation. These 2-5A antisense chimeras have been used successfully to target a variety of cellular and viral RNAs. Telomerase is a nuclear ribonucleoprotein complex that elongates telomeric DNA and contributes to cellular immortalization. Telomerase is composed of a protein catalytic subunit and an RNA (hTR or TERC) component, both of which are critical for holoenzyme activity. We describe the characterization of 2-5A antisense chimeras targeting the hTR component of telomerase (2-5A antihTR). Newly designed 2-5A anti-hTR molecules were assayed for their abilities to selectively degrade hTR in a cell-free system. Of the five chimeras tested, one (RBI011) degraded hTR by 97%, and two others (RBI013 and RBI009) were also found to be highly active (73-76% degradation). The ability of transfected RBI011, and its homolog RBI254, to degrade hTR in cultured tumor cells was assessed by real-time RT-PCR. In these studies, RBI011 and RBI254 effectively degraded hTR in a variety of hTR-positive tumor cell lines. The hTR degradation studies were extended to growth assays to determine whether hTR ablation affected tumor cell viability or proliferation. RBI254 treatment resulted in reduced tumor cell viability over the course of 4-day growth assays, effects that were augmented by cotreatment with interferon-beta. To extend these results to an in vivo system, nude mice were implanted subcutaneously or orthotopically with hTR-positive prostate tumors and treated with RBI254. RBI254-treated mice exhibited enhanced tumor cell apoptosis and reduced tumor volume as compared with controls. These findings demonstrated the effectiveness of highly active forms of 2-5A antisense against hTR, and also highlight the usefulness of the cell-free system in predicting chimera efficacy before to inception of cell-based and in vivo studies.
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Affiliation(s)
- Jayashree M Paranjape
- Department of Cancer Biology and Immunology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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31
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Zagorevskii DV, Aldersley MF, Ferris JP. MALDI analysis of oligonucleotides directly from montmorillonite. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1265-70. [PMID: 16809045 DOI: 10.1016/j.jasms.2006.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Revised: 05/16/2006] [Accepted: 05/25/2006] [Indexed: 05/10/2023]
Abstract
Oligonucleotides synthesized on a montmorillonite catalyst were analyzed directly. By mixing the catalyst with a matrix (2,4,6-trihydroxyacetophenone or 6-aza-2-thiothymine) and dibasic ammonium citrate, higher molecular weight products were detected compared with "classical" methods such as gel electrophoresis and HPLC with UV as a detector. The oligomers (30-mers and higher) were detected by mass spectrometry even though their concentration was less than 10(-4)% of the total content of the RNA. This method is different from the (MALDI) analysis of the eluates from montmorillonite, which otherwise requires desalting. Placing reaction mixtures with a high concentration of buffers on homoionic, preferably Li-containing, montmorillonite does not require desalting.
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Affiliation(s)
- Dmitri V Zagorevskii
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute,209C Cogswell Laboratory, Troy, New York 12180, USA.
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32
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Fu Y, Xu S, Pan C, Ye M, Zou H, Guo B. A matrix of 3,4-diaminobenzophenone for the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Nucleic Acids Res 2006; 34:e94. [PMID: 16885235 PMCID: PMC1540732 DOI: 10.1093/nar/gkl509] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 07/01/2006] [Accepted: 07/03/2006] [Indexed: 12/04/2022] Open
Abstract
A new matrix of 3,4-diaminobenzophenone (DABP) was demonstrated to be advantageous in the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. With DABP as a matrix, intact oligonucleotide ions can be readily produced with lower laser powers, resulting in better detection limits, less fragmentation and fewer alkali metal ion adducts compared with the results obtained with conventional matrices. Importantly, minimal fragmentation and fewer alkali metal ion adducts were seen even at low concentrations of oligonucleotides. It was also found that samples prepared with DABP are highly homogenous and therefore reducing the need for finding 'sweet' spots in MALDI. In addition, excellent shot-to-shot reproducibility, resolution and signal-to-noise ratio were seen with DABP as the matrix.
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Affiliation(s)
- Yu Fu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Songyun Xu
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Chensong Pan
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Mingliang Ye
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, The Chinese Academy of SciencesDalian 116023, China
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
| | - Hanfa Zou
- To whom correspondence should be addressed. Tel: +86 411 843 79610; Fax: +86 411 843 79620;
| | - Baochuan Guo
- Department of Chemistry, Cleveland State UniversityCleveland, OH 44115, USA
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Mourani R, Damha MJ. Synthesis, characterization, and biological properties of small branched RNA fragments containing chiral (Rp and Sp) 2',5'-phosphorothioate linkages. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:203-29. [PMID: 16541962 DOI: 10.1080/15257770500447004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Synthetic branched RNA fragments were prepared to examine the stereochemical requirements for hydrolysis of RNA lariats by the yeast debranching enzyme (yDBR). Specifically, two branched trinucleoside diphosphates and a tetranucleoside triphosphate containing a 2',5'-linked phosphorothioate linkage of defined stereochemistry, namely Rp-A(2'ps5'G)pC, Sp-A(2'ps5'G)pC and Sp-ApA(2'ps5'G)pC, were prepared via solution-phase methods. Unlike the all-phosphodiester control, A(2'p5'G)pC, the Rp-thioated trimer was not cleaved by yDBR, demonstrating that changing the pro-Rp oxygen at the 2',5' phosphodiester bond averts hydrolysis by the enzyme. In contrast, the Sp branched compounds (trimer and tetramer) were cleaved yDBR, albeit with reduced efficiency relative to the corresponding all-phosphodiester branched compounds. Furthermore, the small branched RNAs (5 nt) were not cleaved as efficiently as a 18-nt bRNA, suggesting that the enzyme appears to have a stronger preference for larger bRNA substrates. The non-hydrolyzable branched RNA fragments prepared during these studies may be promising candidates for the future co-crystallization and X-ray analyses of DBR:bRNA complexes.
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Affiliation(s)
- Rawan Mourani
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
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34
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Lecchi P, Olson M, Brancia FL. The role of esterification on detection of protonated and deprotonated peptide ions in matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1269-74. [PMID: 15975823 DOI: 10.1016/j.jasms.2005.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 03/15/2005] [Accepted: 03/18/2005] [Indexed: 05/03/2023]
Abstract
Esterification was used to investigate how introduction of aliphatic chains within the peptide structure affects the MALDI response of ions analyzed in both polarity regimes. In binary mixtures containing equimolar amounts of a peptide with its correspondent alkyl ester, derivatization of the carboxylic groups has the tendency to increase MALDI detection of the modified protonated peptide ions. This positive effect on ion yield is more pronounced when longer alcohols are employed. In negative mode, the situation is antithetic and esterification produces a deleterious effect on the ion yield of the corresponding deprotonated species. From the data reported here we postulate that modifications of the acidic character of peptides prevent formation of anionic species under MALDI analysis. Furthermore, suppression of the formation pathway for anions alters the overall number of molecules which can undergo protonation. This results in an increased ion yield for the protonated esters.
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Affiliation(s)
- Paolo Lecchi
- Department of Pharmacology and Physiology, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
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35
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Edwards JR, Ruparel H, Ju J. Mass-spectrometry DNA sequencing. Mutat Res 2005; 573:3-12. [PMID: 15829234 DOI: 10.1016/j.mrfmmm.2004.07.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 07/15/2004] [Indexed: 11/15/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been explored widely for DNA sequencing. Compared to gel electrophoresis based sequencing systems, mass spectrometry produces very high resolution of sequencing fragments, rapid separation on microsecond time scales, and completely eliminates compressions associated with gel-based systems. While most of the research efforts have focused on using mass spectrometers to analyze the DNA products from Sanger sequencing or enzymatic digestion reactions, the read lengths attainable are currently insufficient for large-scale de novo sequencing. The advantage of mass-spectrometry sequencing is that one can unambiguously identify frameshift mutations and heterozygous mutations making it an ideal choice for resequencing projects. In these applications, DNA sequencing fragments that are the same length but with different base compositions are generated, which are challenging to consistently distinguish in gel-based sequencing systems. In contrast, MALDI-TOF MS produces mass spectra of these DNA sequencing fragments with nearly digital resolution, allowing accurate determination of the mixed bases. For these reasons mass spectrometry based sequencing has mainly been focused on the detection of frameshift mutations and single nucleotide polymorphisms (SNPs). More recently, assays have been developed to indirectly sequence DNA by first converting it into RNA. These assays take advantage of the increased resolution and detection ability of MALDI-TOF MS for RNA.
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Affiliation(s)
- John R Edwards
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, Room 405A, Russ Berrie Medical Science Pavilion, New York, NY 10032, USA
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36
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Jurinke C, Oeth P, van den Boom D. MALDI-TOF mass spectrometry: a versatile tool for high-performance DNA analysis. Mol Biotechnol 2004; 26:147-64. [PMID: 14764940 DOI: 10.1385/mb:26:2:147] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has developed during the past decade into a versatile tool for biopolymer analysis. The aim of this review is to summarize this development and outline the applications, which have been enabled for routine use in the field of nucleic acid analysis. These include the analysis of mutations, the resequencing of amplicons with a known reference sequence, and the quantitative analysis of gene expression and allelic frequencies in complex DNA mixtures.
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Meyer K, Fredriksen A, Ueland PM. High-level multiplex genotyping of polymorphisms involved in folate or homocysteine metabolism by matrix-assisted laser desorption/ionization mass spectrometry. Clin Chem 2004; 50:391-402. [PMID: 14752013 DOI: 10.1373/clinchem.2003.026799] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Increased plasma total homocysteine (tHcy), a risk factor for cardiovascular disease, is related to genetic, environmental, and nutritional factors, in particular folate status. Future large epidemiologic studies of the genetic basis of hyperhomocysteinemia will require high-throughput assays for polymorphisms of genes related to folate and Hcy metabolism. METHOD We developed a high-level multiplex genotyping method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the detection of 12 polymorphisms in 8 genes involved in folate or Hcy metabolism. The assay includes methylenetetrahydrofolate reductase (MTHFR) 677C>T and 1298A>C, methionine synthase (MTR) 2756A>G, methionine synthase reductase (MTRR) 66A>G, cystathionine beta-synthase (CBS) 844ins68 and 699C>T, transcobalamin II (TCII) 776C>G and 67A>G, reduced folate carrier-1 (RFC1) 80G>A, paraoxonase-1 (PON1) 575A>G and 163T>A, and betaine homocysteine methyltransferase (BHMT) 742G>A. RESULTS The failure rate of the assay was < or = 1.7% and was attributable to unsuccessful DNA purification, nanoliter dispensing, and spectrum calibration. Most errors were related to identification of heterozygotes as homozygotes. The mean error rate was 0.26%, and error rates differed for the various single-nucleotide polymorphisms. Identification of CBS 844ins68 was carried out by a semiquantitative approach. The throughput of the MALDI-TOF MS assay was 1152 genotypes within 20 min. CONCLUSIONS This high-level multiplex method is able to genotype 12 polymorphisms involved in folate or Hcy metabolism. The method is rapid and reproducible and could facilitate large-scale studies of the genetic basis of hyperhomocysteinemia and associated pathologies.
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Affiliation(s)
- Klaus Meyer
- LOCUS for Homocysteine and Related Vitamins, University of Bergen, Bergen, Norway.
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38
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Carriero S, Damha MJ. Inhibition of pre-mRNA splicing by synthetic branched nucleic acids. Nucleic Acids Res 2003; 31:6157-67. [PMID: 14576302 PMCID: PMC275466 DOI: 10.1093/nar/gkg824] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 08/27/2003] [Accepted: 09/10/2003] [Indexed: 11/15/2022] Open
Abstract
The cellular transformation of a precursor mRNA (pre-mRNA) into its mature or functional form proceeds by way of a splicing reaction, in which the exons are ligated to form the mature linear RNA and the introns are excised as branched or lariat RNAs. We have prepared a series of branched compounds (bRNA and bDNA), and studied the effects of such molecules on the efficiency of mammalian pre-mRNA splicing in vitro. Y-shaped RNAs containing an unnatural L-2'-deoxycytidine unit (L-dC) at the 3' termini are highly stabilized against exonuclease hydrolysis in HeLa nuclear extracts, and are potent inhibitors of the splicing pathway. A bRNA containing internal 2'-O-methyl ribopyrimidine units and L-dC at the 3' ends was at least twice as potent as the most potent of the bRNAs containing no 2' modifications, with an IC50 of approximately 5 micro M. Inhibitory activity was maintained in a branched molecule containing an arabino-adenosine branchpoint which, unlike the native bRNAs, resisted cleavage by the lariat- debranching enzyme. The data obtained suggest that binding and sequestering of a branch recognition factor by the branched nucleic acids is an early event, which occurs prior to the first chemical step of splicing. Probably, an early recognition element preferentially binds to the synthetic branched molecules over the native pre-mRNA. As such, synthetic bRNAs may prove to be invaluable tools for the purification and identification of the putative branchpoint recognition factor.
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Affiliation(s)
- Sandra Carriero
- Department of Chemistry, Otto Maass Chemistry Building, McGill University, 801 Sherbrooke St West, Montreal, QC, H3A 2K6, Canada
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39
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Song F. Evidence for involvement of the backbone in the ionization process of nucleic acids by matrix-assisted laser desorption/ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1095-1098. [PMID: 12720293 DOI: 10.1002/rcm.1026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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40
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Song F. Quinaldic acid as a new matrix for matrix-assisted laser desorption/ionization of nucleic acids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1802-1807. [PMID: 12872286 DOI: 10.1002/rcm.1105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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41
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Garcia BA, Heaney PJ, Tang K. Improvement of the MALDI-TOF analysis of DNA with thin-layer matrix preparation. Anal Chem 2002; 74:2083-91. [PMID: 12033310 DOI: 10.1021/ac011089+] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new method of sample preparation was developed for MALDI-TOF-MS analysis of oligonucleotides. First, aqueous DNA samples are dispensed and allowed to dry. Then 6-aza-2-thiothymine matrix dissolved in nonaqueous volatile solvents is applied on top of the DNA residue to form a thin homogeneous film. MALDI-TOF analysis shows such preparation generates much better shot-to-shot and sample-to-sample reproducibility and essentially eliminates the need to search for "hot" spots. The increased homogeneity of the matrix/analyte crystal distribution results in significant improvement for quantitative and high-throughput analyses of DNA. Using this method, isotopically resolved oligonucleotide spectra up to a 24-mer can also be easily obtained in a reflectron instrument. Due to the ease of preparation, this method could be widely useful for a number of applications such as for assays that are performed on surface in vitro, as the thin-layer matrix could be applied directly for MALDI analysis.
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Koomen JM, Russell WK, Tichy SE, Russell DH. Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:357-371. [PMID: 11948842 DOI: 10.1002/jms.312] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.
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Affiliation(s)
- John M Koomen
- Laboratory for Biological Mass Spectrometry, Texas A&M University, College Station, Texas 77843, USA
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Shahgholi M, Garcia BA, Chiu NH, Heaney PJ, Tang K. Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved. Nucleic Acids Res 2001; 29:E91. [PMID: 11574693 PMCID: PMC60251 DOI: 10.1093/nar/29.19.e91] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) of DNA is critical for obtaining high quality mass spectra. Sample impurity, solvent content, substrate surface and environmental conditions (temperature and humidity) all affect the rate of matrix-analyte co-crystallization. As a result, laser fluence threshold for desorption/ionization varies from spot to spot. When using 3-hydroxypicolinic acid (3-HPA) as the matrix, laser fluence higher than the threshold value reduces mass resolution in time-of-flight (TOF) MS as the excess energy transferred to DNA causes metastable decay. This can be overcome by either searching for 'hot' spots or adjusting the laser fluence. However, both solutions may require a significant amount of operator manipulation and are not ideal for automatic measurements. We have added various sugars for crystallization with the matrix to minimize the transfer of excess laser energy to DNA molecules. Fructose and fucose were found to be the most effective matrix additives. Using these additives, mass resolution for DNA molecules does not show noticeable deterioration as laser energy increases. Improved sample preparation is important for the detection of single nucleotide polymorphisms (SNPs) using primer extension with a single nucleotide. During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization.
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Affiliation(s)
- M Shahgholi
- Sequenom Inc., 3595 John Hopkins Court, San Diego, CA 92121, USA
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Vicens Q, Westhof E. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure 2001; 9:647-58. [PMID: 11587639 DOI: 10.1016/s0969-2126(01)00629-3] [Citation(s) in RCA: 316] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Aminoglycoside antibiotics interfere with translation in both gram-positive and gram-negative bacteria by binding to the tRNA decoding A site of the 16S ribosomal RNA. RESULTS Crystals of complexes between oligoribonucleotides incorporating the sequence of the ribosomal A site of Escherichia coli and the aminoglycoside paromomycin have been solved at 2.5 A resolution. Each RNA fragment contains two A sites inserted between Watson-Crick pairs. The paromomycin molecules interact in an enlarged deep groove created by two bulging and one unpaired adenines. In both sites, hydroxyl and ammonium side chains of the antibiotic form 13 direct hydrogen bonds to bases and backbone atoms of the A site. In the best-defined site, 8 water molecules mediate 12 other hydrogen bonds between the RNA and the antibiotics. Ring I of paromomycin stacks over base G1491 and forms pseudo-Watson-Crick contacts with A1408. Both the hydroxyl group and one ammonium group of ring II form direct and water-mediated hydrogen bonds to the U1495oU1406 pair. The bulging conformation of the two adenines A1492 and A1493 is stabilized by hydrogen bonds between phosphate oxygens and atoms of rings I and II. The hydrophilic sites of the bulging A1492 and A1493 contact the shallow groove of G=C pairs in a symmetrical complex. CONCLUSIONS Water molecules participate in the binding specificity by exploiting the antibiotic hydration shell and the typical RNA water hydration patterns. The observed contacts rationalize the protection, mutation, and resistance data. The crystal packing mimics the intermolecular contacts induced by aminoglycoside binding in the ribosome.
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Affiliation(s)
- Q Vicens
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisation et simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, Cedex 67084, Strasbourg, France
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Yamashita K, Sato S, Takamiya H, Takagi M, Takenaka S. Analysis of the Complex of Oligonucleotide Duplexes with Ligands by MALDI-TOF Mass Spectroscopy. CHEM LETT 2001. [DOI: 10.1246/cl.2001.680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Kim Y, Hurst GB, Doktycz MJ, Buchanan MV. Improving spot homogeneity by using polymer substrates in matrix-assisted laser desorption/ionization mass spectrometry of oligonucleotides. Anal Chem 2001; 73:2617-24. [PMID: 11403308 DOI: 10.1021/ac001392v] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a method for improving the homogeneity of MALDI samples prepared for analysis of small, single-stranded oligonucleotides using the widely used DNA matrix system, 3-hydroxypicolinic acid/picolinic acid/ ammonium citrate. This matrix system typically produces large crystals around the rim of the dried sample and requires tedious searching of this rim with the laser. However, when a substrate is prepared using both Nafion and a hydrophilic, high-molecular-weight polymer, such as linear polyacrylamide, linear poly(ethylene oxide), or methyl cellulose, oligonucleotide-doped matrix crystals tend to be smaller and more uniformly distributed across the entire spot, thus decreasing the time that is required for locating a usable signal. In addition to MALDI characterization of the spatial distribution of "sweet spots," fluorescence microscopy allows for imaging dye-labeled DNA in dried MALDI spots. The mechanism of enhanced uniformity may involve increased viscosity in the MALDI sample droplet due to partial solubilization of the substrate by the MALDI sample solvent as well as partitioning of the matrix or DNA between the solvent and the undissolved portion of the polymer substrate.
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Affiliation(s)
- Y Kim
- Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Tennessee 37831-6365, USA
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47
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Distler AM, Allison J. 5-Methoxysalicylic acid and spermine: a new matrix for the matrix-assisted laser desorption/ionization mass spectrometry analysis of oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:456-462. [PMID: 11322192 DOI: 10.1016/s1044-0305(01)00212-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
5-Methoxysalicylic acid (MSA) is demonstrated to be a useful matrix for matrix-assisted laser desorption/ionization time-of-flight (TOF) mass spectrometry of oligonucleotides, when desorption/ionization without fragmentation is desired. When MSA is combined with the additive spermine, the need for desalting is reduced. The MSA/spermine matrix yields linear TOF mass spectra with improved resolution, less fragmentation, and less intense alkali ion adduct peaks than those spectra obtained using 3-hydroxypicolinic acid and 6-aza-2-thiothymine with spermine or diammonium hydrogen citrate as additives. Instrumental conditions are discussed to improve the spectral resolution, specifically the use of longer delay times in the delayed-extraction ion source.
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Affiliation(s)
- A M Distler
- Department of Chemistry, Michigan State University, East Lansing 48824-1322, USA
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Davis DL, O'Brien EP, Bentzley CM. Analysis of the degradation of oligonucleotide strands during the freezing/thawing processes using MALDI-MS. Anal Chem 2000; 72:5092-6. [PMID: 11055733 DOI: 10.1021/ac000225s] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Synthetic oligonucleotide strands ranging from 5 to 25 units in length are commonly used as standards, probes, and templates in various bioanalytical applications. Until recently, their preparation, storage, and handling were regarded as unimportant, but this work provides valuable information to the contrary. The systematic degradation of oligonucleotide strands during sample preparation is investigated by repeatedly freezing/thawing short strands followed by matrix-assisted laser desorption ionization mass spectrometric (MALDI-MS) analysis. It is shown here that the longevity of an oligonucleotide strand is dependent on several factors including base composition, solution concentrations, and strand length as well as thawing conditions. Several trends in strand robustness were established. Our studies reveal that the robustness of strands is base-dependent: T-mer > A-mer > C-mer > G-mer. Likewise, an increase in the length of the strands increases the tendency of a sample to degrade. Another observation included that samples of mixed bases degrade according to structural conformations. All of these observations are attributed to the fact that the samples undergo degradation during sample/solvent isolation during freezing.
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Affiliation(s)
- D L Davis
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Pennsylvania 19104, USA
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49
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Koomen JM, Russell WK, Hettick JM, Russell DH. Improvement of resolution, mass accuracy, and reproducibility in reflected mode DE-MALDI-TOF analysis of DNA using fast evaporation--overlayer sample preparations. Anal Chem 2000; 72:3860-6. [PMID: 10959974 DOI: 10.1021/ac0001941] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA analysis by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is hindered by two processes: alkali metal adduction and fragmentation of the intact ionized molecule. The adverse effects of both processes can be reduced by adding ammonium ion salts or compounds such as fructose to the sample preparations. Matrix additives improve sensitivity and resolution of DNA analysis by MALDI. In addition, spot-to-spot reproducibility, resolution, and mass accuracy for DNA oligonucleotides (< or = 12 mer) can be improved by the use of overlayer sample preparations with matrixes that have low aqueous solubilities, such as alpha-cyano-4-hydroxycinnamic acid, ferulic acid, and 2,4,6-trihydroxyacetophenone. For example, resolution for 5-12-mer oligonucleotides is greater than 7000 using overlayer matrix preparations and mass accuracy values are well below 20 ppm. In addition to these methods, a new method for analyzing DNA in positive ion mode is reported using acidified 3-hydroxypicolinic acid. This method does not lose sensitivity for higher mass oligonucleotides as quickly as overlayer methods, and spectra retain > 6000 resolution and mass accuracies of approximately 20 ppm between different overlayer depositions.
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Affiliation(s)
- J M Koomen
- Chemistry Department, Texas A&M University, College Station 77843, USA
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50
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Geselowitz DA, Cramer H, Wondrak EM, Player MR, Torrence PF. Fluorescence resonance energy transfer analysis of RNase L-catalyzed oligonucleotide cleavage. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2000; 10:45-51. [PMID: 10726660 DOI: 10.1089/oli.1.2000.10.45] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A method is described for monitoring the cleavage of an oligoribonucleotide substrate by the 2-5A-dependent RNase L based on fluorescence resonance energy transfer (FRET). The oligoribonucleotide, rC11U2C7, was labeled covalently at its 5'-terminus with fluorescein and at its 3'-terminus with rhodamine to provide a substrate for RNase L. On cleavage, the fluorescence at 538 nm (with 485 nm excitation) increased by a factor of 2.8, allowing real-time quantitation of the reaction progress. The method was performed easily in a 96-well plate format and allowed quantitative high throughput analyses of RNase L activity with different activators.
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Affiliation(s)
- D A Geselowitz
- Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892-0805, USA
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