Molecular Characterization of the Interaction between siRNA and PAMAM G7 Dendrimers by SAXS, ITC, and Molecular Dynamics Simulations

Abstract

A prerequisite for the use of dendrimers as drug delivery vehicles is the detailed molecular understanding of the drug interaction. The purpose of this study was to characterize the self-assembly process between siRNA and generation 7 poly(amidoamine) dendrimers and the resulting dendriplexes in aqueous solution using structural and calorimetric methods combined with molecular dynamics simulations. Complexes with a length scale of 150 nm showed a decreasing size with increasing amine-to-phosphate ratio by dynamic light scattering. At the molecular level, individual dendrimers studied by small-angle X-ray scattering (SAXS) showed no change in size upon siRNA binding, suggesting a rigid sphere behavior. Isothermal titration calorimetry (ITC) demonstrated exothermic binding with a concentration-dependent collapse of complexes. Both the experimentally determined ΔH(bind) and size were in close accordance with molecular dynamics simulations. This study demonstrates the unique complementarity of SAXS, ITC, and modeling for the detailed description of the molecular interactions between dendrimers and siRNA during dendriplex formation.

Effect of Synthetic Polymers on tRNA Nanoparticle Formation

“…Hence the PEG-3350 complexes contain in average one tRNA molecules, the anthracene complexes five molecules and the PEG-6000 complexes ten molecules ( Figure 1-panel A). The tRNA aggregation and particle formation in the presence of PEG and mPEG-anthracene were very similar to those of PEG-DNA complexes recently reported [21,22]. Similarly in the cases of dendrimers and PEGylated dendrimers, the mica surface was covered by a layer that attributed to a mixture of free dendrimer, free pegylated dendrimers and free tRNA ( Figure 1-panel B).…”

“…It has been shown that synthetic polymers induce significant changes in DNA and RNA solubility and structure under given conditions [8][9][10][11][12][13][14][15][16][17][18][19][20]. Synthetic polymers are also used to transport miRNA and siRNA in vitro [11][12][13][14][15][16][17][18][19][20][21][22][23][24]. PEGylation of synthetic polymers such as dendrimers is shown to reduce toxicity and increase biocompatibility and DNA Transfection [6,7,9].…”

Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A

“…The four metastates (m1-m4) witnessed in the single Anton trajectory have chemical shifts similar to those of the ground state, maintain the F helix as a 3 10 helix separate from the G helix, and position F114 just outside of the buried cavity despite fluctuation in cavity volume and changes in F114-V103 internal distances throughout these metastates (Fig. 1).…”

“…Long-timescale molecular dynamics (MD) simulations now make it possible to witness atomic motions on the nanosecond to microsecond timescale, with a suitable level of agreement with experiment (8)(9)(10)(11). Additionally, with recent advances in specialized computational architectures like Anton, simulation timescales on the order of microseconds to milliseconds in a single trajectory are within reach (7,(12)(13)(14).…”

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

“…The binding strength between dendrimer-guest complexes has been determined by isothermal titration calorimetry(ITC) [26][27][28][29], high performance liquid chromatography (HPLC) [30] and fluorescence spectroscopy [31][32][33]. Detailed conformations of dendrimers interacting with guest molecules have been studied by nuclear magnetic resonance(NMR) [34][35][36] and the size of the dendrimer-guest complexes has been measured by dynamic light scattering (DLS) [22,31].…”