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Apostle A, Fang S. Dissolve-spin: Desalting oligonucleotides for MALDI MS analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4893. [PMID: 36415947 DOI: 10.1002/jms.4893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Desalting oligonucleotides (ONs) for matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) analysis was achieved using a simple dissolve-spin approach. The ON is dissolved in an organic solvent. Insoluble salts are removed by centrifugation. ONs are highly polar molecules and are generally believed insoluble in organic solvents with moderate polarity such as acetonitrile (ACN), 1,4-dioxane, ethyl acetate, and THF. However, we found that in the presence of a suitable proton source such as pyridinium chloride, a quantity of ON that is sufficient for MALDI MS analysis could be dissolved. Because inorganic salts are insoluble in such relatively non-polar solvents, the finding can be utilized for desalting ONs for MALDI MS analysis. Comparisons of MS spectra of intentionally salted ONs that underwent the new desalting procedure with those that did not undergo the procedure provided unambiguous evidence that the desalting method is highly effective.
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Affiliation(s)
- Alexander Apostle
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Shiyue Fang
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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2
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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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Zhu L, Yin L, Xue J, Wang Z, Nie Z. Mass Spectrometry Genotyping of Human Papillomavirus Based on High-Efficiency Selective Enrichment of Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2018; 10:41178-41184. [PMID: 30406990 DOI: 10.1021/acsami.8b16694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This work developed a novel spermine-modified nanodiamonds (SP-NDs)-based method to selectively enrich oligonucleotides for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of human papillomavirus (HPV) virus. Our results showed that SP-NDs can effectively extract and enrich DNA oligonucleotides from sodium dodecyl sulfonate and urea solution. In addition, SP-NDs can also selectively extract oligonucleotides from enzymes digestion products of polymerase chain reaction-restriction fragment mass polymorphism (PCR-RFMP) of HPV virus. Then, the extract can be detected by MALDI-TOF MS directly without further purification. According to the MS results, the HPV genotyping can be achieved. More importantly, with SP-NDs extraction, clinical samples infected with HPV genotype 16 and 18 can be identified. The described method shows great advantages of simplicity, high selectivity, and good reliability in real clinical samples. Due to our methods improvement on DNA enrichment, extraction and purification, the PCR-based MALDI-TOF MS for the analysis of oligonucleotides maybe become more rapid, sensitive, and high-throughput, is promising for analysis for DNA methylation, single-nucleotide polymorphisms, and other virus typing.
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Affiliation(s)
- Li Zhu
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , Beijing 100029 , China
- National Institutes for Food and Drug Control , Beijing 102629 , China
| | - Lihui Yin
- National Institutes for Food and Drug Control , Beijing 102629 , China
| | - JinJuan Xue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Zhihua Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
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Moskovets E, Misharin A, Laiko V, Doroshenko V. A comparative study on the analytical utility of atmospheric and low-pressure MALDI sources for the mass spectrometric characterization of peptides. Methods 2016; 104:21-32. [DOI: 10.1016/j.ymeth.2016.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/19/2015] [Accepted: 02/16/2016] [Indexed: 11/16/2022] Open
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Silvestri C, Brodbelt JS. Tandem mass spectrometry for characterization of covalent adducts of DNA with anticancer therapeutics. MASS SPECTROMETRY REVIEWS 2013; 32:247-66. [PMID: 23150278 PMCID: PMC3578003 DOI: 10.1002/mas.21363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 05/17/2023]
Abstract
The chemotherapeutic activities of many anticancer and antibacterial drugs arise from their interactions with nucleic acid substrates. Some of these ligands interact with DNA in a way that causes conformational changes or damage to the nucleic acid targets, ultimately altering recognition by key DNA-specific enzymes, interfering with DNA transcription or prohibiting replication, and terminating cell growth and proliferation. The design and synthesis of ligands that bind to nucleic acids remains a dynamic field in medicinal chemistry and pharmaceutical research. The quest for more selective and efficacious DNA-interactive anticancer chemotherapeutics has likewise catalyzed the need for sensitive analytical methods that can provide structural information about the nature of the resulting DNA adducts and provide insight into the mechanistic pathways of the DNA/drug interactions and the impact on the cellular processes in biological systems. This review focuses on the array of tandem mass spectrometric strategies developed and applied for characterization of covalent adducts formed between DNA and anticancer ligands.
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Affiliation(s)
- Catherine Silvestri
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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6
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Holzhauser S, Freiwald A, Weise C, Multhaup G, Han CT, Sauer S. Screening und Charakterisierung von Protein-modifizierenden Naturstoffen durch MALDI-Massenspektrometrie bringen starke SIRT1- und p300-Inhibitoren hervor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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7
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Holzhauser S, Freiwald A, Weise C, Multhaup G, Han C, Sauer S. Discovery and Characterization of Protein‐Modifying Natural Products by MALDI Mass Spectrometry Reveal Potent SIRT1 and p300 Inhibitors. Angew Chem Int Ed Engl 2013; 52:5171-4. [DOI: 10.1002/anie.201207325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/12/2012] [Indexed: 01/08/2023]
Affiliation(s)
- Susanne Holzhauser
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
- Fachbereich Biologie, Chemie, Pharmazie/Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3/Thielallee 63, 14195 Berlin (Germany)
| | - Anja Freiwald
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
| | - Christoph Weise
- Fachbereich Biologie, Chemie, Pharmazie/Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3/Thielallee 63, 14195 Berlin (Germany)
| | - Gerd Multhaup
- Fachbereich Biologie, Chemie, Pharmazie/Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3/Thielallee 63, 14195 Berlin (Germany)
| | - Chung‐Ting Han
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
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8
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Limanskaia OI, Fesenko TV, Pokrovskiĭ VA, Mukhina TN, Stepanshina VN, Shemiakin IG, Limanskiĭ AP. [Characterization of oligonucleotides with LNA-monomers for PCR detection of point mutations in mycobacteria tuberculosis genome]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2012; 58:199-210. [PMID: 22724359 DOI: 10.18097/pbmc20125802199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Point mutations associated with isoniazid resistance in Mycobacterium tuberculosis (MTB) have been analyzed in codon 315 of the katG gene by conventional polymerase chain reaction (PCR) using primers containing locked nucleic acid (LNA) modified nucleotides. Purity and structure of primers containing 5 LNA monomers of 17 nucleotides in length were characterized by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and a 17-mer duplex formed by two complementary oligonucleotides was characterized by the method of thermal denaturation. The duplex containing five LNA monomers per each strand was characterized by a higher melting temperature than it was expected using extrapolation of theoretical calculation for nucleotide modification of one strand of the duplex. Detection of any of six possible mutations in katG codon 315 (i.e. discrimination between sensitive and resistant MTB) requires just one PCR employing a set of two primers with one LNA-modified primer; this is an important advantage of oligonucleotides containing LNA over unmodified nucleotides: employment of multiplex PCR would require up to 12 primers. Problems of control of oligonucleotide modification by LNA monomers are discussed.
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9
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Phenotypic diversity and epigenomic variation – The utility of mass spectrometric analysis of DNA methylation. J Proteomics 2012; 75:3400-9. [DOI: 10.1016/j.jprot.2012.01.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 01/09/2012] [Accepted: 01/30/2012] [Indexed: 01/10/2023]
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10
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Limanskaya OY, Limanskii OP. Molecular technologies used in detecting of sensitive and isoniazid-resistant Mycobacterium tuberculosis. CYTOL GENET+ 2011. [DOI: 10.3103/s0095452711060041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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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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12
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Dong Y, McGown LB. Incorporation of guanosine gels into sieving matrices for length- and sequence-based separation of DNA in capillary electrophoresis. Electrophoresis 2011; 32:1209-16. [PMID: 21544840 DOI: 10.1002/elps.201000545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Sieving gels are used in capillary gel electrophoresis to resolve DNA strands of different lengths. For complex samples, however, such as those encountered in metagenomic analysis of microbial communities or biofilms, length-based separation may mask the true genetic diversity of the community since different organisms may contribute same-length DNA with different sequences. There is a need, therefore, for DNA separations based on both the length and sequence. Previous work has demonstrated the ability of guanosine gels (G-gels) to separate four single-stranded DNA 76-mers that differ by only a few A/G base substitutions. The goal of the present work is to determine whether G-gels could be combined with commercial sieving gels in order to simultaneously separate DNA based on both length and sequence. The results are given for the four 76-mers and for a standard dsDNA ladder. Commercial sieving gels were used alone and in combination with G-gels. For the 76-mers, the combined medium was less efficient than the G-gel alone but was able to achieve partial resolution. The combined medium was at least as effective as the sieving gel alone at resolving the denatured DNA ladder and showed indications of sequence-based resolution as well, as supported by MALDI-MS. The results show that the combined sieving gel/G-gel medium retains the selectivity of the individual media, providing a promising approach to simultaneous length- and sequence-based DNA separation for metagenomic analysis of complex systems.
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Affiliation(s)
- Yingying Dong
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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13
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Hostetter AA, Miranda ML, DeRose VJ, McFarlane Holman KL. Ru binding to RNA following treatment with the antimetastatic prodrug NAMI-A in Saccharomyces cerevisiae and in vitro. J Biol Inorg Chem 2011; 16:1177-85. [PMID: 21739255 DOI: 10.1007/s00775-011-0806-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/11/2011] [Indexed: 11/24/2022]
Abstract
[ImH][trans-Ru(III)Cl(4)(DMSO)(Im)] (where DMSO is dimethyl sulfoxide and Im is imidazole) (NAMI-A) is an antimetastatic prodrug currently in phase II clinical trials. The mechanisms of action of this and related Ru-based anticancer agents are not well understood, but several cellular targets have been suggested. Although Ru has been observed to bind to DNA following in vitro NAMI-A exposure, little is known about Ru-DNA interactions in vivo and even less is known about how this or related metallodrugs might influence cellular RNA. In this study, Ru accumulation in cellular RNA was measured following treatment of Saccharomyces cerevisiae with NAMI-A. Drug-dependent growth and cell viability indicate relatively high tolerance, with approximately 40% cell death occurring at 6 h for 450 μM NAMI-A. Significant dose-dependent accumulation of Ru in cellular RNA was observed by inductively coupled plasma mass spectrometry measurements on RNA extracted from yeast treated with NAMI-A. In vitro, binding of Ru species to drug-treated model DNA and RNA oligonucleotides at pH 6.0 and 7.4 was characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in the presence and absence of the reductant ascorbate. The extent of Ru-nucleotide interactions increases slightly with lower pH and significantly in the presence of ascorbate, with differences in observed species distribution. Taken together, these studies demonstrate the accumulation of aquated and reduced derivatives of NAMI-A on RNA in vitro and in cellulo, and enhanced binding with nucleic acid targets in a tumorlike acidic, reducing environment. To our knowledge, this is also the first study to characterize NAMI-A treatment of S. cerevisiae, a genetically tractable model organism.
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Cassidy LM, Dong Y, Joshi PC, Aldersley MF, Ferris JP, McGown LB. Signal enhancement of abiotically-synthesized RNA oligonucleotides and other biopolymers using unmodified fused silica in MALDI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1100-1104. [PMID: 21953051 DOI: 10.1007/s13361-011-0113-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 02/21/2011] [Accepted: 02/21/2011] [Indexed: 05/31/2023]
Abstract
Metal is the standard desorption platform for MALDI-MS but other surfaces have been shown to offer advantages for particular types of analytes or applications. One such substrate is fused silica, which has been employed for matrix-free detection of low mass analytes and for affinity MALDI-MS in which binding ligands are immobilized at the fused silica surface. The present work reports improved MALDI-MS detection of RNA oligonucleotides, including polyA, polyU, and polyA/U, at the high end of the mass range when unmodified fused silica is used instead of stainless steel as the MALDI target. The RNA oligonucleotides were abiotically synthesized from activated monomers on catalytic clay surfaces. Further investigation found enhanced signals as well for other anionic biopolymers, including DNA oligonucleotides and heparin. Enhancement also was observed for dextran, which is neutral, indicating that the effect is not restricted to anionic biopolymers. Among more general analytical applications, the results are particularly relevant to rapid screening of abiotic RNA polymerization toward elucidating pathways to life on Earth.
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Affiliation(s)
- Lauren M Cassidy
- Department of Chemistry and Chemical Biology The New York Center for Astrobiology, Rensselaer Polytechnic Institute, Troy, NY, USA
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Serrano CA, Zhang Y, Yang J, Schug KA. Matrix-assisted laser desorption/ionization mass spectrometric analysis of aliphatic biodegradable photoluminescent polymers using new ionic liquid matrices. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1152-1158. [PMID: 21488114 DOI: 10.1002/rcm.4974] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this study, two novel ionic liquid matrices (ILMs), N,N-diisopropylethylammonium 3-oxocoumarate and N,N-diisopropylethylammonium dihydroxymonooxoacetophenoate, were tested for the structural elucidation of recently developed aliphatic biodegradable polymers by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The polymers, formed by a condensation reaction of three components, citric acid, octane diol, and an amino acid, are fluorescent, but the exact mechanism behind their luminescent properties has not been fully elucidated. In the original studies, which introduced the polymer class (J. Yang et al., Proc. Natl. Acad. Sci. USA 2009, 106, 10086-10091), a hyper-conjugated cyclic structure was proposed as the source for the photoluminescent behavior. With the use of the two new ILMs, we present evidence that supports the presence of the proposed cyclization product. In addition, the new ILMs, when compared with a previously established ILM, N,N-diisopropylethylammonium α-cyano-3-hydroxycinnimate, provided similar signal intensities and maintained similar spectral profiles. This research also established that the new ILMs provided good spot-to-spot reproducibility and high ionization efficiency compared with corresponding crystalline matrix preparations. Many polymer features revealed through the use of the ILMs could not be observed with crystalline matrices. Ultimately, the new ILMs highlighted the composition of the synthetic polymers, as well as the loss of water that was expected for the formation of the proposed cyclic structure on the polymer backbone.
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Affiliation(s)
- Carlos A Serrano
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
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Meyer K, Ueland PM. Use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for multiplex genotyping. Adv Clin Chem 2011; 53:1-29. [PMID: 21404912 DOI: 10.1016/b978-0-12-385855-9.00001-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
After completion of the human genome project, the focus of geneticists has shifted to elucidation of gene function and genetic diversity to understand the mechanisms of complex diseases or variation of patient response in drug treatment. In the past decade, many different genotyping techniques have been described for the detection of single-nucleotide polymorphisms (SNPs) and other common polymorphic variants. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is among the most powerful and widely used genotyping technologies. The method offers great flexibility in assay design and enables highly accurate genotyping at high sample throughput. Different strategies for allele discrimination and quantification have been combined with MALDI (hybridization, ligation, cleavage, and primer extension). Approaches based on primer extension have become the most popular applications. This combination enables rapid and reliable multiplexing of SNPs and other common variants, and makes MALDI-TOF-MS well suited for large-scale studies in fine-mapping and verification of genome-wide scans. In contrast to standard genotyping, more demanding approaches have enabled genotyping of DNA pools, molecular haplotyping or the detection of free circulating DNA for prenatal or cancer diagnostics. In addition, MALDI can also be used in novel applications as DNA methylation analysis, expression profiling, and resequencing. This review gives an introduction to multiplex genotyping by MALDI-MS and will focus on the latest developments of this technology.
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Oberacher H. Frontiers of mass spectrometry in nucleic acids analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:351-365. [PMID: 20530841 DOI: 10.1255/ejms.1045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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Il’ina EN, Govorun VM. Mass spectrometry of nucleic acids in molecular medicine. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009. [DOI: 10.1134/s1068162009020010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kouvonen P, McDonnell LA, Heeren RMA, Corthals GL. Nitromatrix provides improved LC-MALDI signals and more protein identifications. Proteomics 2009; 9:1662-71. [DOI: 10.1002/pmic.200800302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Misra A, Kim S. Microbead device for isolating biotinylated oligonucleotides for use in mass spectrometric analysis. Anal Biochem 2008; 384:96-100. [PMID: 18823931 DOI: 10.1016/j.ab.2008.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 08/26/2008] [Accepted: 09/02/2008] [Indexed: 10/21/2022]
Abstract
We describe a prototypical device for isolating biotinylated oligonucleotides for use in mass spectrometric analysis. It consists of monomeric avidin-coated microbeads trapped in a pipette tip and has been used for genotyping single nucleotide polymorphisms (SNPs) with the previously developed solid phase capture-single base extension (SPC-SBE) method. The device reduces processing time for genotyping by SPC-SBE and allows direct spotting of sample for rapid analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In addition, it allows simultaneous processing of multiple samples and can be reused after regeneration of beads with no carryover effects. These results indicate that the microbead device is a low-cost tool that enhances sample cleanup prior to MS for SNP genotyping.
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Affiliation(s)
- Ashish Misra
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Castleberry CM, Chou CW, Limbach PA. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of oligonucleotides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2008; Chapter 10:Unit 10.1. [PMID: 18551426 DOI: 10.1002/0471142700.nc1001s33] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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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