Conformations of poly{G}–poly{C} π stacks with high hole mobility

Abstract

Charge transfer properties of DNA depend strongly on the stack conformation. In the present paper, we identify conformations of homogeneous poly-͕G͖-poly-͕C͖ stacks that should exhibit high charge mobility. Two different computational approaches were applied. First, we calculated the electronic coupling squared, V 2 , between adjacent base pairs for all 1 ps snapshots extracted from 15 ns molecular dynamics trajectory of the duplex G 15 . The average value of the coupling squared ͗V 2 ͘ is found to be 0.0065 eV 2 . Then we analyze the base-pair and step parameters of the configurations in which V 2 is at least an order of magnitude larger than ͗V 2 ͘. To obtain more consistent data, ϳ65 000 configurations of the ͑G:C͒ 2 stack were built using systematic screening of the step parameters shift, slide, and twist. We show that undertwisted structures ͑twistϽ 20°͒ are of special interest, because the stack conformations with strong electronic couplings are found for a wide range of slide and shift. Although effective hole transfer can also occur in configurations with twist= 30°and 35°, large mutual displacements of neighboring base pairs are required for that. Overtwisted conformation ͑twistജ 38°͒ seems to be of limited interest in the context of effective hole transfer. The results may be helpful in the search for DNA based elements for nanoelectronics.

π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

“…Accordingly, some complementary approaches would be welcome in order to get a more detailed picture of the optimal DNA stack configurations. 5,6,11 Spurred by these results, in the present work we shall study the physical role of collective twist motions of the bps which occur in a synchronized manner, giving rise to the emergence of helicoidal standing waves in the DNA duplex. The resulting structural patterns will be described in the framework of dynamical phyllotaxis, by focusing on the presence of long-range spatial correlation effects mediated by twist phonons coupling.…”

“…As a result, the -orbital overlapping is substantially reduced as compared to that corresponding to the optimal geometrical configuration ͓e.g., t = 0.047 eV for the previously considered ͑G:C͒ 2 stack in this case͔. 5 In addition, at physiological temperatures the relative orientation of neighboring bases becomes a function of time due to thermal fluctuations, thereby modifying their mutual overlapping in an oscillatory way. Accordingly, the electronic coupling between nucleobases is very sensitive to structural fluctuations and the Condon approximation is rather limited.…”

“…9 In fact, recent studies have revealed that transfer integral values are extremely sensitive to conformational fluctuations, so that the transport efficiency calculated ignoring dynamical effects can be underestimated by several orders of magnitude. 5,10 Thus, depending on the DNA sequence composition, its length and effective temperature, reported transfer integral values can vary over a relatively broad interval, ranging from t = 0.01 to t = 0.4 eV. 6,[11][12][13][14][15][16][17][18][19][20][21] These figures imply charge migration time scales within the range ប / t Ӎ 2 -66 fs for coherent tunneling.…”

“…Among all possible configurations of a given base pairs ͑bps͒ stack, the so-called eclipsed one ͑i.e., vanishing relative twist angle between neighboring bps͒ exhibits the strongest electronic coupling for charge transfer ͓e.g., t ‫ء‬ = 0.372 eV for a ͑G:C͒ 2 stack with an interplanar separation of 0.34 nm͔. 5 However, in the canonical B-DNA form, consecutive bps are twisted an angle 0 Ӎ / 5 at equilibrium conditions. As a result, the -orbital overlapping is substantially reduced as compared to that corresponding to the optimal geometrical configuration ͓e.g., t = 0.047 eV for the previously considered ͑G:C͒ 2 stack in this case͔.…”

“…9,33,34 In fact, recent quantum-mechanics/ molecular-dynamics studies of a duplex ͑GT͒ 15 oligomer have shown the presence of large fluctuations of t 2 ͑the magnitude determining the charge-transfer rate͒ about one order of magnitude larger than the averaged ͗t 2 ͘ value, occurring every 1 ps on the average. 5 Following this approach, a systematic study of those stack conformations leading to higher mobilities has been performed for several DNA duplex oligomers. 10 However, the analysis of the obtained molecular-dynamics snapshots does not provide a clear enough picture on the spatial stack structures showing the best hole mobility.…”