Do d(GCGAAGC) Cations Retain the Hairpin Structure in the Gas Phase? A Cyclic Ion Mobility Mass Spectrometry and Density Functional Theory Computational Study

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F23%3A00577006" target="_blank" >RIV/61388971:_____/23:00577006 - isvavai.cz</a>

Alternative codes found

RIV/61989592:15310/23:73621803

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/jasms.3c00228" target="_blank" >https://pubs.acs.org/doi/10.1021/jasms.3c00228</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/jasms.3c00228" target="_blank" >10.1021/jasms.3c00228</a>

Result language

angličtina

Original language name

Do d(GCGAAGC) Cations Retain the Hairpin Structure in the Gas Phase? A Cyclic Ion Mobility Mass Spectrometry and Density Functional Theory Computational Study

Original language description

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.

Czech name

—

Czech description

—

Type

J_SC - Article in a specialist periodical, which is included in the SCOPUS database

CEP classification

—

OECD FORD branch

10606 - Microbiology

Project

<a href="/en/project/GA23-07254S" target="_blank" >GA23-07254S: Shape of mobility peaks as a tool for discrimination of isomers by ion mobility-mass spectrometry</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of the American Society for Mass Spectrometry

ISSN

1044-0305

e-ISSN

1879-1123

Volume of the periodical

34

Issue of the periodical within the volume

10

Country of publishing house

US - UNITED STATES

Number of pages

18

Pages from-to

2323-2340

UT code for WoS article

001167008400001

EID of the result in the Scopus database

2-s2.0-85172921038