Anna Garbesi

G-quartet biomolecular nanowires

We present a first-principle investigation of quadruple helix nanowires, consisting of stacked planar hydrogen-bonded guanine tetramers. Our results show that long wires form and are stable in potassium-rich conditions. We present their electronic band structure and discuss the interpretation in terms of effective wide-band-gap semiconductors. The microscopic structural and electronic properties of the guanine quadruple helices make them suitable candidates for molecular nanoelectronics.

Ab initio study of model guanine assemblies: The role of π-π coupling and band transport

Several assemblies of guanine molecules are investigated by means of first-principles calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the

Porphyrin Intercalation in G4-DNA Quadruplexes by Molecular Dynamics Simulations

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Lyomesophases formed by the dinucleoside phosphate d(GpG)

orbitals in adjacent guanine molecules.

Chromonic lyomesophases formed by the self-assembly of the cyclic dinucleotide d(cGpGp)

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Self-assembled guanine ribbons as wide-bandgap semiconductors

coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The band structure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.

Biomolecular Electronic Devices Based on Self‐Organized Deoxyguanosine Nanocrystals

We investigated the intercalation of a porphyrin derivative (TMPyP) between guanine tetrads (G4-tetrads, G4ts) in 4-stranded G4-DNA oligomers by classical molecular dynamics simulations. Contrary to experimental evidence on very short oligomers that contain stabilizing cations, we find that TMPyP can stack with the G4-tetrads in the absence of interplane cations. A high TMPyP/G4t stoichiometric ratio of 1/2 induces strong deformations of the G4-quadruplexes. A lower ratio of 1/8 is better compatible with the helical conformation. When a TMPyP is accommodated between two tetrads, the stacking distance between the intercalated molecule and a G4-tetrad is approximately 4.3-4.7 A. We find that the possibility of regular TMPyP intercalation depends on the length of the quadruplex, on the stoichiometric ratio and on the edge termination motif.

A study of the structure of the lyomesophases formed by the dinucleoside phosphate d(GpG). An approach by X-ray diffraction and optical microscopy

Abstract The sodium salt of the dinucleoside phosphate d(GpG), dissolved in water, forms two mesophases which have been characterized, by optical microscopy, as being of the cholesteric (columnar chiral nematic, N∗) and hexagonal (M) type.

Stability and migration of metal ions in G4-wires by molecular dynamics simulations.

Abstract The cyclic dinucleotide d(cGpGp) undergoes a self-association process in water to give, first, columnar aggregates similar to the four-stranded helix of poly(G). Successively, at higher concentration, these aggregates self-organize to give a cholesteric and a hexagonal mesophase, the former of which appears only in biphasic systems. The self-assembly process in isotropic solution has been studied by CD spectroscopy and the structure of the mesophases was investigated by optical microscopy and X-ray diffraction.

Electron Channels in Biomolecular Nanowires

Abstract We present a first principle study about the stability and the electronic properties of a new biomolecular solid-state material, obtained by the self-assembling of guanine (G) molecules. We consider hydrogen-bonded planar ribbons in isolated and stacked configurations. These aggregates present electronic properties similar to inorganic wide-band gap semiconductors. The formation of Bloch-type orbitals is observed along the stacking direction, while it is negligible in the ribbon plane. Global band-like conduction may be affected by a dipole-field which spontaneously arises along the ribbon axis. Our results indicate that G-ribbon assemblies are promising materials for biomolecular nanodevices, consistently with recent experimental results.