Interbase electronic coupling for transport through DNA

Abstract

We develop a new approach to derive single state tight binding (SSTB) model for electron transport in the vicinity of valence-conduction bands of poly(G)-poly(C) and poly(A)-poly(T) DNA. The SSTB parameters are derived from first principles and are used to model charge transport through finite length DNA. We investigate the rigor of reducing the full DNA Hamiltonian to SSTB model to represent charge transport in the vicinity of valence-conduction band. While the transmission coefficient spectrum is preserved, its position shifts in energy. Thymine is poorly represented and its peak height is substantially reduced. This is attributed to the abstraction of the HOMO-LUMO coupling to other eigen-states in the nearest neighbor DNA bases, and can be corrected within 2 nd order time independent perturbation theory. Inter-strand charge transport has also been analyzed and it is found that hopping to the nearest neighbor in the complementary strand is the most important process except in the valence band of poly(G)-poly(C), where hopping to the second nearest neighbor between 3 ′ −ends is the most dominant process. As a result, transport between 3 ′ −ends and 5 ′ −ends in the vicinity of valence band of polyG-polyC is asymmetric.

Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy

“…The figure demonstrates that the counterions (green curve) indeed contribute new empty electron states in the gap between the G (∼−0.5 eV) and the C (∼2 eV) peaks, with a very low DOS relative to the G and C features, yet a finite number of discrete levels scattered throughout the G-C gap and roughly centred around 1 eV. Let us now discuss why the Na + levels, which are a direct output of our calculations, may help explain the observations, contrary to unsatisfactory attempts that are based only on the ground-state electronic structure on G and C. Ab initio DFT electronic structure calculations of G-rich DNA polymers usually report a π-π * G-C energy gap of ∼2−3 eV, depending on the exact polymer sequence and computational details 23,24,30,31 , consistent with our findings. Taking into account that ground-state DFT results underestimate the gap between occupied and unoccupied states by as much as 100% and even more, the measurement of an average fundamental gap of ∼2.5 eV (Table 1) cannot be explained naively in terms of a G-C gap, because the theoretical prediction should be shifted to roughly 5-6 eV.…”

“…In the latter case, the nature of the electron states is known from the ab initio calculations: however, only those states that are included in the model will play a role. For instance, if we assume that only the bases 30 contribute to the electron tunnelling with no role of the backbone and counterions, this assumption will affect the results.…”

Electrical Conductance in Biological Molecules

“…These works were successful in qualitatively (and sometimes even quantitatively) describing numerous experimental data (see, for example, [42,56,57,82,83] and the references therein) on transfer of injected single holes (or injected single electrons) through DNA duplexes. Such a kind of "tight-binding philosophy" has been analyzed in detail in the work [84] . This work studies homooligonucleotides with regular sequences (dA) n -(dT) n and Thus, the nucleotides as the "tight-binding sites" are just reduced here to hydrogen atoms.…”

Interband optical transitions in DNA-like systems

“…1 Much earlier, it was predicted by theoretical calculations. 16 Effective Hamiltonian models, based on the tight-binding approximation, [17][18][19][20][21][22][23][24][25][26][27] provide a reasonable description of the semiconductor gap observed in experiments. In this contribution we point out that the underlying electronic band structure with full valence band and empty conduction band suggests that interband optical transitions can occur in DNA.…”