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Brundridge NM, Dickerhoff J, Yang D, McLuckey SA. Gas-Phase Fragmentation as a Probe of G-Quadruplex Formation. Anal Chem 2023; 95:15057-15067. [PMID: 37774231 PMCID: PMC11022955 DOI: 10.1021/acs.analchem.3c03143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
G-quadruplex (G4) DNA is found in oncogene promoters and human telomeres and is an attractive anticancer target. Stable G4 structures form in guanine-rich sequences in the presence of metal cations and can stabilize further with specific ligand adduction. To explore the preservation and stability of this secondary structure with mass spectrometry, gas-phase collision-induced dissociation kinetics of G4-like and non-G4-like ion structures were determined in a linear quadrupole ion trap. This study focused on a sequence from the promoter of the MYC oncogene, MycG4, and a mutant non-G4-forming sequence, MycNonG4. At relatively high ion activation energies, the backbone fragmentation patterns of the MycG4 and MycNonG4 are similar, while potassium ion-stabilized G4-folded [MycG4 + 2K-7H]5- and counterpart [MycG4-5H]5- ions are essentially indistinguishable, indicating that high-energy fragmentation is not sensitive to the G4 structure. At low energies, the backbone fragmentation patterns of MycG4 and MycNonG4 are significantly different. For MycG4, fragmentation over time differed significantly between the potassium-bound and free structures, reflecting the preservation of the G4 structure in the gas phase. Kinetic measurements revealed the [MycG4 + 2K-7H]5- ions to fragment two to three times more slowly than the [MycG4-5H]5-. Results for the control MycNonG4 indicated that the phenomena noted for [MycG4 + 2K-7H]5- ions are specific to G4-folding. Therefore, our data show that gentle activation conditions can lead to fragmentation behavior that is sensitive to G-quadruplex structure, revealing differences in kinetic stabilities of isomeric structures as well as the regions of the sequence that are directly involved in forming these structures.
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Affiliation(s)
- Nicole M Brundridge
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Danzhou Yang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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2
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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3
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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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4
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Li W, Mjekiqi E, Douma W, Wang X, Kavatsyuk O, Hoekstra R, Poully J, Schlathölter T. Hole Migration in Telomere-Based Oligonucleotide Anions and G-Quadruplexes. Chemistry 2019; 25:16114-16119. [PMID: 31614016 PMCID: PMC6972685 DOI: 10.1002/chem.201904105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/11/2019] [Indexed: 01/24/2023]
Abstract
Vacuum ultraviolet photoionization of a gas-phase oligonucleotide anion leads to the formation of a valence hole. This hole migrates towards an energetically favorable site where it can weaken bonds and ultimately lead to bond cleavage. We have studied Vacuum UV photoionization of deprotonated oligonucleotides containing the human telomere sequence dTTAGGG and G-quadruplex structures consisting of four dTGGGGT single strands, stabilized by NH4 + counter ions. The oligonucleotide and G-quadruplex anions were confined in a radiofrequency ion trap, interfaced with a synchrotron beamline and the photofragmentation was studied using time-of-flight mass spectrometry. Oligonucleotide 12-mers containing the 5'-TTAGGG sequence were found to predominantly break in the GGG region, whereas no selective bond cleavage region was observed for the reversed 5'-GGGATT sequence. For G-quadruplex structures, fragmentation was quenched and mostly non-dissociative single and double electron removal was observed.
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Affiliation(s)
- Wen Li
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Edita Mjekiqi
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Wessel Douma
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Xin Wang
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Oksana Kavatsyuk
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
- University College GroningenUniversity of GroningenHoendiepskade 23/249718 BGGroningenThe Netherlands
| | - Ronnie Hoekstra
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jean‐Christophe Poully
- CIMAP laboratory UMR 6252Université de Caen Normandie/CEA/CNRS/ENSICAENBd Becquerel14070CAEN Cedex 5France
| | - Thomas Schlathölter
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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5
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Ickert S, Beck S, Linscheid MW, Riedel J. VUV Photodissociation Induced by a Deuterium Lamp in an Ion Trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2114-2122. [PMID: 31429053 DOI: 10.1007/s13361-019-02282-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 05/16/2023]
Abstract
Tandem mass spectrometry represents an important analytical tool to unravel molecular structures and to study the gas-phase behavior of organic molecules. Besides commonly used methods like collision-induced dissociation and electron capture or transfer dissociation, new ultraviolet light-based techniques have the potential to synergistically add to the activation methods. Here, we present a new simple, yet robust, experimental design for polychromatic activation of trapped ions using the 115-160 nm output of a commercially available deuterium lamp. The resulting continuous dissociative excitation with photons of a wide energy range from 7.7 to 10.8 eV is studied for a comprehensive set of analyte classes in both positive and negative ion modes. While being simple, affordable, compact, and of low maintenance, the new setup initiates fragmentation of most precursor ions via their known dissociation pathways. Additionally, some new fragmentation patterns were discovered. Especially, electron loss and electron capture reactions with subsequent fragmentations were observed. For oligonucleotides, peptides, carbohydrates, and organic dyes, in comparison to collision-induced dissociation, a significantly wider fragment distribution was obtained, resulting in an information increase. Since the individual photons carry enough energy to post-ionize the nascent fragments, a permanent vacuum ultraviolet light exposure inside the ion trap potentially goes along with a general increase in detection capability.
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Affiliation(s)
- Stefanie Ickert
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
- Bundesanstalt für Materialforschung und -prüfung, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Sebastian Beck
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Michael W Linscheid
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Jens Riedel
- Bundesanstalt für Materialforschung und -prüfung, Richard-Willstätter-Str. 11, 12489, Berlin, Germany.
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6
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Ickert S, Schwaar T, Springer A, Grabarics M, Riedel J, Beck S, Pagel K, Linscheid MW. Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:402-411. [PMID: 30771235 DOI: 10.1002/jms.4344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences-bearing mismatch positions and abasic sites of complementary DNA 15-mers-were investigated to unravel general trends in their stability in the gas phase. Single-stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.
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Affiliation(s)
- Stefanie Ickert
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Timm Schwaar
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Andreas Springer
- Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin, Germany
| | - Márkó Grabarics
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Jens Riedel
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Sebastian Beck
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Kevin Pagel
- Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin, Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
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7
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Daly S, Porrini M, Rosu F, Gabelica V. Electronic spectroscopy of isolated DNA polyanions. Faraday Discuss 2019; 217:361-382. [DOI: 10.1039/c8fd00207j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We address whether action spectroscopy could be used to investigate structural changes in gas-phase biomolecule (e.g. nucleic acid) ions, owing to changes in the environments of their chromophores, while taking advantage of the additional spectrometric separation of complex mixtures.
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Affiliation(s)
- Steven Daly
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
| | - Massimiliano Porrini
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie
- Université de Bordeaux
- CNRS & Inserm (IECB, UMS3033, US001)
- 33607 Pessac
- France
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle
- Université de Bordeaux
- Inserm & CNRS (ARNA, U1212, UMR5320)
- IECB
- 33607 Pessac
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8
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Benigni P, Sandoval K, Thompson CJ, Ridgeway ME, Park MA, Gardinali P, Fernandez-Lima F. Analysis of Photoirradiated Water Accommodated Fractions of Crude Oils Using Tandem TIMS and FT-ICR MS. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5978-5988. [PMID: 28457132 PMCID: PMC5661887 DOI: 10.1021/acs.est.7b00508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
For the first time, trapped ion mobility spectrometry (TIMS) in tandem with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is applied to the analysis of the low energy water accommodated fraction (WAF) of a crude oil as a function of the exposure to light. The TIMS-FT-ICR MS analysis provided, in addition to the heteroatom series identification, new insights into the WAF isomeric complexity (e.g., [m/z; chemical formula; collision cross section] data sets) for a better evaluation of the degree of chemical and structural photoinduced transformations. Inspection of the [m/z; chemical formula; collision cross section] data sets shows that the WAF composition changes as a function of the exposure to light in the first 115 h by initial photosolubilization of HC components and their photo-oxidation up to O4-5 of mainly high double bond equivalence species (DBE > 9). The addition of high resolution TIMS (resolving power of 90-220) to ultrahigh resolution FT-ICR MS (resolving power over 400k) permitted the identification of a larger number of molecular components in a single analysis (e.g., over 47k using TIMS-MS compared to 12k by MS alone), with instances of over 6-fold increase in the number of molecular features per nominal mass due to the WAF isomeric complexity. This work represents a stepping stone toward a better understanding of the WAF components and highlights the need for better experimental and theoretical approaches to characterize the WAF structural diversity.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Kathia Sandoval
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Piero Gardinali
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Southeast Environmental Research Center, Florida International University, Miami, Florida 33199, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199
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9
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Benigni P, Fernandez-Lima F. Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry Coupled to FT-ICR MS: Fundamentals and Applications. Anal Chem 2016; 88:7404-12. [DOI: 10.1021/acs.analchem.6b01946] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry and ‡Biomolecular Sciences
Institute, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry and ‡Biomolecular Sciences
Institute, Florida International University, Miami, Florida 33199, United States
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10
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Doussineau T, Paletto P, Dugourd P, Antoine R. Multiphoton dissociation of electrosprayed megadalton-sized DNA ions in a charge-detection mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:7-13. [PMID: 25348472 DOI: 10.1007/s13361-014-1011-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/17/2014] [Accepted: 09/20/2014] [Indexed: 06/04/2023]
Abstract
Charge detection mass spectrometry in combination with a linear electrostatic ion trap coupled to a continuous wavelength infrared CO2 laser has been used to study the multiphoton dissociation of DNA macromolecular ions. Samples, with masses ranging from 2.23 to 31.5 MDa, include single strand circular M13mp18, double strand circular M13mp18, and double strand linear LambdaPhage DNA fragments. Their activation energies for unimolecular dissociation were determined. Activation energy values slightly increase as a function of the molecular weight. The most important result is the difference between the fragmentations observed for hybridized double-strands and dimers of single strands.
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Affiliation(s)
- Tristan Doussineau
- Université Claude Bernard Lyon1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
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11
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Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
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12
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Weber JM, Marcum J, Nielsen SB. UV Photophysics of DNA and RNA Nucleotides In Vacuo: Dissociation Channels, Time Scales, and Electronic Spectra. PHOTOPHYSICS OF IONIC BIOCHROMOPHORES 2013. [DOI: 10.1007/978-3-642-40190-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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13
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Doussineau T, Antoine R, Santacreu M, Dugourd P. Pushing the Limit of Infrared Multiphoton Dissociation to Megadalton-Size DNA Ions. J Phys Chem Lett 2012; 3:2141-2145. [PMID: 26295761 DOI: 10.1021/jz300844e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report the use of infrared multiphoton dissociation (IRMPD) for the determination of relative activation energies for unimolecular dissociation of megadalton DNA ions. Single ions with masses in the megadalton range were stored in an electrostatic ion trap for a few tens of milliseconds and the image current generated by the roundtrips of ions in the trap was recorded. While being trapped, single ions were irradiated by a CO2 laser and fragmented, owing to multiphoton IR activation. The analysis of the single-ion image current during the heating period allows us to measure changes in the charge of the trapped ion. We estimated the activation energy associated with the dissociation of megadalton-size DNA ions in the frame of an Arrhenius-like model by analyzing a large set of individual ions in order to construct a frequency histogram of the dissociation rates for a collection of ions.
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Affiliation(s)
- Tristan Doussineau
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Rodolphe Antoine
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Marion Santacreu
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
| | - Philippe Dugourd
- Université de Lyon, CNRS, UMR5579, LASIM, Université Lyon 1, Villeurbanne, F-69622 Lyon, France
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14
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Vonderach M, Ehrler OT, Matheis K, Weis P, Kappes MM. Isomer-selected photoelectron spectroscopy of isolated DNA oligonucleotides: phosphate and nucleobase deprotonation at high negative charge states. J Am Chem Soc 2012; 134:7830-41. [PMID: 22524691 DOI: 10.1021/ja300619j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Fractionation according to ion mobility and mass-to-charge ratio has been used to select individual isomers of deprotonated DNA oligonucleotide multianions for subsequent isomer-resolved photoelectron spectroscopy (PES) in the gas phase. Isomer-resolved PE spectra have been recorded for tetranucleotides, pentanucleotides, and hexanucleotides. These were studied primarily in their highest accessible negative charge states (3-, 4-, and 5-, respectively), as provided by electrospraying from room temperature solutions. In particular, the PE spectra obtained for pentanucleotide tetraanions show evidence for two coexisting classes of gas-phase isomeric structures. We suggest that these two classes comprise: (i) species with excess electrons localized exclusively at deprotonated phosphate backbone sites and (ii) species with at least one deprotonated base (in addition to several deprotonated phosphates). By permuting the sequence of bases in various [A(5-x)T(x)](4-) and [GT(4)](4-) pentanucleotides, we have established that the second type of isomer is most likely to occur if the deprotonated base is located at the first or last position in the sequence. We have used a combination of molecular mechanics and semiempirical calculations together with a simple electrostatic model to explore the photodetachment mechanism underlying our photoelectron spectra. Comparison of predicted to measured photoelectron spectra suggests that a significant fraction of the detected electrons originates from the DNA bases (both deprotonated and neutral).
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Affiliation(s)
- Matthias Vonderach
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
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15
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Sun X, Lee JK. Stability of DNA Duplexes Containing Hypoxanthine (Inosine): Gas versus Solution Phase and Biological Implications. J Org Chem 2010; 75:1848-54. [DOI: 10.1021/jo9023683] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xuejun Sun
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
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16
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Barlow CK, Hodges BDM, Xia Y, O'Hair RAJ, McLuckey SA. Gas-phase ion/ion reactions of transition metal complex cations with multiply charged oligodeoxynucleotide anions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:281-293. [PMID: 18083525 DOI: 10.1016/j.jasms.2007.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Revised: 10/15/2007] [Accepted: 10/15/2007] [Indexed: 05/25/2023]
Abstract
Multiply deprotonated hexadeoxyadenylate anions, (A6-nH)(n-), where n = 3-5, have been subjected to reaction with a range of divalent transition-metal complex cations in the gas phase. The cations studied included the bis- and tris-1,10-phenanthroline complexes of CuII, FeII, and CoII, as well as the tris-1,10-phenanthroline complex of RuII. In addition, the hexadeoxyadenylate anions were subjected to reaction with the singly charged FeIII and CoIIIN,N'-ethylenebis(salicylideneiminato) complexes. The major competing reaction channels are electron-transfer from the oligodeoxynucleotide anion to the cation, the formation of a complex between the anion and cation, and the incorporation of the transition-metal into the oligodeoxynucleotide. The latter process proceeds via the anion/cation complex and involves displacement of the ligand(s) in the transition-metal complex by the oligodeoxynucleotide. Competition between the various reaction channels is governed by the identity of the transition-metal cation, the coordination environment of the metal complex, and the oligodeoxynucleotide charge state. In the case of the divalent metal phenanthroline complexes, competition between electron-transfer and metal ion incorporation is particularly sensitive to the coordination number of the reagent metal complexes. Both electron-transfer and metal ion incorporation occur to significant extents with the bis-phenanthroline ions, whereas the tris-phenanthroline ions react predominantly by metal ion incorporation. To our knowledge this work reports the first observations of the gas-phase incorporation of multivalent transition-metal cations into oligodeoxynucleotide anions and represents a means for the selective incorporation of transition-metal counter-ions into gaseous oligodeoxynucleotides.
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Abstract
With the development of electrospray and matrix-assisted laser desorption ionization, mass spectrometry (MS) evolved into a powerful tool in the field of biochemistry. Whereas MS is primarily analytical in nature, an increasing number of MS research groups employ the method to address fundamental biochemical questions. Probing the interaction of noncovalently bound molecules in the mass spectrometer is one of the most interesting MS-based experiments possible today, with the potential of making a significant contribution to the basic understanding of the structure and function of biochemical complexes. Here we review a number of current research efforts employing primarily MS techniques to investigate intermolecular interactions in biochemical systems. Examples chosen include the interaction of biomolecules with solvent molecules; interactions between nucleic-acid molecules, in particular, interactions in duplex and quadruplex structures; and interactions between proteins involved in neurodegenerative diseases. Finally we conclude by presenting a few examples of very large biomolecular assemblies in the mega-Dalton range analyzed by MS.
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Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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Delvolvé A, Tabet JC, Bregant S, Afonso C, Burlina F, Fournier F. Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:1498-508. [PMID: 17103389 DOI: 10.1002/jms.1124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.
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Affiliation(s)
- Alice Delvolvé
- University Pierre et Marie Curie, CNRS-UMR 7613, Synthèse, Structure et Fonction de Molécules Bioactives, FR 2769, Case Courrier 45, 4 place Jussieu, 75005 Paris, France
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19
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Daneshfar R, Klassen JS. Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1229-38. [PMID: 16782356 DOI: 10.1016/j.jasms.2006.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 05/05/2006] [Accepted: 05/05/2006] [Indexed: 05/10/2023]
Abstract
Arrhenius activation parameters (E(a), A) for the loss of neutral nucleobases from a series of T-rich, doubly and triply deprotonated 15- and 20-mer oligodeoxynucleotides (ODN) containing a single reactive base (X = A or C) with the sequence, XT14, XT19 and T19X, have been determined using the blackbody infrared radiative dissociation technique. The A-containing anions are significantly more reactive (> or =3000 times) than the C-containing ions over the temperature range investigated. Importantly, the Arrhenius parameters for the loss of AH exhibit a strong dependence on size of the ODN and, to some extent, the charge state; the Arrhenius parameters increase with size and charge (Ea = 29-39 kcal mol(-1), A = 10(15)-10(20) s(-1)). In contrast, the parameters for the loss of CH are much less sensitive to size (Ea = 35-39 kcal mol(-1), A = 10(14)-10(17) s(-1)). The results are consistent with a greater contribution from the internal solvation of the reactive base to the Arrhenius parameters for the loss of A, compared with C, from the 15- and 20-mers. To further probe differences in internal solvation of A and C, hydrogen/deuterium exchange was carried out on AT19(-3), T19A(-3), CT19(-3) and T19C(-3) using D2O as the exchange reagent. However, the H/D exchange results did not reveal any differences in internal solvation within the ODN anions. Arrhenius parameters for the dissociation of noncovalent complexes of T20(-3) and the neutral nucleobase AH or CH have also been determined. Differences in the parameters indicate differences in the nature of the intermolecular interactions. It is proposed that neutral A-T interactions (i.e., base-base), which originate in solution, dominate in the case of (T20 + AH)(-3), while charge solvation, involving CH and a deprotonated phosphate group, is present for (T20 + CH)(-3).
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Affiliation(s)
- Rambod Daneshfar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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20
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Boxford WE, Dessent CEH. Probing the intrinsic features and environmental stabilization of multiply charged anions. Phys Chem Chem Phys 2006; 8:5151-65. [PMID: 17203139 DOI: 10.1039/b609123g] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Multiply charged anions (MCAs) represent exotic, highly energetic species in the gas-phase due to their propensity to undergo unimolecular decay via electron loss or ionic fragmentation. There is considerable fundamental interest in these systems since they display novel potential energy surfaces that are characterized by Coulomb barriers. Over recent years, considerable progress has been made in understanding the factors that affect the stability, decay pathways and reactivity of gas-phase MCAs, mainly as a result of the application of electrospray ionization as a generic technique for transferring solution-phase MCAs into the gas-phase for detailed characterization. We review contemporary work in this field, focusing on the factors that control the intrinsic stability of MCAs, both as isolated gas-phase ions, and on their complexation with solvent molecules and counter-ions. While studies of MCAs are primarily of fundamental interest, several classes of important biological ions are commonly observed as MCAs in the gas-phase (e.g. oligonucleotides, sugars). Recent results for biologically relevant ions are emphasised, since a fundamental understanding of the properties of gas-phase MCAs will be highly valuable for developing further analytical methods to study these important systems.
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Pan S, Verhoeven K, Lee JK. Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: charge level-related base loss. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1853-65. [PMID: 16198120 DOI: 10.1016/j.jasms.2005.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 07/08/2005] [Accepted: 07/08/2005] [Indexed: 05/04/2023]
Abstract
The charge state distribution and CID fragmentation of two series of deprotonated oligodeoxynucleotide (ODN) 9-mers (5'-GGTTXTTGG-3' and 5'-CCAAYAACC-3', X/Y = G, C, A, or T) have been studied in detail in an ion trap in an effort to understand the intrinsic properties of DNA in vacuo. The distribution of charge states (-2 to -6) is similar for both the X- and Y-series, with the most abundant being the -4 charge state. The T-rich X-series prefers higher charge states (-6 and -5) than does the Y-series. Calculations show that phosphate groups located nearest a thymine are more acidic than those near an adenine, cytosine, or guanine, thus explaining why the X-series prefers higher charge states. We use the term "charge level" to define the ratio of the charge state to the total number of phosphate groups present in the ODN. We find, consistent with previous studies, that the initial step of fragmentation is loss of nucleobase either as an anion or as a neutral. We observe the former for ODNs with charge levels greater than 50% and the latter for ODNs with charge levels below 50%. The overall anionic base loss follows the trend A(-) >> G(-) approximately T(-) > C(-); electrostatic potential calculations indicate that this trend follows delocalization of electron density for each anion, with A(-) being the most stabilized through delocalization. For neutral base loss, thymine (TH) is rarely cleaved, while the preferences for AH, GH, and CH loss vary. Proton affinity (PA) calculations show that a nearby negatively charged phosphate enhances the PA of proximally located nucleobases; this PA enhancement probably plays a role in promoting neutral base loss. The trends differ by charge level. At a charge level of 37.5% (-3 charge state), AH loss is preferred over CH and GH loss, regardless of sequence. However, at a charge level of 25% (-2 charge state), the terminal bases are preferentially lost over the internal bases, regardless of identity. By reconstructing the ODN sequences from structurally informative (a-BH) and w ions, we are able to identify the charge locations for the -3 and -2 charge states. For the -3 charge state, one charge resides on each "most terminal" phosphate, with the third being in the middle. For the -2 charge state, each charge resides on the penultimate phosphate groups. We compare our data to earlier experiments in an effort to generalize trends.
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Affiliation(s)
- Su Pan
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
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22
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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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23
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Sleno L, Volmer DA. Ion activation methods for tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2004; 39:1091-112. [PMID: 15481084 DOI: 10.1002/jms.703] [Citation(s) in RCA: 311] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This tutorial presents the most common ion activation techniques employed in tandem mass spectrometry. In-source fragmentation and metastable ion decompositions, as well as the general theory of unimolecular dissociations of ions, are initially discussed. This is followed by tandem mass spectrometry, which implies that the activation of ions is distinct from the ionization step, and that the precursor and product ions are both characterized independently by their mass/charge ratios. In collision-induced dissociation (CID), activation of the selected ions occurs by collision(s) with neutral gas molecules in a collision cell. This experiment can be done at high (keV) collision energies, using tandem sector and time-of-flight instruments, or at low (eV range) energies, in tandem quadrupole and ion trapping instruments. It can be performed using either single or multiple collisions with a selected gas and each of these factors influences the distribution of internal energy that the activated ion will possess. While CID remains the most common ion activation technique employed in analytical laboratories today, several new methods have become increasingly useful for specific applications. More recent techniques are examined and their differences, advantages and disadvantages are described in comparison with CID. Collisional activation upon impact of precursor ions on solid surfaces, surface-induced dissociation (SID), is gaining importance as an alternative to gas targets and has been implemented in several different types of mass spectrometers. Furthermore, unique fragmentation mechanisms of multiply-charged species can be studied by electron-capture dissociation (ECD). The ECD technique has been recognized as an efficient means to study non-covalent interactions and to gain sequence information in proteomics applications. Trapping instruments, such as quadrupole ion traps and Fourier transform ion cyclotron resonance instruments, are particularly useful for the photoactivation of ions, specifically for fragmentation of precursor ions by infrared multiphoton dissociation (IRMPD). IRMPD is a non-selective activation method and usually yields rich fragmentation spectra. Lastly, blackbody infrared radiative dissociation is presented with a focus on determining activation energies and other important parameters for the characterization of fragmentation pathways. The individual methods are presented so as to facilitate the understanding of each mechanism of activation and their particular advantages and representative applications.
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Affiliation(s)
- Lekha Sleno
- National Research Council, Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, Canada, B3H 3Z1
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24
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Dunbar RC. BIRD (blackbody infrared radiative dissociation): evolution, principles, and applications. MASS SPECTROMETRY REVIEWS 2004; 23:127-158. [PMID: 14732935 DOI: 10.1002/mas.10074] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Blackbody infrared radiative dissociation (BIRD) describes the observation of ion-dissociation reactions at essentially zero pressure by the ambient blackbody radiation field, which is usually studied in the ion-trapping ion cyclotron resonance (ICR) mass spectrometer. A brief summary of the historical context and evolution is provided. Focussing on the quantitative observation of the temperature dependence of BIRD rates, methods are developed for connecting BIRD observations with activation parameters and dissociation thermochemistry. Three regimes are differentiated and described, comprising large molecules, small molecules, and intermediate-sized molecules. The different approaches to interpreting BIRD kinetics in those three regimes are discussed. In less than a decade since its inception, this approach to studying gas-phase ions has spread over a wide variety of applications, which are surveyed. Some major areas of activity are: the characterization of solvent-molecule detachment from solvated ions; dissociation reactions of biomolecules (polypeptides, oligonucleotides, complexes involving polysaccharides) and the structural information to be deduced from them; and dissociations of proton-bound and metal-ion-containing complexes. Studies of blackbody-radiation-driven evaporation of water molecules from large water-cluster ions are surveyed briefly. Several techniques related to BIRD are noted, including collisional dissociation in the FT-ICR ion trap; high-pressure thermal dissociation in quadrupole ion traps and in heated inlet capillary regions; hot-filament-assisted dissociation; and infrared multiphoton dissociation (IRMPD).
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Affiliation(s)
- Robert C Dunbar
- Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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25
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Daneshfar R, Klassen JS. Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:55-64. [PMID: 14698556 DOI: 10.1016/j.jasms.2003.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Arrhenius activation parameters (E(a) and A) for the loss of neutral nucleobase from a series of doubly deprotonated oligodexoynucleotide 10-mers of the type XT(9), T(9)X, and T(5)XT(4), where X = A, C, and G, have been determined using the blackbody infrared radiative dissociation technique. At temperatures of 120 to 190 degrees C, the anions dissociate exclusively by the loss of a neutral nucleobase (XH), followed by cleavage of the sugar 3' C-O bond leading to (a-XH) and w type ions or, in the case of the T(9)X(2-) ions, the loss of H(2)O. The dissociation kinetics and energetics are sensitive to the nature and position of X. Over the temperature range investigated, the kinetics for the loss of AH and GH were similar, but approximately 100 times faster than for the loss of CH. For the loss of AH and GH, the values of E(a) are sensitive to the position of the base. The order of the E(a)s for the loss of XH from the 5' and 3' termini is: C > G > A; while for T(5)XT(4) the order is: C > A > G. The trends in the values of E(a) do not parallel the trend in deprotonation enthalpies or proton affinities of the nucleobases in the gas phase, indicating that the energetic differences do not simply reflect differences in their gas phase acidity or basicity. The pre-exponential factors (A) vary from 10(10) to 10(15) s(-1), depending on the nature and position of X. These results suggest that the reactivity of individual nucleobases is influenced by stabilizing intramolecular interactions.
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Affiliation(s)
- Rambod Daneshfar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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26
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Xiang Y, Abliz Z, Li LJ, Takayama M. Characteristic fragmentation behavior of deoxytetranucleotides by positive ion electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1220-1224. [PMID: 12772280 DOI: 10.1002/rcm.990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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27
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Armentrout PB. Threshold Collision-Induced Dissociations for the Determination of Accurate Gas-Phase Binding Energies and Reaction Barriers. Top Curr Chem (Cham) 2003. [DOI: 10.1007/3-540-36113-8_7] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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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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29
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Kitova EN, Bundle DR, Klassen JS. Thermal dissociation of protein-oligosaccharide complexes in the gas phase: mapping the intrinsic intermolecular interactions. J Am Chem Soc 2002; 124:5902-13. [PMID: 12010066 DOI: 10.1021/ja017213o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11.
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Affiliation(s)
- Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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30
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Luo H, Lipton MS, Smith RD. Charge effects for differentiation of oligodeoxynucleotide isomers containing 8-oxo-dG residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:195-199. [PMID: 11908798 DOI: 10.1016/s1044-0305(01)00353-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Dissociation reactions of a series of multiply charged oligodeoxynucleotide (ODN) 12-mer anions were studied using an ion trap mass spectrometer. These mixed nucleobase 12-mers fragment first by loss of a neutral nucleobase (A, G, C, and/or 5-methyl-cytosine) followed by cleavage at 3' C-O bond of the sugar from which the base is lost to produce the complementary sequence ions, i.e., [a - B] and w type of ions. No detectable loss of 8-oxo-guanine and/or thymine from these 12-mers is observed under gentle collision conditions in the ion trap. The primary loss of a nucleobase and the subsequent backbone cleavage to generate sequence ions strongly depend on the charge state of the parent molecular ion. For low charge states (2- and 3-), product ions due to the loss of a neutral guanine base and related sequence ions are dominant in the tandem mass spectra. However, preferential loss of a neutral adenine becomes the primary reaction channel from the 5- charge state of the molecular ion. Such charge state dependent fragmentation behavior was utilized to determine the site of 8-oxo-dG residue in a series of structural isomers. The position of 8-oxo-dG residue can be simply determined from the fragmentation pattern of 3- charge state, but not of 5- charge state. It is suggested that in addition to specific modification that affects the N-glycosidic bond strength, total charge content of an ODN is an important factor for determining the differential fragmentation behavior.
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Affiliation(s)
- Hai Luo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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31
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O'Connor PB. Considerations for design of a Fourier transform mass spectrometer in the 4.2 K cold bore of a superconducting magnet. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:1160-1167. [PMID: 12112266 DOI: 10.1002/rcm.685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An external source Fourier transform mass spectrometer (FTMS) constructed inside the vertical cold bore of a superconducting magnet will have dramatic advantages in effective magnetic field, noise figures, and base pressure over current commercially available external source FTMS systems. There are substantial, but solvable, difficulties in the design, primarily with regard to control of the helium boiloff rate to an acceptable level, as well as relatively minor design challenges with heat sinks, contraction of metallic ion optic elements in the extreme temperature, and tandem mass spectrometry experiments. However, the ability to construct the FTMS inside the narrow bore tube of existing, commercially available vertical bore NMR magnets will allow access to the upper magnetic field limit currently used by 900 MHz (21 Tesla) - 1 GHz (23.3 Tesla) NMR experiments. The vacuum system, simply by being held inside the cold bore at 4.2 K, will cryopump itself dropping base pressures substantially, and heat sinking the input resistor of the preamplifier to this cryogenically cooled vacuum chamber will allow reduction of the input Johnson noise by a factor of 8.4 with associated 8.4-fold improvement in signal/noise, sensitivity, and dynamic range. The simultaneous improvement of three fundamental limiting factors in the FTMS (field strength, base pressure, and Johnson noise figure) will clearly outweigh the concomitant increased helium boiloff rate particularly if this rate can be dropped to the estimated <5 L/day range. The additional use of modern cryorefrigerators will further reduce helium boiloff to zero except during MS(n) experiments and system cooldown.
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Affiliation(s)
- Peter B O'Connor
- Department of Biochemistry, Mass Spectrometry Resource, Boston University School of Medicine, 715 Albany St., R806, Boston, MA 02118, USA.
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32
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Gabelica V, De PE. Comparison of the collision-induced dissociation of duplex DNA at different collision regimes: evidence for a multistep dissociation mechanism. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:91-98. [PMID: 11777205 DOI: 10.1016/s1044-0305(01)00335-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The dissociation mechanism of duplex DNA has been investigated in detail by collision-induced dissociation experiments at different collision regimes. MS/MS experiments were performed either in a quadrupole collision cell (hybrid quadrupole-TOF instrument) or in a quadrupole ion trap with different activation times and energies. In addition to the noncovalent dissociation of the duplex into the single strands, other covalent bond fragmentation channels were observed. Neutral base loss from the duplex is favored by slow activation. In fast activation conditions, however, the major reaction channel is the noncovalent dissociation into single strands, which is highly entropy-favored. Fast activation regimes can favor the entropy-driven noncovalent dissociation, while in slow heating conditions the competition with enthalpy-driven covalent fragmentation can completely hinder the dissociation of the complex. We also evidence that the noncovalent dissociation of DNA duplex is a multistep process involving a progressive unzipping, preferentially at terminal positions. This is proposed to be a general feature for complexes containing a high number of contributing interactions organized at the interface of the ligands. The overall (observed) dissociation kinetics of noncovalent complexes can therefore depend on a complicated mechanism for which a single transition state description of the kinetics is too simplistic.
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Affiliation(s)
- Valérie Gabelica
- Mass Spectrometry Laboratory, Department of Chemistry, University of Liege, Belgium.
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33
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Freitas MA, Hendrickson CL, Marshall AG. Determination of Relative Ordering of Activation Energies for Gas-Phase Ion Unimolecular Dissociation by Infrared Radiation for Gaseous Multiphoton Energy Transfer. J Am Chem Soc 2000. [DOI: 10.1021/ja9925397] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael A. Freitas
- Contribution from the Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310
| | - Christopher L. Hendrickson
- Contribution from the Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310
| | - Alan G. Marshall
- Contribution from the Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310
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Rodgers MT, Armentrout PB. Noncovalent metal-ligand bond energies as studied by threshold collision-induced dissociation. MASS SPECTROMETRY REVIEWS 2000; 19:215-247. [PMID: 10986693 DOI: 10.1002/1098-2787(200007)19:4<215::aid-mas2>3.0.co;2-x] [Citation(s) in RCA: 245] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This review focuses on noncovalent metal ion-ligand complexes and measurements of the bond energies of such species. The method utilized in this work is threshold collision-induced dissociation (CID), as achieved using a guided ion beam tandem mass spectrometer. Accurate determination of bond energies requires attention to many details of the experiments and data analysis. These details are discussed thoroughly and compared to other methods. A comprehensive listing of metal-ligand bond dissociation energies determined by threshold CID is provided. This list includes a variety of metals (alkalis, magnesium, aluminum, and first and second row transition metals), many different types of ligands, and variations in the number of ligands. The trends in these values are discussed, and we elucidate the importance of ion-dipole and ion-induced dipole interactions, chelation, different conformers and tautomers, steric interactions, solvation phenomena, and electronic effects such as hybridization and promotion.
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Affiliation(s)
- MT Rodgers
- Chemistry Department, Wayne State University, Detroit, MI, USA
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Freitas MA, Hendrickson CL, Marshall AG. Gas phase activation energy for unimolecular dissociation of biomolecular ions determined by focused RAdiation for gaseous multiphoton ENergy transfer (FRAGMENT). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 1999; 13:1639-1642. [PMID: 10421907 DOI: 10.1002/(sici)1097-0231(19990815)13:15<1639::aid-rcm691>3.0.co;2-s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a novel approach for the determination of activation energy for the unimolecular dissociation of a large (>50 atoms) ion, based on measurement of the unimolecular dissociation rate constant as a function of continuous-wave CO(2) laser intensity. Following a short ( approximately 1 s) induction period, CO(2) laser irradiation produces an essentially blackbody internal energy distribution, whose 'temperature' varies inversely with laser intensity. The only currently available method for measuring such activation energies is blackbody infrared radiative dissociation (BIRD). Compared with BIRD, FRAGMENT: (a) eliminates the need to heat the surrounding ion trap and vacuum chamber to each of several temperatures (each requiring hours for temperature equilibration); (b) offers a three-fold wider range of effective blackbody temperature; and (c) extends the range of applications to include initially cold ions (e.g., gas-phase H/D exchange). Our FRAGMENT-determined activation energy for dissociation of protonated bradykinin, 1.2 +/- 0.1 eV, agrees within experimental error to the value, 1.3 +/- 0.1 eV, previously reported by Williams et al. from BIRD experiments. Copyright 1999 John Wiley & Sons, Ltd.
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Affiliation(s)
- MA Freitas
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, FL 32310, USA
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