Direct measurement of hole transport dynamics in DNA

Lewis, Frederick D.; Liu, Xiaoyang; Liu, Jian‐Qin; Miller, Scott E.; Hayes, Rachel M.; Wasielewski, Michael R.

doi:10.1038/35017524

Cited by 346 publications

(380 citation statements)

References 20 publications

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“…Oscillatory frequencies in the range 10 7 to 10 11 s −1 have been reported [18][19][20]. Single strands have been observed to be less conductive than double strands [2], which agrees with the circuit model prediction because only double strands constitute closed circuits in each grid, allowing for proper conduction.…”

Section: Model Discussion and Predictionssupporting

confidence: 74%

Stepwise oscillatory circuits of a DNA molecule

2009

J Biol Phys

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A DNA molecule is characterized by a stepwise oscillatory circuit where every base pair is a capacitor, every phosphate bridge is an inductance, and every deoxyribose is a charge router. The circuitry accounts for DNA conductivity through both short and long distances in good agreement with experimental evidence that has led to the identification of the so-called super-exchange and multiple-step hopping mechanisms. However, in contrast to the haphazard hopping and super-exchanging events, the circuitry is a well-defined charge transport mechanism reflecting the great reliability of the genetic substance in delivering electrons. Stepwise oscillatory charge transport through a nucleotide sequence that directly modulates the oscillation frequency may have significant biological implications.

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Section: Model Discussion and Predictionssupporting

confidence: 74%

Stepwise oscillatory circuits of a DNA molecule

2009

J Biol Phys

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“…21,22 By analyzing the detailed kinetics of electron transfer reactions, Lewis, Wasielewski and co-workers determined the rate constants of forward-and back-transfer from single G to a GG doublet and a GGG triplet. 23,24 The free energy values for these reversible hole transfer reactions are ~ − 0.052 V and −0.077 V, respectively. The rate constants for oxidation of isolated guanines vs. 5′-guanines in a GG sequence context was elucidated by Sistare et al using an electrochemical method.…”

Section: Introductionmentioning

confidence: 99%

Oxidation of Guanine in G, GG, and GGG Sequence Contexts by Aromatic Pyrenyl Radical Cations and Carbonate Radical Anions: Relationship between Kinetics and Distribution of Alkali-Labile Lesions

et al. 2008

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Oxidatively generated DNA damage induced by the aromatic radical cation of the pyrene derivative 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), and by carbonate radicals anions, was monitored from the initial one-electron transfer, or hole injection step, to the formation of hot alkali-labile chemical end-products monitored by gel electrophoresis. The fractions of BPT molecules bound to double-stranded 20-35-mer oligonucleotdes with noncontiguous guanines G, and grouped as contiguous GG and GGG sequences, were determined by a fluorescence quenching method. Utilizing intense nanosecond 355 nm Nd: Yag laser pulses, the DNA-bound BPT molecules were photoionized to BPT •+ radicals by a consecutive two-photon ionization mechanism. The BPT •+ radicals thus generated within the duplexes selectively oxidize guanine by intraduplex electron transfer reactions, and the rate constants of these reactions follow the trend 5′-..GGG.. > 5′-..GG.. > 5′-..G… In the case of CO 3 •− radicals, the oxidation of guanine occurs by intermolecular collision pathways and the bimolecular rate constants are independent of base sequence context. However, the distributions of the end-products generated by CO 3 •− radicals, as well as by BPT •+ , is base sequence context-dependent and is greater than in isolated guanines at the 5′-G in 5′-…GG… sequences, and the first two 5′-guanines in the 5′-..GGG sequences. These results help to clarify the conditions that lead to a similar or different base sequence dependence of the initial hole injection step and the final distribution of oxidized, alkalilabile guanine products. In the case of the intermolecular one-electron oxidant CO 3 •− , the rate constant of hole injection is similar for contiguous and isolated guanines, but the subsequent equilibration of holes by hopping favors trapping and product formation at contiguous guanines, and the sequence dependence of these two phenomena are not correlated. In contrast, in the case of the DNA bound oxidant BPT •+ , the hole injection rate constants, as well as hole equilibration, exhibit a similar dependence on base sequence context, and are thus correlated to one another.

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“…the dynamics of holes in DNA, was studied intensely in the late nineties and onwards. It was rapidly established that holes can travel long distances [17,18], via a hopping mechanism between trapping sites. Trapped holes couple to lattice distortions forming polarons [19], and preferentially localise in guanine-rich regions, although they appear to be delocalised over a few bases rather than on a single one [20].…”

Section: Radiation Damage Of Dnamentioning

confidence: 99%

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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Abstract. DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts from the interaction of radiation -either photons or swift ions -with the biological medium. Such interactions cause electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, in particular strand breaks in plasmid DNA [1]. These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage.In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.

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Direct measurement of hole transport dynamics in DNA

Cited by 346 publications

References 20 publications

Stepwise oscillatory circuits of a DNA molecule

Stepwise oscillatory circuits of a DNA molecule

Oxidation of Guanine in G, GG, and GGG Sequence Contexts by Aromatic Pyrenyl Radical Cations and Carbonate Radical Anions: Relationship between Kinetics and Distribution of Alkali-Labile Lesions

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

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