title: A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra.
abstract: A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures.
authors.affiliation: Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo , Caixa Postal 66318, 05314-970 Sao Paulo, Brazil.|Department of Engineering and Sciences, Federal University of Paraná , 85950-000 Palotina, Paraná, Brazil.
authors.forename: Cassio
authors.initials: C
authors.lastname: Alves
authors.affiliation: Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy.
authors.forename: Federico
authors.initials: F
authors.lastname: Iacovelli
authors.affiliation: Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy.
authors.forename: Mattia
authors.initials: M
authors.lastname: Falconi
authors.affiliation: Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Cardamone
authors.affiliation: Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy.
authors.forename: Blasco
authors.initials: B
authors.lastname: Morozzo Della Rocca
authors.affiliation: Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo , Caixa Postal 66318, 05314-970 Sao Paulo, Brazil.
authors.forename: Cristiano L P
authors.initials: CL
authors.lastname: de Oliveira
authors.affiliation: Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Desideri
mesh_terms: D001331:Automation; D059371:DNA, B-Form / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation
chemical_list: D059371:DNA, B-Form