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.

Alves, C., Iacovelli, F., Falconi, M., Cardamone, F., MOROZZO DELLA ROCCA, B., de Oliveira, C., et al. (2016). A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56(5), 941-949 [10.1021/acs.jcim.5b00586].

A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra

Iacovelli, F;FALCONI, MATTIA;MOROZZO DELLA ROCCA, BLASCO;DESIDERI, ALESSANDRO
2016-05-23

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.
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore BIO/11
English
Alves, C., Iacovelli, F., Falconi, M., Cardamone, F., MOROZZO DELLA ROCCA, B., de Oliveira, C., et al. (2016). A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56(5), 941-949 [10.1021/acs.jcim.5b00586].
Alves, C; Iacovelli, F; Falconi, M; Cardamone, F; MOROZZO DELLA ROCCA, B; de Oliveira, C; Desideri, A
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2108/144567
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