Structure and Dynamics of Oligonucleotides in the Gas Phase

By combining ion‐mobility mass spectrometry experiments with sub‐millisecond classical and ab initio molecular dynamics we fully characterized, for the first time, the dynamic ensemble of a model nucleic acid in the gas phase under electrospray ionization conditions. The studied oligonucleotide unfo...

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Published inAngewandte Chemie (International ed.) Vol. 54; no. 2; pp. 467 - 471
Main Authors Arcella, Annalisa, Dreyer, Jens, Ippoliti, Emiliano, Ivani, Ivan, Portella, Guillem, Gabelica, Valérie, Carloni, Paolo, Orozco, Modesto
Format Journal Article
LanguageEnglish
Published Weinheim WILEY-VCH Verlag 07.01.2015
WILEY‐VCH Verlag
Wiley Subscription Services, Inc
EditionInternational ed. in English
Subjects
ab initio calculations
Charge
DNA
Dynamics
gas phase
Gases - chemical synthesis
Ionization
Ions
Mass spectrometry
Molecular dynamics
Molecular Structure
Oligonucleotides
Oligonucleotides - chemistry
Vaporization
gas phase
mass spectrometry
ab initio calculations
molecular dynamics
DNA
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Summary:By combining ion‐mobility mass spectrometry experiments with sub‐millisecond classical and ab initio molecular dynamics we fully characterized, for the first time, the dynamic ensemble of a model nucleic acid in the gas phase under electrospray ionization conditions. The studied oligonucleotide unfolds upon vaporization, loses memory of the solution structure, and explores true gas‐phase conformational space. Contrary to our original expectations, the oligonucleotide shows very rich dynamics in three different timescales (multi‐picosecond, nanosecond, and sub‐millisecond). The shorter timescale dynamics has a quantum mechanical nature and leads to changes in the covalent structure, whereas the other two are of classical origin. Overall, this study suggests that a re‐evaluation on our view of the physics of nucleic acids upon vaporization is needed. Molecular dynamics calculations and mass spectrometry are combined to obtain an atomistic description of DNA under vacuum after electrospray vaporization under mild ionization conditions. After vaporization, gas‐phase ions with different mass/charge (m/z) ratios are produced and for the most abundant charge state, the structure preserves a memory of the native conformation.
Bibliography:Spanish National Institute of Bioinformatics
ark:/67375/WNG-R2GN3GH1-3
ICREA-Academia
European Research Council
This work is supported by the Spanish MINECO (BIO2012-32868), the Spanish National Institute of Bioinformatics (INB) and the European Research Council (ERC). M.O. is an ICREA-Academia fellow and G.P. is a Sara Borell Fellow. Moreover, the authors gratefully acknowledge the Gauss Centre for Supercomputing (GCS) for providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS share of the supercomputer JUQUEEN at the Jülich Supercomputing Centre (JSC).
ERC
Spanish MINECO - No. BIO2012-32868
INB
istex:7FB700B39135D762DD0D7EE448015E6616448C82
ArticleID:ANIE201406910
This work is supported by the Spanish MINECO (BIO2012‐32868), the Spanish National Institute of Bioinformatics (INB) and the European Research Council (ERC). M.O. is an ICREA‐Academia fellow and G.P. is a Sara Borell Fellow. Moreover, the authors gratefully acknowledge the Gauss Centre for Supercomputing (GCS) for providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS share of the supercomputer JUQUEEN at the Jülich Supercomputing Centre (JSC).
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1433-7851
1521-3773
DOI:10.1002/anie.201406910