Sage Journals: Discover world-class research

Abstract

Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n = 15–40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence.

Keywords

Collision-induced dissociation mass spectrometry oligonucleotide fragmentation ion mobility tandem-MS

Get full access to this article

View all access options for this article.

References

McLuckey

. Gas-phase fragmentation of oligonucleotide ions. Int J Mass Spectrom 2004; 237: 197–241.

Gidden

Bowers

. Gas-phase conformations of deprotonated trinucleotides (dGTT-, dTGT-, and dTTG-): the question of zwitterion formation. J Am Soc Mass Spectrom 2003; 14: 161–170.

Pan

Verhoeven

Lee

. Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: charge level-related base loss. J Am Soc Mass Spectrom 2005; 16: 1853–1865.

McLuckey

Vaidyanathan

. Charge state effects in the decompositions of single-nucleobase oligonucleotide polyanions. Int J Mass Spectrom Ion Process 1997; 162: 1–16.

Favre

Gonnet

Tabet

. Location of the negative charge(s) on the backbone of single-stranded deoxyribonucleic acid in the gas phase. Eur J Mass Spectrom 2000; 6: 389–396.

McLuckey

Van Berkel

Goeringer

et al.

Ion trap mass spectrometry. Using high-pressure ionization. Anal Chem 1994; 66: 737A–743A.

Bartlett

McCloskey

Manalili

et al.

The effect of backbone charge on the collision-induced dissociation of oligonucleotides. J Mass Spectrom 1996; 31: 1277–1283.

Rosu

Gabelica

Joly

et al.

Zwitterionic i-motif structures are preserved in DNA negatively charged ions produced by electrospray mass spectrometry. Phys Chem Chem Phys 2010; 12: 13448–13454.

Arcella

Dreyer

Ippoliti

et al.

Structure and dynamics of oligonucleotides in the gas phase. Angew Chem Int Ed Engl 2015; 54: 467–471.

10.

Lopez

Tiller

Senko

et al.

Automated strategies for obtaining standardized collisionally induced dissociation spectra on a benchtop ion trap mass spectrometer. Rapid Commun Mass Spectrom 1999; 13: 663–668.

11.

Allen

Giles

Gilbert

et al.

Ion mobility mass spectrometry of peptide, protein, and protein complex ions using a radio-frequency confining drift cell. Analyst 2016; 141: 884–891.

12.

Revercomb

Mason

. Theory of plasma chromatography gaseous electrophoresis – review. Anal Chem 1975; 47: 970–983.

13.

Von Helden

Kemper

Gotts

et al.

Isomers of small carbon cluster anions – linear-chains with up to 20 atoms. Science 1993; 259: 1300–1302.

14.

McLuckey

Habibi-Goudarzi

. Ion trap tandem mass spectrometry applied to small multiply charged oligonucleotides with a modified base. J Am Soc Mass Spectrom 1994; 5: 740–747.

15.

Morsa

Gabelica

Rosu

et al.

Dissociation pathways of benzylpyridinium “Thermometer” ions depend on the activation regime: an IRMPD spectroscopy study. J Phys Chem Lett 2014; 5: 3787–3791.

16.

Larriba-Andaluz

Hogan

. Collision cross section calculations for polyatomic ions considering rotating diatomic/linear gas molecules. J Chem Phys 2014; 141: 194107.

17.

Siems

Viehland

Hill

. Improved momentum-transfer theory for ion mobility. 1. Derivation of the fundamental equation. Anal Chem 2012; 84: 9782–9791.

18.

Abi-Ghanem

Gabelica

. Nucleic acid ion structures in the gas phase. Phys Chem Chem Phys 2014; 16: 21204–21218.

Supplementary Material

Please find the following supplemental material available below.

For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.

For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.

0.00 MB

0.15 MB

Charge-induced geometrical reorganization of DNA oligonucleotides studied by tandem mass spectrometry and ion mobility

Abstract

Keywords

Get full access to this article

References

Supplementary Material