A DNA nanocage has been recently characterized by small-angle X-ray scattering (SAXS) and cryotransmission 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.

Falconi, M., Oteri, F., Chillemi, G., Andersen, F., Tordrup, D., Oliveira, C., et al. (2009). Deciphering the Structural Properties That Confer Stability to a DNA Nanocage. ACS NANO, 3(7), 1813-1822 [10.1021/nn900468y].

Deciphering the Structural Properties That Confer Stability to a DNA Nanocage.

FALCONI, MATTIA;DESIDERI, ALESSANDRO
2009-01-01

Abstract

A DNA nanocage has been recently characterized by small-angle X-ray scattering (SAXS) and cryotransmission 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.
2009
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore BIO/11 - BIOLOGIA MOLECOLARE
English
Con Impact Factor ISI
molecular dynamics simulation · SAXS spectroscopy · DNA nanocage structure · DNA flexibility and geometrical parameters · principal component analysis
Falconi, M., Oteri, F., Chillemi, G., Andersen, F., Tordrup, D., Oliveira, C., et al. (2009). Deciphering the Structural Properties That Confer Stability to a DNA Nanocage. ACS NANO, 3(7), 1813-1822 [10.1021/nn900468y].
Falconi, M; Oteri, F; Chillemi, G; Andersen, F; Tordrup, D; Oliveira, C; Pedersen, J; Knudsen, B; Desideri, A
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/28508
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