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

Several assemblies of guanine molecules are investigated by means of first-principle 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 pi orbitals in adjacent guanine molecules. pi-pi 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 bandstructure 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.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.

The triple helix: 50 years later, the outcome

Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us

Toward Resolving Model-Measurement Discrepancies of Radon Entry into Houses

Analysis of the literature indicated that radon transport models significantly and consistently underpredict the advective entry into houses of soil-gas borne radon. Advective entry is the dominant mechanism resulting in high concentrations of radon indoors. The author investigated the source of the model-measurement discrepancy via carefully controlled field experiments conducted at an experimental basement located in natural soil in Ben Lomond, California. Early experiments at the structure confirmed the existence and magnitude of the model-measurement discrepancy, ensuring that it was not merely an artifact of inherently complex and poorly understood field sites. The measured soil-gas entry rate during structure depressurization was found to be an order of magnitude larger than predicted by a current three-dimensional numerical model of radon transport. The exact magnitude of the discrepancy depends on whether the arithmetic or geometric mean of the small-scale measurements of permeability is used to estimate the effective permeability of the soil. This factor is a critical empirical input to the model and was determined for the Ben Lomond site in the typical fashion using single-probe static depressurization measurements at multiple locations. The remainder of the dissertation research tests a hypothesis to explain the observed discrepancy: that soil permeability assessed using relatively small-scale probe measurements does not reflect bulk soil permeability for flows that is likely to occur at larger scales of several meters or more in real houses and in the test structure. The idea is that soil heterogeneity is of a nature that, as flows occur over larger scales, larger scales of heterogeneity are encountered that facilitate larger flux rates, resulting in a scale dependence of effective soil permeability