title: Deciphering the structural properties that confer stability to a DNA nanocage.
abstract: A DNA nanocage has been recently characterized by small-angle X-ray scattering (SAXS) and cryo-transmission electron microscopy as a DNA octahedron having a central cavity larger than the apertures in the surrounding DNA lattice. Starting from the SAXS data, a DNA nanocage has been modeled and simulated by classical molecular dynamics to evaluate in silico its structural properties and stability. Global properties, principal component analysis, and DNA geometrical parameters, calculated along the entire trajectory, indicate that the cage is stable and that the B-DNA conformation, also if slightly distorted, is maintained for all the simulation time. Starting from the initial model, the nanocage scaffold undergoes a contraction of the thymidine strands, connecting the DNA double helices, suggesting that the length of the thymidine strands is a crucial aspect in the modulation of the nanocage stability. A comparison of the average structure as obtained from the simulation shows good agreement with the SAXS experimental data.
authors: Department of Biology and Center of Biostatistics and Bioinformatics, University of Rome "Tor Vergata", Via della Ricerca Scientifica 1, 00133 Rome, Italy.
authors: Mattia
authors: M
authors: Falconi
authors: Francesco
authors: F
authors: Oteri
authors: Giovanni
authors: G
authors: Chillemi
authors: Felicie F
authors: FF
authors: Andersen
authors: David
authors: D
authors: Tordrup
authors: Cristiano L P
authors: CL
authors: Oliveira
authors: Jan S
authors: JS
authors: Pedersen
authors: Birgitta R
authors: BR
authors: Knudsen
authors: Alessandro
authors: A
authors: Desideri