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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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2
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Wang P, Shah GL, Landau H, Coulter ME, Walsh CA, Roider E, Kramer CS, Beuning PJ, Giese RW. Jettison-MS of Nucleic Acid Species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1641-1646. [PMID: 32551641 DOI: 10.1021/jasms.0c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
While MALDI-MS of intact genomic DNA is unheard of, actually many DNA adducts can be detected in this way under certain MALDI conditions: relatively high molar ratio of DNA nucleobases to matrix (0.01 to 0.3), hot matrix (CCA), and high laser fluence. This is because many DNA adducts create "bubbles" on dsDNA (disruption of base pairing), making it easier for these adducts as modified nucleobases to be jettisoned by the laser-derived energy of MALDI (jettison mass spectrometry or JeMS). The method also works for other nucleic acid species, namely nucleobases, nucleosides, nucleotides, and RNA. Examples of what we have detected in this way are as follows: methyladenine in E. coli DNA, 5-hydroxymethylcytosine in human brain DNA, melphalan-adenine in leukocyte DNA from patients on corresponding chemotherapy, wybutosine in tRNA, benzyl DNA adducts in E. coli cell culture treated with benzyl bromide, and various DNA adducts formed in test tube exposure experiments with calf thymus DNA. Noteworthy, in the chemotherapy study, principle component analysis of the data encourages the hypothesis that patient DNA undergoes much more damage than just melphalan adducts. Overall, our work leads to the preliminary generalization that about 5 fmol of a nucleobase deficient in base pairing, and present in a MALDI spot, will be detected by JeMS (on the equipment that we used), irrespective of the type of nucleic acid species which houses it, as long as the nucleobase is relatively basic such as A, C, or G.
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Affiliation(s)
- Poguang Wang
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115, United States
| | - Gunjan L Shah
- Department of Medicine, Weill Cornell Medical College, New York, New York 10021, United States
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Heather Landau
- Department of Medicine, Adult Bone Marrow Transplant Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Michael E Coulter
- Center for Integrative Neuroscience, UCSF, San Francisco, California 94158, United States
- Division of Genetics and Genomics, Boston Children's Hospital, Center for Life Sciences, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Center for Life Sciences, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Elisabeth Roider
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Caitlin S Kramer
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Roger W Giese
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115, United States
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Mauger F, Tabet JC, Gut IG. A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1433-1443. [PMID: 24861592 DOI: 10.1002/rcm.6913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/01/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE High-energy collision-induced dissociation (CID) spectra of isomeric RNA/DNA chimeras using matrix-assisted laser desorption/ionization time-of-flight LIFT mass spectrometry (MALDI-LIFT-TOF/TOF) can potentially be applied for an exhaustive fragment characterization in a nucleic acid sequencing scheme. These chimeras contain deoxynucleotides and at the 3'-end a ribonucleotide with a 3'-phosphate group. METHODS Deprotonated RNA/DNA chimeras of 4-, 5-, 7- and 10-mers are analyzed by CID. This enhances consecutive dissociations from both the precursor and prompt product anions generated by MALDI and metastable fragmentations prior to entering the LIFT cell. RESULTS Gas-phase fragmentations of 4- and 5-mers produced many fragment ions, from base release prior to consecutive cleavage of the nucleotide phosphate bond linkage phosphate. The unusual a4(-) product ion is a specific and diagnostic dissociation of the 4-mer if the ribonucleotide contains cytosine. As the size of RNA/DNA chimeras increase, several abundant product ions are generated mainly from zwitterionic forms (deprotonated phosphate ester and protonated base sites): [(M-H)-BiH](-), [ai-BiH](-), wj(-), [wj, (ai-BiH)](-) (if Bi ≠ T) as internal product ion, and more rarely [wj-BiH](-). The absence of the majority of the [ai-BiH](-) series although the wj (-) series suggested that the higher critical energy processes with a loose transition state are favored yielding the wj(-) series. A large number of abundant fragment ions are detected which enable each isomer to be sequenced. CONCLUSIONS This sequencing method is high-throughput, accurate and could be used to sequence isomers of up to 10-mers and also oligonucleotides of unknown sequence. However, RNA/DNA chimeras without thymine must be sufficiently concentrated to reach desorption of deprotonated molecular species to be selected in LIFT to produce all fragment ions within measurable abundances.
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Affiliation(s)
- Florence Mauger
- CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex, France
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Gao L, Zhang L, Cho BP, Chiarelli MP. Sequence verification of oligonucleotides containing multiple arylamine modifications by enzymatic digestion and liquid chromatography mass spectrometry (LC/MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1147-1155. [PMID: 18524623 PMCID: PMC2819294 DOI: 10.1016/j.jasms.2008.04.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 04/25/2008] [Accepted: 04/25/2008] [Indexed: 05/26/2023]
Abstract
An analytical method for the structure differentiation of arylamine modified oligonucleotides (ODNs) using on-line LC/MS analysis of raw exonuclease digests is described. Six different dodeca ODNs derived from the reaction of N-acetoxy-N-(trifluoroacetyl)-2-aminofluorene with the dodeca oligonucleotide 5'-CTCGGCGCCATC-3' are isolated and sequenced with this LC/MS method using 3'- and 5'-exonucleases. When the three products modified by a single aminofluorene (AF) are subjected to 3'-exonuclease digestion, the exonuclease will cleave a modified nucleotide but when di-AF modified ODNs are analyzed the 3'-exonuclease ceases to cleave nucleotides when the first modification is exposed at the 3'-terminus. Small abundances of ODN fragments formed by the cleavage of an AF-modified nucleotide were observed when two of the three di-AF modified ODNs were subjected to 5'-exonuclease digestion. The results of the 5'-exonuclease studies of the three di-AF modified ODNs suggest that as the number of unmodified bases between two modifications in an ODN sequence increases, the easier it becomes to sequence beyond the modification closest to the 5'-terminus. The results of this study indicate that the LC/MS method described here would be useful in sequencing ODNs modified by multiple arylamines to be used as templates for site-specific mutagenesis studies.
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Affiliation(s)
- Lan Gao
- Department of Chemistry, Loyola University, 1068 W. Sheridan Road, Chicago, IL 60626, USA
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6
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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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7
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Papanastasiou D, Belgacem O, Sudakov M, Raptakis E. Ion thermalization using pressure transients in a quadrupole ion trap coupled to a vacuum matrix-assisted laser desorption ionization source and a reflectron time-of-flight mass analyzer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2008; 79:055103. [PMID: 18513088 DOI: 10.1063/1.2919881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Efficient trapping and detection of intact peptide ions is demonstrated in a quadrupole ion trap (QIT) coupled to an external vacuum matrix-assisted laser desorption ionization (MALDI) source. Deactivation of metastable ions generated by MALDI is achieved in a pressure transient environment inside the QIT established by pulsing gas to access the higher pressures required for fast thermalization, without affecting vacuum conditions in the ion source and time-of-flight (TOF) mass analyzer. Pressure transients are experimentally determined and a threshold of approximately 10 mTorr is identified where internally excited ions, which commonly observed to dissociate upon injection in a QIT, are stabilized. Fragment-free spectra are presented for a set of peptides by using 2,5-dihydroxybenzoic acid (DHB) as a matrix, and significantly reduced fragmentation is observed by using a-cyano-4-hydroxycinnamic acid (CHCA). Intact peptide spectra of a protein tryptic digest are also recorded with CHCA. The process of translational cooling for externally injected ions in a dynamic pressure environment is visualized by using ion trajectory simulations that employ hard sphere collisions. Statistical theory of dynamic equilibrium of ions stored in rf fields is applied to our QIT to characterize a translationally thermalized ion cloud, to explain observed ejection efficiency into the TOF mass analyzer, and to further discuss collisional deactivation of metastable ions.
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Affiliation(s)
- D Papanastasiou
- Kratos Analytical, Shimadzu Biotech, Manchester M17 1GP, United Kingdom.
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van Kampen JJA, Burgers PC, de Groot R, Osterhaus ADME, Reedijk ML, Verschuren EJ, Gruters RA, Luider TM. Quantitative Analysis of HIV-1 Protease Inhibitors in Cell Lysates Using MALDI-FTICR Mass Spectrometry. Anal Chem 2008; 80:3751-6. [DOI: 10.1021/ac702072c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeroen J. A. van Kampen
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
| | - Peter C. Burgers
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
| | - Ronald de Groot
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
| | - Mariska L. Reedijk
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
| | - Esther J. Verschuren
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
| | - Rob A. Gruters
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
| | - Theo M. Luider
- Department of Neurology, Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics and Department of Virology, Erasmus MC, Rotterdam, The Netherlands, Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia, Rotterdam, The Netherlands, and Department of Pediatrics, UMC St. Radboud, Nijmegen, The Netherlands
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Hofstadler SA, Sannes-Lowery KA, Hannis JC. Analysis of nucleic acids by FTICR MS. MASS SPECTROMETRY REVIEWS 2005; 24:265-285. [PMID: 15389854 DOI: 10.1002/mas.20016] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fourier transform ion cyclotron resonance (FTICR) mass spectrometry represents a unique platform with which to study nucleic acids and non-covalent complexes containing nucleic acids moieties. In particular, systems in which very high mass measurement accuracy is required, very complex mixtures are to be analyzed, or very limited amounts of sample are available may be uniquely suited to interrogation by FTICR mass spectrometry. Although the FTICR platform is now broadly deployed as an integral component of many high-end proteomics-based research efforts, momentum is still building for the application of the platform towards nucleic acid-based analyses. In this work, we review fundamental aspects of nucleic acid analysis by FTICR, focusing primarily on the analysis of DNA oligonucleotides but also describing applications related to the characterization of RNA constructs. The goal of this review article is to give the reader a sense of the breadth and scope of the status quo of FTICR analysis of nucleic acids and to summarize a few recently published reports in which researchers have exploited the performance attributes of FTICR to characterize nucleic acids in support of basic and applied research disciplines including genotyping, drug discovery, and forensic analyses.
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Affiliation(s)
- Steven A Hofstadler
- Ibis Therapeutics, A Division of Isis Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, California 92008, USA.
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Kellersberger KA, Yu ET, Merenbloom SI, Fabris D. Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:199-207. [PMID: 15694770 DOI: 10.1016/j.jasms.2004.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2004] [Revised: 10/26/2004] [Accepted: 10/28/2004] [Indexed: 05/24/2023]
Abstract
Atmospheric pressure (AP) MALDI has been combined with Fourier transform mass spectrometry (FTMS) to obtain the unambiguous characterization of RNA samples modified by solvent accessibility reagents used in structural studies of RNA and protein-RNA complexes. The formation of cation adducts typical of MS analysis of nucleic acids was effectively reduced by extensive washing of the anionic analytes retained onto the probe surface by strong interactions with a cationic layer of poly(diallyldimethylammonium chloride) (PADMAC). This rapid desalting procedure allowed for the detection of DNA and RNA samples in high femtomole quantities distributed over a 4 x 4 mm sample well. AP MALDI-FTMS was shown to provide high-resolution spectra for analytes as large as approximately 6.4 kDa with little or no evidence of metastable decomposition. The absence of significant metastable decay observed for precursor ions selected for tandem experiments offered a further measure of the low energy content typical of ions generated by AP MALDI. This feature proved to be very beneficial in the characterization of chemically modified RNA samples, which become particularly prone to base losses upon alkylation. The high resolution offered by FTMS enabled the application of a data-reduction algorithm capable of rejecting any signal devoid of plausible isotopic distribution, thus facilitating the analysis of complex analyte mixtures produced by nuclease treatment of RNA substrates. Proper selection of nucleases and digestion conditions can ensure the production of hydrolytic fragments of manageable size, which could extend the range of applicability of this bottom-up strategy to the structural investigation of very large RNA and protein-RNA complexes.
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Wang Y, Zhang Q, Wang Y. Tandem mass spectrometry for the determination of the sites of DNA interstrand cross-link. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1565-1571. [PMID: 15519223 DOI: 10.1016/j.jasms.2004.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Revised: 07/16/2004] [Accepted: 07/16/2004] [Indexed: 05/24/2023]
Abstract
Formation of DNA interstrand cross-link is implicated in the mechanism of anticancer activity of some drugs. Here we examined the fragmentation of deprotonated ions of double-stranded oligodeoxynucleotides (ODNs) that are covalently held together with either a mitomycin C or a 4,5',8-trimethylpsoralen. Our results showed that, upon collisional activation, the covalently-bound duplex ODNs cleaved to give a series of wn and [an-base] ions; the sites of interstrand cross-linking could be determined from the mass shifts of some product ions. In addition, compared with the product-ion spectra acquired on an ion trap, those obtained from sustained off-resonance irradiation-collisionally activated dissociation (SORI-CAD) on a Fourier transform mass spectrometer offered high mass-resolving power, which facilitated unambiguous assignment of product ions and made it an effective method for locating the cross-linking sites.
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Affiliation(s)
- Yuesong Wang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521-0403, USA
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12
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Brown K, Harvey CA, Turteltaub KW, Shields SJ. Structural characterization of carcinogen-modified oligodeoxynucleotide adducts using matrix-assisted laser desorption/ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:68-79. [PMID: 12526008 DOI: 10.1002/jms.401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aim of this study was to determine the chemical structure of in vitro 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)-modified oligodeoxynucleotides (ODNs) by exonuclease digestion and matrix-assisted laser desorption/ionization mass spectrometry. A single-stranded 11-mer ODN, 5'-d(CCATCGCTACC), was reacted with N-acetoxy-PhIP, resulting in the formation of one major and eight minor PhIP-ODN adducts. A 10 min treatment of the major and one minor PhIP-ODN adduct with a 3'-exonuclease, bovine intestinal mucosa phosphodiesterase (BIMP), and a 5'-exonuclease, bovine spleen phosphodiesterase, results in inhibition of the primary exonuclease activity at deoxyguanosine (dG) producing 5'-d(CCATCG(PhIP)) and 5'-d(G(PhIP)CTACC) product ions, respectively. Post-source decay (PSD) of these enzymatic end products identifies dG as the sole modification site in two 11-mer ODN-PhIP adducts. PSD of the minor PhIP-ODN adduct digestion end product, 5'-d(CCATCG(PhIP)), also reveals that the PhIP adducted guanine moiety is in an oxidized form. Prolonged treatment of the PhIP-ODN adducts at 37 degrees C with BIMP induces a non-specific, or endonuclease, enzymatic activity culminating in the formation of deoxyguanosine 5'-monophosphate-PhIP (5'-dGMP-PhIP). The PSD fragmentation pattern of the 5'-dGMP-PhIP [M + H](+) ion of the major adduct confirms PhIP binds to the C-8 position of dG. For the minor adduct, PSD results suggest that PhIP binds to the C-8 position of an oxidized guanine, supporting the hypothesis that this adduct arises from oxidative degradation, resulting in a spirobisguanidino structure.
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Affiliation(s)
- Karen Brown
- Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, P.O. Box 808, California 94531, USA
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Frankevich V, Zhang J, Dashtiev M, Zenobi R. Production and fragmentation of multiply charged ions in 'electron-free' matrix-assisted laser desorption/ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:2343-2348. [PMID: 14558136 DOI: 10.1002/rcm.1194] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An unusually large fraction of multiply charged ions is observed in 'electron-free' matrix-assisted laser desorption/ionization (MALDI). Here we investigate how the yield of multiply charged ions depends on experimental parameters in MALDI. It is found to increase if measures are taken to limit the number of electrons in the plume, for example, by using non-metallic MALDI targets or low laser pulse energies. The ionization energy of the matrix is another important parameter that affects the yield of multiply charged ions: matrices with high ionization energies lead to greater intensities of multiply charged ions. It is furthermore proposed that some of the fragment ions observed in MALDI are due to reactions of analyte with electrons in the plume. The possibility of electron capture dissociation of multiply charged ions produced by MALDI is shown.
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Affiliation(s)
- Vladimir Frankevich
- Department of Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, CH-8093 Zürich, Switzerland
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14
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Chan TWD, Fung YME, Li YCL. A study of fast and metastable dissociations of adenine-thymine binary-base oligonucleotides by using positive-ion MALDI-TOF mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:1052-1064. [PMID: 12322953 DOI: 10.1016/s1044-0305(02)00423-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the present study, fast and metastable dissociations of a number of adenine-thymine binary-base oligonucleotides under the conditions of UV matrix-assisted laser desorption/ionization mass spectrometry were investigated. 2-Aminobenzoic acid/ammonium fluoride (ABA/NH4F) matrix system was used. The spectra obtained under metastable and fast dissociation conditions exhibit distinctive dissociation products. From the post-source-decay analysis, all oligonucleotides underwent predominantly metastable dissociations at the 3' C-O linkages to form [a(n)-B]+ and w(n)+ complimentary ion series. Based on the present results, the so-called "[wn+80]+" ions were postulated to be the complimentary [Z(8-n)AH]+ ions rather than the expected phosphate rearrangement products. In addition, these oligonucleotides were found to generate fast dissociation products of b(n)+, d(N)+, w(N)+ and y(N)+ ions through backbone cleavages at 5' C-O, 5' O-P, 3' C-O and 3' P-O linkages, respectively. Product ion series formed under PSD conditions were not observed. The implications of this mutually exclusive occurrence of the two sets of fragment ions under fast and metastable conditions using ABA/NH4F matrix would be discussed. A model of ion activation under UV-MALDI conditions was also proposed.
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Affiliation(s)
- T W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, NT.
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15
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Zhang LK, Rempel D, Gross ML. Matrix-assisted laser desorption/ionization mass spectrometry for locating abasic sites and determining the rates of enzymatic hydrolysis of model oligodeoxynucleotides. Anal Chem 2001; 73:3263-73. [PMID: 11476224 DOI: 10.1021/ac010042l] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method using a combination of exonuclease enzymatic digestion and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was developed to locate model abasic sites in a series of model 21-base oligodeoxynucleotides in which a nucleobase was replaced by a hydrogen atom. The exonuclease digestion rate, with either snake venom phosphodiesterase (SVP) or bovine spleen phosphodiesterase (BSP), clearly slows as the digestion approaches the abasic sites and stops as it reaches it. An oligodeoxynucleotide containing an abasic site in which OH replaces the nucleobase shows similar results. MALDI mass spectra taken at appropriate times during the course of hydrolysis are the basis for rate measurements, and the kinetics also reveal the location of the abasic site. A mathematical treatment of the time-dependent MALDI data was implemented to obtain rate curves and rate constants for the enzymatic digestion of both modified and unmodified oligodeoxynucleotides.
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Affiliation(s)
- L K Zhang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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Christian NP, Reilly JP, Mokler VR, Wincott FE, Ellington AD. Elucidation of the initial step of oligonucleotide fragmentation in matrix-assisted laser desorption/ionization using modified nucleic acids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:744-753. [PMID: 11401165 DOI: 10.1016/s1044-0305(01)00228-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To probe the mechanism of gas-phase oligonucleotide ion fragmentation, modified oligonucleotides were studied using matrix-assisted laser desorption/ionization. The oligonucleotides were of the form 5'-TTTTXTTTTT, where X was a modified nucleotide. Modifications included substitution of hydroxy, methoxy, amino, and allyl groups at the 2'-position of the deoxyribose. The modified ribose contained adenine, guanine, cytosine, or uracil bases. For comparison, we studied oligomers where X was an unmodified adenosine, guanosine, cytidine, thymidine, or uridine deoxyribonucleotide. We found a very strong dependence of the matrix-to-analyte ratio on fragmentation for these oligomers. Analysis of these modifications suggests that the initial fragmentation step in MALDI-MS involves a two-step (E1) elimination of the base.
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Affiliation(s)
- N P Christian
- Department of Chemistry, Indiana University, Bloomington 47505-7102, USA
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17
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Gross J, Hillenkamp F, Wan KX, Gross ML. Metastable decay of negatively charged oligodeoxynucleotides analyzed with ultraviolet matrix-assisted laser desorption/ionization post-source decay and deuterium exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:180-192. [PMID: 11212003 DOI: 10.1016/s1044-0305(00)00209-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In an effort to understand the initiating step in metastable-ion decay of UV matrix-assisted laser desorption/ionization (MALDI)-produced ions, we conducted experiments in which we exchanged all active protons for deuterons of tetrameric and hexameric oligodeoxynucleotides. We wish to address the controversial proposal that in the negative-ion mode, as in the positive-ion mode, fragmentation is driven by nucleobase protonation. The results show unambiguously that proton transfer, leading to zwitterion formation, charges a nucleobase prior to its elimination. The zwitterion formation directs fragmentation of both positive and negative oligodeoxynucleotide ions. Poly-T-rich oligodeoxynucleotide tetramers show surprising differences in the negative compared to the positive-ion mode, as thymine is preferentially expelled, instead of a nucleobase with higher proton affinity. For the exceptional case of negatively charged poly-T-rich oligodeoxynucleotide tetramers generated by MALDI, we propose that zwitterion formation with positive charging of a nucleobase leads to base stabilization in the negative-ion mode through an interaction of the positive nucleobase with the excess negative charge. Moreover, backbone cleavages (accompanied by H rearrangement) of a phosophodiester bond give first-generation products that can be traced back to this tripolar complex bearing one positive and two negative charges, all of which may be interacting.
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Affiliation(s)
- J Gross
- Institute for Medical Physics and Biophysics, University of Muenster, Germany
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18
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O'Connor PB, Costello CE. A high pressure matrix-assisted laser desorption/ionization Fourier transform mass spectrometry ion source for thermal stabilization of labile biomolecules. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2001; 15:1862-8. [PMID: 11565105 DOI: 10.1002/rcm.447] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A high pressure matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) ion source was designed and tested. With this design, pressure is pulsed to an estimated 1-10 mbar in the region of the MALDI sample during desorption with the result of significantly decreased fragmentation compared to similar systems operating with pressures of <0.1 mbar. The thermal stabilization of vibrationally excited ions under these conditions is shown with small peptides desorbed from the "hot" matrix alpha-cyano-4-hydroxycinnamic acid, and with the highly labile oxidized beta-chain of insulin. Fragile gangliosides with several sialic acid residues are desorbed under high pressure and remain intact without the typical losses of sialic acid, and a protein standard, ubiquitin (8565.64 Da), is desorbed with minimal dehydration. Under high pressure collisional cooling conditions, non-covalent matrix adduction to the molecular ions becomes prominent, but with the trapped ions in an FT mass spectrometer, the ions can be mildly activated to detach the matrix adducts. The new source, additionally, generates significant levels of the multiply charged ions which are commonly seen in MALDI-TOFMS, but are rarely observed in MALDI-FTMS. This effect is more likely due to the elimination of a mass filtering effect in the previous FTMS ion source than to collisional cooling of the ions.
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Affiliation(s)
- P B O'Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 715 Albany St., R806, Boston, MA 02118, USA.
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19
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Wu H, Aboleneen H. Sequencing oligonucleotides with blocked termini using exonuclease digestion and electrospray mass spectrometry. Anal Biochem 2000; 287:126-35. [PMID: 11078592 DOI: 10.1006/abio.2000.4827] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A method for sequencing ODNs with both termini blocked using mass spectrometry (MS) is reported. The ladder sequencing method is based on our investigation and understanding of critical factors affecting snake venom phosphodiesterase (SVP) digestion of such ODNs. To produce sequence ladders suitable for MS analysis, digestion conditions such as SVPs from three snake species and pH values of digestion buffer were investigated. SVP of Crotalus duressus terrificus (SVP I) was found to be the most suitable for sequencing ODNs with both termini blocked. The pH value of 9.4, which is optimal for SVP digestion of unmodified ODNs, was found to be unsuitable for ladder sequencing ODNs with both termini blocked. Instead, digestion in a wide range of pH values (pH 5-8), including rarely used acidic conditions, was found to be necessary to obtain otherwise unobtainable sequence information. With digestion buffer of desired pH values, sequence ladders which are recorded as MWs of truncated ODNs from SVP digestion are obtained. Examples of sequencing ODNs up to 26 bases long with both termini blocked are demonstrated in this work.
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Affiliation(s)
- H Wu
- Abbott Laboratories, Diagnostics Division, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA.
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20
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O'Connor PB, Costello CE. Application of multishot acquisition in Fourier transform mass spectrometry. Anal Chem 2000; 72:5125-30. [PMID: 11055737 DOI: 10.1021/ac0005565] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new method of ion injection and trapping is discussed wherein ions are accumulated over several laser shots in the FT-ICR cell prior to detection. This allows accumulation of ion signal without accumulating noise so that the signal/noise ratio is much improved provided that the "space-charge" limit of the total number of ions in the cell is not exceeded. "In-cell" ion accumulation allows selected ion accumulation by simply sweeping unwanted ions out of the cell prior to subsequent ion trapping events and also allows shifted ion accumulations to correct for time-of-flight distortions in the ion abundance distributions.
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Affiliation(s)
- P B O'Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, Massachusetts 02118, USA.
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21
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Wang Y, Taylor JS, Gross ML. Differentiation of isomeric photomodified oligodeoxynucleotides by fragmentation of ions produced by matrix-assisted laser desorption ionization and electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1999; 10:329-338. [PMID: 10197353 DOI: 10.1016/s1044-0305(98)00158-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
UV irradiation of oligodeoxynucleotides at 254 nm generates several different types of DNA photoproducts, including cis-syn cyclobutane pyrimidine dimers, pyrimidine[6-4] pyrimidone photoproducts and their Dewar valence isomers, and thymine-adenine photoproducts (TA*). Studies of photoproducts in oligodeoxynucleotides require the development of suitable structure determination methods such as mass spectrometry. In an earlier study (Vollmer et al. Int. J. Mass Spectrom. Ion Processes 1997, 165/166, 487-496), we showed that fast atom bombardment and tandem sector mass spectrometry can be used to locate the site of photomodification and identify most of the photoproducts of d(TATTAT). One goal of the present research was to expand the method to the more sensitive electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) methods. A second goal was to test the generality of the methods by investigating not only the photoproducts of d(TATTAT) but also those of three other oligodeoxynucleotides, d(GTATTAT), d(GGCTATAA), and d(AATTAA). The photoproducts of these sequences were separated by HPLC and gave characteristic fragment ions in postsource decompositions of MALDI-produced ions and collisionally activated decompositions of ESI-produced ions.
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Affiliation(s)
- Y Wang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA.
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22
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Gross J, Leisner A, Hillenkamp F, Hahner S, Karas M, Schäfer J, Lützenkirchen F, Nordhoff E. Investigations of the metastable decay of DNA under ultraviolet matrix-assisted laser desorption/ionization conditions with post-source-decay analysis and hydrogen/deuterium exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1998; 9:866-878. [PMID: 9725011 DOI: 10.1016/s1044-0305(98)00058-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The fragmentation of positive ions of DNA under the conditions of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was investigated by post-source decay (PSD) analysis and hydrogen/deuterium (H/D) exchange. Spectra of five different synthetic 4mer oligonucleotides were recorded. As a main result the hypothesis was confirmed that for these ions all fragment ions result from processes, initiated by protonation/deuteration of a suitable base followed by a loss of this base as a neutral or ion and further backbone cleavages. The three bases adenine, guanine, and cytosine all exhibit comparable lability for fragmentation. The spectra show evidence for an interaction of the adenine base with the phosphate backbone. Signals of fragments containing TT- and CT-cycloadducts were observed in the spectra.
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Affiliation(s)
- J Gross
- Institut fuer Medizinische Physik und Biophysik, Universitaet Muenster, Germany
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23
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Wang Z, Wan KX, Ramanathan R, Taylor JS, Gross ML. Structure and fragmentation mechanisms of isomeric T-rich oligodeoxynucleotides: a comparison of four tandem mass spectrometric methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1998; 9:683-691. [PMID: 9879378 DOI: 10.1016/s1044-0305(98)00178-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding the product-ion spectra of T-rich tetradeoxynucleotides is a starting point in the development of a mass spectrometric scheme to determine the mutagenicity of individual types of DNA damage. We obtained product-ion spectra for electrospray-produced ions that were activated in the ion source (electrospray ionization-source collision-activated-dissociation) and by high-energy collisions in the MS/MS mode of a four-sector instrument. We also activated singly and doubly charged ions by low-energy collisions in an ion-trap mass spectrometer and investigated post source decompositions of matrix-assisted laser desorbed ions in a time-of-flight mass spectrometer. The various methods of extracting structural information give remarkably consistent results. The difference in the relative abundances of wn and dn ions of the singly charged oligonucleotides and the formation of [a3-B3] ions, where B3 is the base on the third position, are effective for identification and distinction of pairs of isomeric tetranucleotides. A sufficient number of tetramers and pentamers were studied to enable us to propose a charge-remote mechanism for the formation of site-specific [an-Bn] ion.
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Affiliation(s)
- Z Wang
- Department of Chemistry, Washington University, St. Louis, MO 63130-4899, USA
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24
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Abstract
Recent advances in the use of mass spectrometry for the determination of the molecular weight and sequencing of oligonucleotides are discussed. Matrix-assisted laser desorption (MALDI) and electrospray ionization (ESI) mass spectrometry have been shown to be especially important techniques for both molecular weight assignment and sequencing of oligonucleotides, and are the focus of this article which covers the literature through early 1996.
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Affiliation(s)
- P Miketova
- Department of Pharmacology and Toxicology, University of Arizona, College of Pharmacy, Tucson 85721, USA
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25
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Structure determination of isomeric hexadeoxynucleotide photoproducts by high-field NMR and fast atom bombardment/ tandem mass spectrometry. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0168-1176(97)00181-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Charge state effects in the decompositions of single-nucleobase oligonucleotide polyanions. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0168-1176(96)04473-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Mouradian S, Skogen JW, Dorman FD, Zarrin F, Kaufman SL, Smith LM. DNA analysis using an electrospray scanning mobility particle sizer. Anal Chem 1997; 69:919-25. [PMID: 9068276 DOI: 10.1021/ac960785k] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A scanning mobility particle sizer (SMPS) allows size separation of gas phase particles according to their electrophoretic mobilities. The addition of an electrospray source (ES) recently allowed extension of SMPS analysis to the macromolecular range. We demonstrate here the application of ES-SMPS to nucleic acids analysis. Single- and double-stranded DNA molecules ranging from 6.1 kDa (single-stranded DNA 20 nucleotides in length) to 300 kDa (500 base-pair double-stranded DNA) were separated and detected by ES-SMPS at the picomole to femtomole levels. The measured electrophoretic mobility diameters were found to correlate with the analytes' molecular weights, while the peak areas could yield quantitative information. No fragmentation of DNA was observed under the conditions employed. Different apparent densities were observed for single-stranded and double-stranded DNAs, showing a different behavior for each type of biomolecule. The total analysis time was about 3 min/spectrum. Further optimization of ES-SMPS is expected to make it a fast and sensitive technique for biopolymer characterization.
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Affiliation(s)
- S Mouradian
- Department of Chemistry, University of Wisconsin, Madison 53706-1396, USA
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28
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Li Y, Tang K, Little DP, Köster H, Hunter RL, McIver RT. High-resolution MALDI Fourier transform mass spectrometry of oligonucleotides. Anal Chem 1996; 68:2090-6. [PMID: 9027224 DOI: 10.1021/ac9601268] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The matrix-assisted laser desorption/ionization (MALDI) method has been used with an external ion source Fourier transform mass spectrometer (FIMS) to analyze single-stranded, mixed-base oligomers of DNA. It is demonstrated that ultrahigh mass resolution (830 000 fwhm) can be achieved for small oligomers, and high resolution (136 000 fwhm) can be achieved for a 25-mer at m/z 7634. MALDI-FTMS can clearly separate the molecular ion peaks from analyte-matrix adduct peaks and alkali metal-containing species that result from replacement of hydrogen ions with sodium or potassium ions at multiple sites along the phosphate backbone. Previous MALDI-FTMS studies of oligonucleotides had two limitations: (1) low sensitivity due to difficulty in trapping the high kinetic energy ions made by the laser and (2) fragmentation of the ions due to the long delay (tens to hundreds of milliseconds) between their formation and detection. Both of these problems are alleviated in the present study. With the external ion source FTMS instrument, ions made by MALDI are injected at low energy into the analyzer cell by a rf-only quadrupole ion guide, captured by gating the voltage on the trapping plates, and cooled by a 0.5-s pulse of argon gas. Under these conditions, fragmentation is minimized, and DNA ions can be trapped in the FTMS analyzer cell for greater than 50 s. Sensitivity is also improved, as demonstrated by detection of 1 pmol of a single-stranded, mixed-base 20-mer of DNA, with a signal-to-noise ratio greater than 20:1.
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Affiliation(s)
- Y Li
- IonSpec Corporation, Irvine, California 92714, USA
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29
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Affiliation(s)
- A L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA
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30
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Limbach PA. Indirect mass spectrometric methods for characterizing and sequencing oligonucleotides. MASS SPECTROMETRY REVIEWS 1996; 15:297-336. [PMID: 27082835 DOI: 10.1002/(sici)1098-2787(1996)15:5<297::aid-mas2>3.0.co;2-d] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/1996] [Revised: 01/09/1997] [Accepted: 01/09/1997] [Indexed: 06/05/2023]
Abstract
The use of mass spectrometry for the characterization and sequence determination of oligonucleotides is reviewed. This review focuses primarily on the use of mass spectrometry to analyze sequence-specific fragments of oligonucleotides that are generated via solution-phase chemical reactions. The majority of these "indirect" sequencing methods are a result of recent advances in electrospray ionization and matrix-assisted laser desorption/ionization for the generation of intact gas-phase ions from oligonucleotides. Descriptions of the current indirect sequencing protocols will be presented as well as a comparison of the applicability of these procedures for analyzing "real world" samples. The applicability of indirect mass spectrometric sequencing to antisense oligonucleotides will be discussed in detail. © 1997 John Wiley & Sons, Inc.
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Affiliation(s)
- P A Limbach
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803
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31
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Dienes T, Pastor SJ, Schürch S, Scott JR, Yao J, Cui S, Wilkins CL. Fourier transform mass spectrometry-advancing years (1992-mid. 1996). MASS SPECTROMETRY REVIEWS 1996; 15:163-211. [PMID: 27082513 DOI: 10.1002/(sici)1098-2787(1996)15:3<163::aid-mas2>3.0.co;2-g] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/1996] [Revised: 10/18/1996] [Accepted: 10/22/1996] [Indexed: 06/05/2023]
Abstract
This article is one of a series of Fourier transform mass spectrometry (FTMS) reviews that has appeared in this journal at ca. 3-4 year intervals. A comprehensive review of the recent theoretical developments, instrumental developments, electrospray ionization (ESI), and MALDI is given. Ion dissociation techniques are also discussed because of their contributions to gaining insight into chemical structure. Special sections have been devoted to discussing the emerging fields of surface analysis, polymer analysis, Buckminsterfullerenes (buckyballs), and hydrogen/deuterium exchange studies. This review, although not all-inclusive, is intended to be a starting point for those wishing to learn more about the current status of FTMS, and also as a representative cross-section of the literature for those familiar with the technique. © 1997 John Wiley & Sons, Inc.
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Affiliation(s)
- T Dienes
- Department of Chemistry, University of California-Riverside, Riverside, California 92521
| | - S J Pastor
- Department of Chemistry, University of California-Riverside, Riverside, California 92521
| | - S Schürch
- Department of Chemistry, University of California-Riverside, Riverside, California 92521
| | - J R Scott
- Department of Chemistry, University of California-Riverside, Riverside, California 92521
| | - J Yao
- Department of Chemistry, University of California-Riverside, Riverside, California 92521
| | - S Cui
- Department of Chemistry, University of California-Riverside, Riverside, California 92521
| | - C L Wilkins
- Department of Chemistry, University of California-Riverside, Riverside, California 92521
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32
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Nordhoff E, Kirpekar F, Roepstorff P. Mass spectrometry of nucleic acids. MASS SPECTROMETRY REVIEWS 1996; 15:67-138. [PMID: 27082318 DOI: 10.1002/(sici)1098-2787(1996)15:2<67::aid-mas1>3.0.co;2-8] [Citation(s) in RCA: 222] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/1996] [Revised: 10/30/1996] [Accepted: 11/01/1996] [Indexed: 06/05/2023]
Abstract
The present article is a survey of ESI and MALDI mass spectrometric analysis of nucleic acid oligomers and polymers. In order to limit the extent of the review, mass spectrometry of mononucleotides is generally not considered, except where such data are important for an understanding of the analysis of larger nucleic acids. The first part of the review is a condensed description of the structure and the acid-base properties of nucleic acids. The remaining part is divided into three main sections, dealing with the practical aspects of the two ionization techniques, fragmentation, and applications, respectively. The first section includes an extensive discussion of experimental parameters and problems, which are important for the analysis of different types of nucleic acid samples, including noncovalent complexes and mixtures. At the end of this section, as well as the following one, a comparison between MALDI and ESI as ionization techniques for nucleic acid is given. In addition to a detailed discussion of ion fragmentation, the fragmentation section includes an overview of the direct mass spectrometric sequencing of nucleic acids performed with either technique. The fragmentation reactions occurring upon MALDI and ESI are compared. The last section describes the life science applications of ESI-MS and MALDI-MS of nucleic acids; an account of experiments demonstrating the potential of a method, and of the bona fide solving of problems by ESI and MALDI is given. © 1997 John Wiley & Sons, Inc.
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Affiliation(s)
- E Nordhoff
- Department of Molecular Biology, University of Odense, Campusvej 55, 5230 Odense M, Denmark
| | - F Kirpekar
- Department of Molecular Biology, University of Odense, Campusvej 55, 5230 Odense M, Denmark
| | - P Roepstorff
- Department of Molecular Biology, University of Odense, Campusvej 55, 5230 Odense M, Denmark
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33
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Mouradian S, Nelson CM, Smith LM. A Self-Assembled Matrix Monolayer for UV-MALDI Mass Spectrometry. J Am Chem Soc 1996. [DOI: 10.1021/ja953585j] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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