Andrea Danani

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In this study, simulation challenges intuitive models of "flexible" and "rigid" generation two triazine dendrimers as it pertains to solution conformation and conformation on binding DNA or siRNA sequences. These results derive from structural and energetic analyses of the binding events. Simulations of the rigid structure reinforce the role of the(More)
Polycationic nanocarriers attract increasing attention to the field of siRNA delivery. We investigated the self-assembly of siRNA vs pDNA with polycations, which are broadly used for nonviral gene and siRNA delivery. Although polyethyleneimine (PEI) was routinely adopted as siRNA carrier based on its efficacy in delivering pDNA, it has not been investigated(More)
This paper reports a molecular dynamic study to explore the diverse behavior of different generations of poly(amidoamine) (PAMAM) dendrimers in binding siRNA. Our models show good accordance with experimental measurements. Simulations demonstrate that the molecular flexibility of PAMAMs plays a crucial role in the binding event, which is controlled by the(More)
This paper reports the application of molecular dynamics methods to understand the interactions between dendritic molecules with spermine surface groups and double-helical DNA. Importantly, we are able to reproduce the binding effects observed experimentally, indicating that this type of modeling is robust and reliable. The energetic effects were(More)
In this work, we present a molecular dynamics study to gain an insight into the binding of nucleic acids with spermine functionalized dendrons. We compare UV-degradable dendrons with nondegradable dendrons studied in our previous works. These two dendritic architectures have the same functional surface; however, the branching scaffold exhibits different(More)
Toll-like receptor protein 7 is a transmembrane protein playing a crucial role in the signaling pathways involved in innate immunity. Its crystal structure is not yet available, but there are several proteins possessing domains of sufficiently high homology, which enabled us to build a model of the toll-like receptor protein 7 monomer and gain insights into(More)
We present an in-depth analysis of the geometrical percolation behavior in the continuum of random assemblies of hard oblate ellipsoids of revolution. Simulations were carried out by considering a broad range of aspect ratios, from spheres up to aspect-ratio-100 platelike objects, and with various limiting two-particle interaction distances, from 0.05 times(More)
We report the synthesis, DNA binding ability and preliminary gene delivery profiles of dendrons with different amine surface groups, 1,3-diaminopropane (DAP), N,N-di-(3-aminopropyl)-N-(methyl)amine (DAPMA) and spermine (SPM). By using a combination of ethidium bromide displacement, gel electrophoresis and transfection assays, it is shown that the dendrons(More)
Polymer micelles can be used to facilitate the aqueous solubilization of lipophilic, poorly water-soluble compounds and drugs. Even if the evaluation of the efficiency of drug incorporation into such micelles can be tested experimentally, a theoretical approach based on molecular simulation can constitute a useful tool that reduces time and cost. Here we(More)
Short double-stranded RNAs, which are known as short interfering RNA (siRNA), can be used to specifically down-regulate the expression of the targeted gene in a process known as RNA interference (RNAi). However, the success of gene silencing applications based on the use of synthetic siRNA critically depends on efficient intracellular delivery. Polycationic(More)