Analysis of the interband optical transitions: Characterization of synthetic DNA band structure

Abstract

We analyze the band structure and interband optical transitions in a dangling backbone ladder DNA model. Using this model, semiconducting synthetic poly͑G͒-poly͑C͒ DNA is studied by means of a tight-binding model traditionally used for transport studies. Numerical calculations for optical absorption spectra are also presented. By studying the eigenstates' symmetries in uniform and nonuniform DNA chains, we conclude that, in both cases, the transitions are almost vertical in K space. The optical gap turns out larger than the electronic one, and an indirect band gap electronic structure for this DNA model is revealed. The effects of the environment, which are relevant for the wet form of DNA, are taken into account by introducing disorder in the backbone levels. We demonstrate that they affect more the spectra in the case of parallel polarization of the incoming light ͑with respect to the molecule axis͒. In such a case, the closure of the gap appears for a large enough disorder. We also consider the natural helix DNA conformation and find unusual selection rules for interband optical transitions. We propose that a comparison between the obtained spectra and the experiments can provide an insight into the electronic band structure of DNA.

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

“…This procedure is important when environmentally induced effects are considered [29]. For example, the FLM can be reduced into an LM via a one-step renormalization procedure [53], or to an even simpler WM via a two-step renormalization procedure [54,55].…”

Influence of backbone on the charge transport properties of G4-DNA molecules: a model-based calculation

“…Figure 1(b) shows a schematic illustration of a fragment of the G4-DNA within the dangling backbone model. It is worth mentioning that similar models, including the dangling backbone sites, have been extensively adopted to investigate the transport properties of the dsDNA molecules [18][19][20][21][22][23], where the obtained results can provide a qualitative even quantitative explanation of the experimental data. We expect that the transport properties of the G4-DNA molecules can be analyzed in great detail within the framework of the effective tight-binding Hamiltonian given by equation (1).…”

“…Because of its negatively charged phosphates and its outmost location in the quadruple-helical structure, the backbone will be more easily affected by the environmental conditions than other parts of the G4-DNA. In aqueous buffer solutions, the backbone has a propensity to interact with counterions and solute molecules and these interactions can lead to variations in the on-site energies ν j,n [19,22,23,25]. Even for a dried G4-DNA, the backbone's conformation can be quite different in various experiments because a few counterions and water molecules may still randomly reside on the phosphates of the backbone.…”

“…It is now widely accepted that to understand the transport properties of DNA molecules one should consider the contributions coming from the backbone system and the environment [18][19][20][21][22][23]. Accordingly, in this paper we propose an effective tight-binding Hamiltonian, including the sugar-phosphate backbone, to mimic the G4-DNA and explicitly address the influence of backbone energetics on the charge transport properties of the G4-DNA for this model, where each base and backbone site contributes one orbital.…”

Energy structure and charge transport-transfer in molecular wires

“…This procedure is important when environmentally induced effects are considered [77]. For example, the FLM can be reduced into an LM via a one-step renormalization procedure [104], or to an even simpler WM via a two-step renormalization procedure [105,106].…”