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Structure of Nucleic Acids in the Gas Phase

  • Annalisa Arcella
  • Guillem Portella
  • Modesto Orozco
Chapter
Part of the Physical Chemistry in Action book series (PCIA)

Abstract

Evolution has refined nucleic acids to display well-defined three-dimensional structures that are functional under aqueous physiological conditions. While the structure of nucleic acids is well known in solution, it is unclear how nucleic acids react when transferred to a fully anhydrous environment. Simple physical chemistry considerations suggest that a heavily charged poly-anion would adopt fully extended conformations in vacuum, and that multistranded structure would dissociate, to guarantee that charged residues separate as much as possible to reduce Coulomb repulsion. However, and quite counterintuitively, a vast amount of experiments demonstrate that this is not the case and that oligomeric nucleic acids adopt quite compact structures in the gas phase, which in some cases might preserve memories of the original conformation in solution. In this chapter, we review our current understanding of nucleic acid structure in the gas phase.

Keywords

Nucleic acids Gas phase Electrospray Soft Ionization Mass spectrometry Molecular dynamics Ion mobility spectrometry DNA Simulation 

Abbreviations

ESI-MS

Electrospray soft ionization mass spectrometry

IMS

Ion mobility spectrometry

IVNT

In vacuum native structure

XFEL

X-ray free electron laser

CCS

Collision cross section

MD

Molecular dynamics

QM

Quantum mechanics

DFT

Density functional theory

CCSD(T)/CBS

Coupled cluster with single, double, and triple excitation/complete basis set

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Annalisa Arcella
    • 1
    • 2
  • Guillem Portella
    • 1
    • 2
  • Modesto Orozco
    • 1
    • 2
    • 3
  1. 1.Institute for Research in Biomedicine (IRB Barcelona)BarcelonaSpain
  2. 2.Joint Research Program in Computational BiologyInstitute for Research in Biomedicine and Barcelona Supercomputing CenterBarcelonaSpain
  3. 3.Department of Biochemistry and Molecular BiologyUniversity of BarcelonaBarcelonaSpain

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