Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation

Abstract

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH4 + from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH4 + or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.

On the Chemistry of Aqueous Ammonium Acetate Droplets during Native Electrospray Ionization Mass Spectrometry

“…MD has become an important tool for probing ESI mechanisms, ,− but there appear to be no previous MD studies on the ESI behavior of NH 4 Ac. Proton transfer cannot be modeled using standard MD methods, , although this reaction is a key feature of NH 4 Ac (eq ).…”

“…Proton transfer cannot be modeled using standard MD methods, , although this reaction is a key feature of NH 4 Ac (eq ). Some efforts have been made to conduct MD with proton transfer, ,,,, but NH 4 Ac has not been tackled yet. Here, we present a strategy for MD simulations on NH 4 Ac-containing ESI droplets.…”

Mechanism of Magic Number NaCl Cluster Formation from Electrosprayed Water Nanodroplets

“…MD simulations have become a key tool for addressing ESI mechanistic questions. ,− Using this approach, we previously demonstrated that NaCl-containing aqueous ESI droplets liberate Na n Cl m ( n – m )+ clusters via the CRM . Unfortunately, those earlier efforts failed to reproduce the preferential formation of MNCs.…”

Exploring the Conformational Landscape of Poly(l-lysine) Dendrimers Using Ion Mobility Mass Spectrometry

“…As a result of the wide application scope for dendrimers, several analytical methods have been used to characterize them including NMR and size exclusion chromatography. , In part due to their monodispersity and broad mass range (700–30,000 Da), dendrimers have previously also been proposed as MS calibrants, for example, in MALDI-MS and as IM calibrants for CCS calculations . Recently, Saintmot et al used IM-MS, coupled to molecular dynamics simulations, to investigate the conformations of dendrimers and dendriplexes . Here, we investigated a family of polylysine dendrimers (Figure and Table ), where the number of surface amino groups (−NH 2 ) doubled in number with the increasing generation, allowing for greater charge accommodation (e.g., generation 2 (G2) has eight surface groups, Figure A).…”