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Do d(GCGAAGC) Cations Retain the Hairpin Structure in the Gas Phase? A Cyclic Ion Mobility Mass Spectrometry and Density Functional Theory Computational Study
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SYSNO ASEP 0577006 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Do d(GCGAAGC) Cations Retain the Hairpin Structure in the Gas Phase? A Cyclic Ion Mobility Mass Spectrometry and Density Functional Theory Computational Study Tvůrce(i) Wan, J. (US)
Nytka, M. (CZ)
Qian, H. (US)
Lemr, Karel (MBU-M) RID, ORCID
Tureček, F. (US)Zdroj.dok. Journal of the American Society for Mass Spectrometry. - : American Chemical Society - ISSN 1044-0305
Roč. 34, č. 10 (2023), s. 2323-2340Poč.str. 18 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova Computation theory ; Density functional theory ; Dissociation ; Electrospray ionization ; Gases ; Hydrogen bonds ; Ion mobility spectrometers ; Mass spectrometry ; Oligonucleotides Obor OECD Microbiology Způsob publikování Omezený přístup Institucionální podpora MBU-M - RVO:61388971 UT WOS 001167008400001 EID SCOPUS 85172921038 DOI 10.1021/jasms.3c00228 Anotace d(GCGAAGC) is the smallest oligonucleotide with a well-defined hairpin structure in solution. We report a study of multiply protonated d(GCGAAGC) and its sequence-scrambled isomers, d(CGAAGCG), d(GCGAACG), and d(CGGAAGC), that were produced by electrospray ionization with the goal of investigating their gas-phase structures and dissociations. Cyclic ion mobility measurements revealed that dications of d(GCGAAGC) as well as the scrambled-sequence ions were mixtures of protomers and/or conformers that had collision cross sections (CCS) within a 439-481 & Aring,(2) range. Multiple ion conformers were obtained by electrospray under native conditions as well as from aqueous methanol. Arrival time distribution profiles were characteristic of individual isomeric heptanucleotides. Extensive Born-Oppenheimer molecular dynamics (BOMD) and density functional theory (DFT) calculations of d(GCGAAGC)(2+) isomers indicated that hairpin structures were high-energy isomers of more compact distorted conformers. Protonation caused a break up of the C2<middle dot><middle dot><middle dot>G6 pair that was associated with the formation of strong hydrogen bonds in zwitterionic phosphate anion-nucleobase cation motifs that predominated in low energy ions. Multiple components were also obtained for d(GCGAAGC)(3+) trications under native and denaturing electrospray conditions. The calculated trication structures showed disruption of the G<middle dot><middle dot><middle dot>C pairs in low energy zwitterions. A hairpin trication was calculated to be a high energy isomer. d(GCGAAGC)(4+) tetracations were produced and separated by c-IMS as two major isomers. All low energy d(GCGAAGC)(4+) ions obtained by DFT geometry optimizations were zwitterions in which all five purine bases were protonated, and the ion charge was balanced by a phosphate anion. Tetracations of the scrambled sequences were each formed as one dominant isomer. The CCS calculated with the MobCal-MPI method were found to closely match experimental values. Collision-induced dissociation (CID) spectra of multiply charged heptanucleotides showed nucleobase loss and backbone cleavages occurring chiefly at the terminal nucleosides. Electron-transfer-CID tandem mass spectra were used to investigate dissociations of different charge and spin states of charge-reduced heptanucleotide cation radicals. Pracoviště Mikrobiologický ústav Kontakt Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Rok sběru 2024 Elektronická adresa https://pubs.acs.org/doi/10.1021/jasms.3c00228
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