AI Article Synopsis
- A DNA nanocage, modeled as an octahedron with a large central cavity, was studied using small-angle X-ray scattering (SAXS) and cryo-transmission electron microscopy.
- The simulation through classical molecular dynamics demonstrated that the nanocage remains stable and maintains a slightly distorted B-DNA conformation throughout the testing period.
- Changes in the length of thymidine strands, which connect the DNA helices, are identified as a key factor affecting the stability of the nanocage, with the simulation results aligning well with the SAXS data.
Article 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.
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| http://dx.doi.org/10.1021/nn900468y | DOI Listing |
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