Modeling the bandstructures of B-DNA base stacks

Abstract

A pseudohelical approximation for the calculation of the bandstructures of DNA base homostacks in B conformation is introduced. It consists of choosing a unit cell of only two nucleobases with relative parallel displacement and twist that locally mimic the helical conformation. It is tested employing the extended Hückel method with a unique Wolfsberg-Helmholtz parameter. The resulting bandgaps and ionization potential trend agree well with the ones reported in the literature employing the full screw-axis symmetry and higher levels of theory. The electron and hole effective masses extracted from the bandstructures follow the same trends as the experimentally reported mobilities

Length-independent transport rates in biomolecules by quantum mechanical unfurling

“…Previous work on DNA bridges (poly-A, in particular) has shown that the hole orbitals tend to delocalize over several nucleobases in such structures. 10 , 12 , 17 , 19 , 29 – 32 Indeed, the inclusion of long range correlations within a stepwise kinetic model (the variable range hopping model 22 ) significantly improved the success of the hopping model to describe weak length dependence of the rate for transport through long (⪆10 base pairs) bridges. 22 , 30 Moreover, the possibilities of coherent hole scattering 33 – 37 or ballistic transport of hole wave packets 38 , 39 through DNA bridges were attributed to the presence of delocalized states in a band-like electronic structure.…”

“…Nevertheless, an approximate glimpse into the electronic structure of long DNA molecules can be based on their local building blocks and the interactions between them. 29 , 42 – 47 Neighboring nucleobases in DNA are coupled via local π-stacking interactions imposed by the double helix structure, where the local ionization potential (hole energy) and the inter-base coupling depend on the relative orientation between the nucleobases. 29 , 42 – 47 The positively charged DNA is represented below as a tight-binding ladder molecular Hamiltonian.…”

“… 29 , 42 – 47 Neighboring nucleobases in DNA are coupled via local π-stacking interactions imposed by the double helix structure, where the local ionization potential (hole energy) and the inter-base coupling depend on the relative orientation between the nucleobases. 29 , 42 – 47 The positively charged DNA is represented below as a tight-binding ladder molecular Hamiltonian. 31 , 33 , 34 The model takes explicit account of the building blocks of the double stranded DNA, [5′-G(T) N GGG-3′] + .…”

Early Events in Radiobiology: Isolated and Cluster DNA Damage Induced by Initial Cations and Nonionizing Secondary Electrons

“…35,36,41 A more quantitative analysis of the transmission curves of Figure 1 is possible by estimating electron transmission and reflection coefficients at the vacuum interface and the band structure of the DNA film (Supporting Information). 35,42,43 As shown in the Supporting Information, positive hole currents are 3.4 and 4.5 larger than the incident electron current at 60 and 100 eV, respectively (i.e., for every electron entering the film there are 3.4 and 4.5 holes created, which corresponds to 6.8 and 9 ionizations per plasmid, respectively). This simple transmission measurement indicates that most holes (i.e., cations) are trapped and do not recombine with electrons in our f ilms, within the time scale (50 ms) of the measurements (Supporting Information).…”

“…Consequently, the large difference between curve A of Figure and the others (curves B–D) result essentially from electron scattering from DNA molecules and the transmission coefficients of electrons coming in and out of the film at the vacuum interface . , The transmission method and the underlying phenomena have been amply explained in the literature. ,, A more quantitative analysis of the transmission curves of Figure is possible by estimating electron transmission and reflection coefficients at the vacuum interface and the band structure of the DNA film (Supporting Information). ,, As shown in the Supporting Information, positive hole currents are 3.4 and 4.5 larger than the incident electron current at 60 and 100 eV, respectively (i.e., for every electron entering the film there are 3.4 and 4.5 holes created, which corresponds to 6.8 and 9 ionizations per plasmid, respectively). This simple transmission measurement indicates that most holes (i.e., cations) are trapped and do not recombine with electrons in our films, within the time scale (50 ms) of the measurements (Supporting Information).…”