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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: 34] [Impact Index Per Article: 11.3] [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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Cheng R, Loire E, Martens J, Fridgen TD. An IRMPD spectroscopic and computational study of protonated guanine-containing mismatched base pairs in the gas phase. Phys Chem Chem Phys 2020; 22:2999-3007. [DOI: 10.1039/c9cp06393e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Infrared multiple photon dissociation spectroscopy has been used to probe the structures of the three protonated base-pair mismatches containing 9-ethylguanine (9eG) in the gas phase. Some of these protonated base-pairs have been identified in RNA.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | - Estelle Loire
- Laboratoire Chimie Physique – CLIO
- Campus Universite d’Orsay
- France
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Nijmegen
- The Netherlands
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3
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Cheng R, Loire E, Fridgen TD. Hydrogen bonding in alkali metal cation-bound i-motif-like dimers of 1-methyl cytosine: an IRMPD spectroscopic and computational study. Phys Chem Chem Phys 2019; 21:11103-11110. [PMID: 31094375 DOI: 10.1039/c9cp01223k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The structures of alkali metal cation bound 1-methylcytosine (1-mCyt) dimers were explored using vibrational spectroscopy in the form of infrared multiple photon dissociation (IRMPD) spectroscopy and by computational methods. For the smaller alkali metal cations, Li+ and Na+, only non-hydrogen bonded symmetric anti-parallel structures were observed in agreement with the lowest energy computed structures. For K+, Rb+, and Cs+ the vibrational spectra in the N-H stretch region showed strong evidence for hydrogen bonding in agreement with the lowest energy structures which contained hydrogen bonding interactions between the amine group of one cytosine and the carbonyl oxygen of the other cytosine. The lowest energy structures for these complexes were compared to previously studied cytosine complexes [(Cyt)2M]+ where M = Li, Na, and K. The calculations are in agreement that only the non-hydrogen bonded structures would be observed for these cytosine complexes.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry, Memorial University, St. John's, NL A1B 3 × 7, Canada.
| | - Estelle Loire
- Laboratoire Chimie Physique - CLIO, Batiment 201, Porte 2, Campus Universite d'Orsay, 91405, France
| | - Travis D Fridgen
- Department of Chemistry, Memorial University, St. John's, NL A1B 3 × 7, Canada.
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4
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Gad SF, El-Demerdash SH, El-Mehasseb IM, El-Nahas AM. Structure, stability and conversions of tautomers and rotamers of azulene-based uracil analogue. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Cheng R, Rose VE, Power B, Fridgen TD. Self-assembled uracil complexes containing tautomeric uracils: an IRMPD spectroscopic and computation study of the structures of gaseous uracilnCa2+ (n = 4, 5, or 6) complexes. Phys Chem Chem Phys 2018; 20:572-580. [DOI: 10.1039/c7cp07128k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structures of doubly-charged uracil (U) complexes with Ca2+, UnCa2+ (n = 4, 5, 6), were studied by infrared multiphoton dissociation (IRMPD) spectroscopy and computational methods.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | | | - Barry Power
- Department of Chemistry
- Memorial University
- St. John's
- Canada
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6
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Na N, Shi R, Long Z, Lu X, Jiang F, Ouyang J. Real-time analysis of self-assembled nucleobases by Venturi easy ambient sonic-spray ionization mass spectrometry. Talanta 2014; 128:366-72. [DOI: 10.1016/j.talanta.2014.04.080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/23/2014] [Accepted: 04/29/2014] [Indexed: 11/24/2022]
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7
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Sun J, Qin Z, Liu J, Zhang C, Luo H. Highly sensitive and specific detection of histamine via the formation of a self-assembled magic number cluster with thymine by mass spectrometry. Analyst 2014; 139:3154-9. [DOI: 10.1039/c3an02354k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-assembled magic number cluster of thymine (T) significantly enhanced the MS signal of histamine with high specificity.
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Affiliation(s)
- Jiamu Sun
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China
| | - Zhen Qin
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China
| | - Jia Liu
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China
| | - Chengsen Zhang
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China
| | - Hai Luo
- Beijing National Laboratory for Molecular Sciences
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China
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Emilie-Laure Z. Large mixed complexes involving uracil, cytosine, thymine and/or 1-methyl uracil around Ca2+ ions: an electrospray ionization/MS study. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:438-447. [PMID: 23584937 DOI: 10.1002/jms.3175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 12/27/2012] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Abstract
We investigated the possible formation of mixed B(n)B'(n')Ca(2+) complexes where B and B' are two different nucleobases. Electrospray ionization (ESI) mass spectrometric experiments from solutions containing two different kinds of nucleobases and calcium ions were carried out to investigate the formation of magic number clusters that may be relevant in a biological point of view. The results presented here clearly show that mixed complexes can be formed and are stable in the gas phase. This represents an important step toward more complex solutions in which several nucleobases are present simultaneously and may compete in the formation of cationized clusters. We believe that thorough investigations on such systems may help understanding biological processes that may effect the tridimensional structure of the DNA macromolecule. The formation of mixed hexamers, decamers, dodecamers and tetradecamers are clearly favored from solution containing uracil (Ura), thymine (Thy) and Ca(2+), whereas mixed octamers are preferred from 1-methyl uracil (MeU), uracil and Ca(2+) mixtures. Cytosine (Cyto) can form mixed complexes with either uracil or 1-methyl uracil or thymine. On the other hand, the main species formed in these latter cases are mixed tetramers.
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Affiliation(s)
- Zins Emilie-Laure
- Laboratoire de Dynamique, Interactions et Réactivité (LADIR), UPMC Université Paris 06, CNRS, UMR 7075, 4 place Jussieu, F-75005, Paris, France
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Gillis EAL, Demireva M, Nanda K, Beran G, Williams ER, Fridgen TD. Structures and energetics of electrosprayed uracilnCa2+clusters (n = 14–4) in the gas phase. Phys Chem Chem Phys 2012; 14:3304-15. [DOI: 10.1039/c1cp22984b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Szolomájer J, Paragi G, Batta G, Guerra CF, Bickelhaupt FM, Kele Z, Pádár P, Kupihár Z, Kovács L. 3-Substituted xanthines as promising candidates for quadruplex formation: computational, synthetic and analytical studies. NEW J CHEM 2011. [DOI: 10.1039/c0nj00612b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Zins EL, Pepe C, Schröder D. Decameric uracil complexes around Li+. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:740-749. [PMID: 20564575 DOI: 10.1002/jms.1764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings.
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Affiliation(s)
- Emilie-Laure Zins
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 16610 Prague 6, Czech Republic.
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Zins EL, Rochut S, Pepe C. Formation of complexes between uracil and calcium ions: an ESI/MS/MS study in combination with theoretical calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:813-820. [PMID: 19199276 DOI: 10.1002/jms.1561] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cationized uracil clusters around calcium metal ions were generated in the gas phase by electrospray ionization (ESI). A previous study showed that with particular experimental conditions, hexamer, octamer, decamer, dodecamer and tetradecamer uracil clusters are present in high quantities. New experiments were carried out to understand the reasons for the particular stability of these complexes. MS/MS experiments suggested that these uracil clusters belong to the same family. Based on ab initio and DFT quantum chemistry calculations, structures in agreement with experimental results are proposed for these clusters.
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Affiliation(s)
- Emilie-Laure Zins
- Laboratoire de Dynamique, Interactions et Réactivité, Université Pierre et Marie Curie, 4 place Jussieu, 75 005 Paris, CNRS, UMR 7075, France.
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