title: Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.
abstract: Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.
authors: Departamento de Química Inorgánica, Orgánica y Bioquímica, Facultad de Medicina, Universidad de Castilla-La Mancha, Albacete, Spain.
authors: José Ramón
authors: JR
authors: Blas
authors: Oscar
authors: O
authors: Huertas
authors: Carolina
authors: C
authors: Tabares
authors: Bobby G
authors: BG
authors: Sumpter
authors: Miguel
authors: M
authors: Fuentes-Cabrera
authors: Modesto
authors: M
authors: Orozco
authors: Pablo
authors: P
authors: Ordejón
authors: F Javier
authors: FJ
authors: Luque
mesh_terms: D004247:DNA / Q000737:chemistry*; D004579:Electron Transport; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011789:Quantum Theory
chemical_list: D004247:DNA