Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.

We report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, the technique has become popular in structural biology, and the conformati...

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Authors: Porrini, Massimiliano, Rosu, Frédéric, Rabin, Clémence, Darré, Leonardo, Gómez, Hansel, Orozco López, Modesto, Gabelica, Valérie
Format: article
Status:Published version
Publication Date:2017
Country:España
Institution:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repository:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/114913
Online Access:https://hdl.handle.net/2445/114913
Access Level:Open access
Keyword:Àcids nucleics
Espectrometria de masses
Nucleic acids
Mass spectrometry
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spelling Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.Porrini, MassimilianoRosu, FrédéricRabin, ClémenceDarré, LeonardoGómez, HanselOrozco López, ModestoGabelica, ValérieÀcids nucleicsEspectrometria de massesNucleic acidsMass spectrometryWe report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, the technique has become popular in structural biology, and the conformation survival becomes more and more taken for granted. Surprisingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥100 mM aqueous NH4OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for all duplex sizes (gas-phase structures are more compact than canonical B-helices by ∼20% for 12-bp, and by up to ∼30% for 36-bp duplexes), and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semiempirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb repulsion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate–phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.2017201720172017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion23 p.application/pdfhttps://hdl.handle.net/2445/114913Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: http://dx.doi.org/10.1021/acscentsci.7b00084ACS Comb Sci, 2017, vol. 3, num. 5, p. 454-461http://dx.doi.org/10.1021/acscentsci.7b00084info:eu-repo/grantAgreement/EC/FP7/291433info:eu-repo/grantAgreement/EC/FP7/616551(c) American Chemical Society, 2017info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1149132026-05-29T05:05:01Z
dc.title.none.fl_str_mv Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
title Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
spellingShingle Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
Porrini, Massimiliano
Àcids nucleics
Espectrometria de masses
Nucleic acids
Mass spectrometry
title_short Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
title_full Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
title_fullStr Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
title_full_unstemmed Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
title_sort Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.
dc.creator.none.fl_str_mv Porrini, Massimiliano
Rosu, Frédéric
Rabin, Clémence
Darré, Leonardo
Gómez, Hansel
Orozco López, Modesto
Gabelica, Valérie
author Porrini, Massimiliano
author_facet Porrini, Massimiliano
Rosu, Frédéric
Rabin, Clémence
Darré, Leonardo
Gómez, Hansel
Orozco López, Modesto
Gabelica, Valérie
author_role author
author2 Rosu, Frédéric
Rabin, Clémence
Darré, Leonardo
Gómez, Hansel
Orozco López, Modesto
Gabelica, Valérie
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Àcids nucleics
Espectrometria de masses
Nucleic acids
Mass spectrometry
topic Àcids nucleics
Espectrometria de masses
Nucleic acids
Mass spectrometry
description We report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, the technique has become popular in structural biology, and the conformation survival becomes more and more taken for granted. Surprisingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥100 mM aqueous NH4OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for all duplex sizes (gas-phase structures are more compact than canonical B-helices by ∼20% for 12-bp, and by up to ∼30% for 36-bp duplexes), and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semiempirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb repulsion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate–phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.
publishDate 2017
dc.date.none.fl_str_mv 2017
2017
2017
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/114913
url https://hdl.handle.net/2445/114913
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: http://dx.doi.org/10.1021/acscentsci.7b00084
ACS Comb Sci, 2017, vol. 3, num. 5, p. 454-461
http://dx.doi.org/10.1021/acscentsci.7b00084
info:eu-repo/grantAgreement/EC/FP7/291433
info:eu-repo/grantAgreement/EC/FP7/616551
dc.rights.none.fl_str_mv (c) American Chemical Society, 2017
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) American Chemical Society, 2017
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 23 p.
application/pdf
dc.source.none.fl_str_mv Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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