Charge Separation in DNA via Consecutive Adenine Hopping

Takada, Tadao; Kawai, Kiyoshi; Cai, Xichen; Sugimoto, Akihiro; Fujitsuka, Mamoru; Majima, Tetsuro

doi:10.1021/ja035730w

Cited by 151 publications

(230 citation statements)

References 41 publications

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“…In many experiments characterizing DNA CT, a shallow distance dependence in the reaction has been demonstrated (1)(2)(3)(4)(5)(6)(7)(8), and this shallow distance dependence has been explained through models primarily involving long-range diffusive charge-hopping (15,16,34). Models involving a mixture of hopping among low-energy guanine sites and tunneling through AT tracts provided a useful starting point for reconciling many experiments.…”

Section: Discussionmentioning

confidence: 99%

“…Models involving a mixture of hopping among low-energy guanine sites and tunneling through AT tracts provided a useful starting point for reconciling many experiments. Once experiments demonstrated rapid, long-range DNA CT across assemblies containing adenine tracts (5,7,34,35), the model was modified to include also hopping on low-energy adenines (18). These models, however, consistently explain DNA CT in the context solely of base energetics.…”

Section: Discussionmentioning

confidence: 99%

“…charge transport ͉ delocalized domain ͉ radical trap ͉ base dynamics O xidative damage to DNA from a distance through longrange migration of charge has now been established in many DNA assemblies by using different pendant photooxidants through both biochemical and spectroscopic assays (1)(2)(3)(4)(5)(6)(7)(8). The DNA base pair stack can mediate charge transport (CT) over at least 200 Å (2,3), and the reaction is exquisitely sensitive to the dynamic structure and stacking within the DNA duplex (9,10).…”

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confidence: 99%

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Long-range oxidative damage to cytosines in duplex DNA

Shao

O’Neill²,

Barton³

2004

Proc. Natl. Acad. Sci. U.S.A.

140

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Charge transport (CT) through DNA has been found to occur over long molecular distances in a reaction that is sensitive to intervening structure. The process has been described mechanistically as involving diffusive charge-hopping among low-energy guanine sites. Using a kinetically fast electron hole trap, N4-cyclopropylcytosine ( CP C), here we show that hole migration must involve also the higher-energy pyrimidine bases. In DNA assemblies containing either [Rh(phi)2(bpy )] 3؉ or an anthraquinone derivative, two highenergy photooxidants, appreciable oxidative damage at a distant CP C is observed. The damage yield is modulated by lower-energy guanine sites on the same or complementary strand. Significantly, the efficiency in trapping at CP C is equivalent to that at N2-cyclopropylguanosine ( CP G). Indeed, even when CP G and CP C are incorporated as neighboring bases on the same strand, their efficiency of photodecomposition is comparable. Thus, CT is not simply a function of the relative energies of the isolated bases but instead may require orbital mixing among the bases. We propose that charge migration through DNA involves occupation of all of the DNA bases with radical delocalization within transient structure-dependent domains. These delocalized domains may form and break up transiently, facilitating and limiting CT. This dynamic delocalized model for DNA CT accounts for the sensitivity of the process to sequence-dependent DNA structure and provides a basis to reconcile and exploit DNA CT chemistry and physics.charge transport ͉ delocalized domain ͉ radical trap ͉ base dynamics O xidative damage to DNA from a distance through longrange migration of charge has now been established in many DNA assemblies by using different pendant photooxidants through both biochemical and spectroscopic assays (1-8). The DNA base pair stack can mediate charge transport (CT) over at least 200 Å (2, 3), and the reaction is exquisitely sensitive to the dynamic structure and stacking within the DNA duplex (9, 10). This sensitivity to perturbations in base pair stacking has been advantageous in the development of DNA-based sensors for mutational analysis (11) and may provide a role for DNAmediated CT within the cell (12), but it has limited the application of physical techniques to explore CT mechanistically.Although not a robust molecular wire, the DNA duplex has in some experiments been characterized as a wide band gap semiconductor (13,14). More prevalent have been models of incoherent CT involving a mixture of localized charge-hopping among low-energy sites, guanines and sometimes adenines, and tunneling through higher-energy pyrimidine bases (15-18). These mechanisms do not provide a rationale, however, for the sensitivity of CT to DNA structure. We have observed that DNA CT is gated by the dynamical motions of the DNA bases (9, 19) and have described DNA CT as conformationally gated hopping through transient, well stacked DNA domains (20).Our experimental strategy to probe for hole density on pyrimidines exploits the rapid ...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Long-range oxidative damage to cytosines in duplex DNA

Shao

O’Neill²,

Barton³

2004

Proc. Natl. Acad. Sci. U.S.A.

140

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“…Nanosecond transient absorption measurements were performed by using the LFP technique (31,35). The third-harmonic oscillation (355 nm, full width at half maximum of 4 ns, 20 mJ per pulse) from a Q-switched neodymium-doped yttrium aluminum garnet (Nd:YAG) laser (Surelight, Continuum, Santa Clara, CA) was used to excite the NI site selectively because NI showed strong absorption around 355 nm ( 355 Ϸ 8 ϫ 10 3 M Ϫ1 ⅐cm Ϫ1 ) and PTZ showed no absorption at wavelengths longer than 320 nm (32). A xenon flash lamp (XBO-450, Osram, Berlin) was focused into the sample solution as the probe light for the transient absorption measurement.…”

Section: Methodsmentioning

confidence: 99%

“…Previously, we demonstrated that the adenine hopping (Ahopping) occurred very rapidly (Ͼ10 8 s Ϫ1 ) and can be applied to generate a long-lived charge-separated state in DNA (31,32). Accordingly, it is expected that a long-lived hole escaped from charge recombination can be generated effectively in DNA by using the A-hopping mechanism, which enables us to observe the hole-transfer process occurring in the much slower time scale.…”

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confidence: 99%

Direct observation of hole transfer through double-helical DNA over 100 Å

Takada

Kawai

Fujitsuka

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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161

177

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Mechanism of photo-induced electron transfer and the subsequent hole transfer in DNA has been studied extensively, but so far we are not aware of any reliable report of the observation of the long-distance hole-transfer process. In this article, we demonstrate the results of direct observation for the long-distance hole transfer in double-helical DNA over 100 Å with time-resolved transient absorption measurements. DNA conjugated with naphthalimide (NI) and phenothiazine (PTZ) (which worked as electron-acceptor and donor molecules, respectively) at both 5 ends was synthesized to observe the hole-transfer process. Site-selective charge injection into G by means of the adenine-hopping process was accomplished by excitation of NI with a 355-nm laser flash. Transient absorption around 400 nm, which was assigned to the NI radical anion, was observed immediately after the irradiation of a laser flash, indicating that the charge separation between NI and the nearest G occurred. Then, the transient absorption of the PTZ radical cation (PTZ •؉ ) at 520 nm was emerged, which was attributed to the hole transfer through DNA to the PTZ site. By monitoring the time profiles of the transient absorption of PTZ •؉ for NI-A6-(GA)n-PTZ and NI-A6-(GT)n-PTZ (n ‫؍‬ 2, 3, 4, 6, 8, 12) (base sequences correspond to those for DNA modified with NI), the long-distance hole-transfer process from G to PTZ, which occurred in the time scale of microsecond to millisecond, was observed directly. By assuming an average distance of 3.4 Å between base-pairs, total distance reaches 100 Å for n ‫؍‬ 12 sequences. Our results clearly show the direct observation of the long-distance hole transfer over 100 Å.D ouble-helical DNA, which has unique structural properties, is a promising candidate for molecular electronic devices and a scaffold for two-and three-dimensional nanostructures (1, 2). Mechanistic studies of charge transfer in DNA have attracted considerable attention because of their relevance to the development of DNA molecular wires (3) and the involvement in DNA oxidative lesion and strand cleavage (4, 5). There are many mechanistic studies for the ''one-dimensional'' conductivity in the double helix (6-8). Factors controlling charge-transfer properties in DNA (such as electronic coupling between donor and acceptor, structural dynamics, reorganization energy, etc.) have been discussed (9-14), and the mechanism for charge transfer, especially hole transfer over long distances in DNA, is the subject of experimental and theoretical studies.Generally, experimental studies of charge transfer in DNA have been performed by time-resolved measurements and electrophoresis analysis (15)(16)(17)(18)(19). A model of a multistep holehopping mechanism, which was proposed by Giese and coworkers (20), is the most widely adopted. An alternative mechanism in which delocalized hole migrates by means of a polaron-like mechanism was proposed by Schuster and coworkers (18). Strand-cleavage studies using PAGE analysis have provided valuable information about the seque...

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Kinetics of Long‐Range Oxidative Electron Transfer through DNA

Kawai

Majima

2009

Radical and Radical Ion Reactivity in Nucleic Acid Chemistry

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Charge Separation in DNA via Consecutive Adenine Hopping

Cited by 151 publications

References 41 publications

Long-range oxidative damage to cytosines in duplex DNA

Long-range oxidative damage to cytosines in duplex DNA

Direct observation of hole transfer through double-helical DNA over 100 Å

Kinetics of Long‐Range Oxidative Electron Transfer through DNA

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