Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk

Conron, Sarah M.; Thazhathveetil, Arun K.; Wasielewski, Michael R.; Burin, Alexander L.; Lewis, Frederick D.

doi:10.1021/ja106991f

Cited by 89 publications

(119 citation statements)

References 38 publications

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“…An average activation energy of 326 ± 6 meV was observed for T17-A monolayers. A similar value for E A was also found for T17, which is higher than previously reported for Nile blue monolayers 26,28 and similar constructs, 34,47,48 but closer to theoretically anticipated values for CT through DNA. 49,50 Laviron analysis of the T17-A monolayer was also performed and found to give similar rate results (see Supporting Information Figure 4).…”

Section: ■ Results and Discussionsupporting

confidence: 89%

The Electronic Influence of Abasic Sites in DNA

et al. 2015

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Abasic sites in DNA are prevalent as both naturally forming defects and as synthetic inclusions for biosensing applications. The electronic impact of these defects in DNA sensor and device configurations has yet to be clarified. Here we report the effect of an abasic site on the rate and yield of charge transport through temperature-controlled analysis of DNA duplex monolayers on multiplexed devices. Transport yield through the abasic site monolayer strongly increases with temperature, but the yield relative to an undamaged monolayer decreases with temperature. This is opposite to the increasing relative yield with temperature from a mismatched base pair, and these effects are accounted for by the unique structural impact of each defect. Notably, the effect of the abasic site is nearly doubled when heated from room temperature to 37 °C. The rate of transport is largely unaffected by the abasic site, showing Arrhenius-type behavior with an activation energy of ∼300 meV. Detailed abasic site investigation elucidates the electrical impact of these biologically spontaneous defects and aids development of biological sensors.

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Section: ■ Results and Discussionsupporting

confidence: 89%

The Electronic Influence of Abasic Sites in DNA

et al. 2015

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“…In the SH simulations of hole transfer in AAAA, the wave function of the hole remains localized to a single A for most of the time, which is the same appearance that is observed in BO simulations. The rate of next-neighbour hole transfer can be determined in such a case and amounts to ca 100 ns -1 , which is roughly an order of magnitude larger than the experimental estimates [101,102]. This discrepancy may be caused by the preliminary character of the SH implementation, which seems to require additional attention regarding the calculation of hopping probabilities and decoherence behaviour.…”

Section: Mfmentioning

confidence: 84%

A hybrid approach to simulation of electron transfer in complex molecular systems

Kubař

Elstner

2013

J. R. Soc. Interface.

130

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Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors.

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“…As described above, Lewis et al reported that the single-step hopping rate of HT was 4.3 × 10 9 and 1.2 × 10 9 s –1 for G-to-G and A-to-A, respectively. 19 Our research group found that the A-to-A hopping rate was 2 × 10 10 s –1 . 58 Therefore, it became clear that the hopping rate of the excess electron among consecutive T's is faster than the hole hopping rate among A's and G's.…”

Section: Excess Electron Transfer In Dnamentioning

confidence: 88%

“…Recently, Lewis and co-workers estimated the A-to-A and G-to-G hopping rates to be 1.2 × 10 9 and 4.3 × 10 9 s –1 , respectively, based on the direct observation of HT dynamics in a photosensitizing acceptor–DNA–donor system by transient absorption spectroscopy. 19 Thus, it can be concluded that the single step hole hopping time in A's or G's is on the order of several tens to hundreds of picoseconds.…”

Section: Hole Transfer In Dnamentioning

confidence: 99%