Direct Measurement of the Dynamics of Excess Electron Transfer through Consecutive Thymine Sequence in DNA

Park, Man Jae; Fujitsuka, Mamoru; Kawai, Kiyoshi; Majima, Tetsuro

doi:10.1021/ja2068017

Cited by 69 publications

(84 citation statements)

References 41 publications

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“…In all cases, the absorption features due to the charge-separated state are formed within the first 5 ps. Thus, charge-hopping, which is known to occur on a much longer time scale of 10-100 ps (38,39), cannot explain the results. In all mCU a AU (4 − a) oligonucleotides, we observe not only the mC and A bleach but also a very strong bleach of the bridging base U.…”

mentioning

confidence: 81%

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

Bucher

Pilles

Carell

et al. 2014

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

115

139

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Base stacking in DNA is related to long-living excited states whose molecular nature is still under debate. To elucidate the molecular background we study well-defined oligonucleotides with natural bases, which allow selective UV excitation of one single base in the strand. IR probing in the picosecond regime enables us to dissect the contribution of different single bases to the excited state. All investigated oligonucleotides show long-living states on the 100-ps time scale, which are not observable in a mixture of single bases. The fraction of these states is well correlated with the stacking probabilities and reaches values up to 0.4. The longliving states show characteristic absorbance bands that can be assigned to charge-transfer states by comparing them to marker bands of radical cation and anion spectra. The charge separation is directed by the redox potential of the involved bases and thus controlled by the sequence. The spatial dimension of this charge separation was investigated in longer oligonucleotides, where bridging sequences separate the excited base from a sensor base with a characteristic marker band. After excitation we observe a bleach of all involved bases. The contribution of the sensor base is observable even if the bridge is composed of several bases. This result can be explained by a charge delocalization along a well-stacked domain in the strand. The presence of charged radicals in DNA strands after light absorption may cause reactions-oxidative or reductive damagecurrently not considered in DNA photochemistry.DNA photophysics | DNA damage | DNA electron transfer | ultrafast vibrational spectroscopy D NA photophysics is crucial for the understanding of lightinduced damage of the genetic code (1). The excited state of single DNA bases is known to decay extremely fast on the subpicosecond time scale, predominantly via internal conversion (2, 3). This ultrafast decay is assumed to suppress destructive decay channels, thereby protecting the DNA from photodamage and avoiding disintegration of the genetic information. In contrast to this ultrafast deactivation of single nucleobases, the biological relevant DNA strands show further long-living states (4, 5). Several explanations for these long-living states and the size of their spatial extent have been discussed in the literature (5-9). Delocalized excitons (9); excitons that decay to charge-separated states or neutral excimer states (10, 11); exciplexes located on two neighboring bases (5, 8, 12, 13); or even excited single bases, where steric interactions in the DNA strand impedes the ultrafast decay (14), have been proposed. Further computations suggest a decay of an initially populated delocalized exciton to localized neutral or charged excimer states (15-17). However, to our knowledge, a final understanding of the nature of these longliving states has not been reached. Related experiments were performed in the last decade to investigate charge transport processes in DNA, motivated by DNA electronics and oxidative damage (18,19). Charge ...

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mentioning

confidence: 81%

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

Bucher

Pilles

Carell

et al. 2014

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

115

139

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“…, [8] faster than that of HT in DNA. In EET, T is known to be a primal excess-electron carrier, whilst it has been suggested that cytosine (C) is not suitable as an excess-electron carrier because of the rapid protonation of CC À .…”

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confidence: 89%

“…[5][6][7][8][9] Several research groups have revealed that the excess electron can migrate through DNA by a hopping mechanism. [5][6][7][8] However, there remains only limited information on the rate constant for the hopping of excess electrons in DNA. In our previous paper, we showed that the excess electron can migrate through a consecutive sequence of thymine (T) with time constants of the order of 10 10 s…”

Section: Introductionmentioning

confidence: 99%

“…Various compounds have been used as photosensitizing electron donors. [9] In our previous paper, [8] we used the tetramer of thiophene (4T) as the photosensitizing electron donor because of its high donor-ability and well-established spectroscopic properties, which are favorable for a transient absorption spectroscopic study of EET in DNA. In the case of 4T, only T can be reduced upon photoexcitation of 4T to the singlet-excited state ( 1 4T*), because T possesses the highest reduction potential of the four natural nucleobases.…”

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confidence: 99%

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Excess‐Electron Injection and Transfer in Terthiophene‐Modified DNA: Terthiophene as a Photosensitizing Electron Donor for Thymine, Cytosine, and Adenine

Park

Fujitsuka

Kawai

et al. 2012

Chemistry A European J

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Excess-electron transfer (EET) in DNA has attracted wide attention owing to its close relation to DNA repair and nanowires. To clarify the dynamics of EET in DNA, a photosensitizing electron donor that can donate an excess electron to a variety of DNA sequences has to be developed. Herein, a terthiophene (3T) derivative was used as the photosensitizing electron donor. From the dyad systems in which 3T was connected to a single nucleobase, it was revealed that (1) 3T* donates an excess electron efficiently to thymine, cytosine, and adenine, despite adenine being a well-known hole conductor. The free-energy dependence of the electron-transfer rate was explained on the basis of the Marcus theory. From the DNA hairpins, it became clear that (1) 3T* can donate an excess electron not only to the adjacent nucleobase but also to the neighbor one nucleobase further along and so on. From the charge-injection rate, the possibilities of smaller β value and/or charge delocalization were discussed. In addition, EET through consecutive cytosine nucleobases was suggested.

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“…[4] In earlier studies it was shown that the replacement of the natural base pairs by non-hydrogen bonding base surrogates with extended aromatic surfaces such as phenanthrene could have beneficial conducting properties and could overcome the physico-chemical limitations of the natural nucleobases. [5] Regarding the reduction of such base surrogates the choice of the electron injector is crucial for the success of the experiments.…”

mentioning

confidence: 99%

Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates

Roethlisberger

Kaliginedi

Leumann

2017

Chemistry A European J

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The modulation of excess electron transfer (EET) within DNA containing a dimethylaminopyrene (C-AP) as an electron donor and 5-bromouracil ( Br dU) as a electron acceptor through phenanthrenyl pairs (phen-R) could be achieved by modifying the phenanthrenyl base surrogates with electron withdrawing and donating groups. Arranging the phenanthrenyl units to form a descending LUMO gradient increased the EET efficiency compared to the electron transfer through uniform LUMOs or an ascending LUMO gradient.The well-defined double helical structure of DNA with the linear arranged base pairs represents a suitable scaffold for charge transfer and is therefore subject to intense studies in DNA damage, [1] sensors [2] and applications in molecular electronics.[3]The reductive electron transfer also called excess electron transfer (EET) in DNA is a process that is directed through the lowest unoccupied molecular orbital (LUMO) of the DNA bases. Investigations elucidated that the charge transfer over longer distances occurs via electron hopping mostly through thymine bases (k = 10 10 s -1). [4] In earlier studies it was shown that the replacement of the natural base pairs by non-hydrogen bonding base surrogates with extended aromatic surfaces such as phenanthrene could have beneficial conducting properties and could overcome the physico-chemical limitations of the natural nucleobases.[5] Regarding the reduction of such base surrogates the choice of the electron injector is crucial for the success of the experiments. Investigations by Grigorenko et. al. revealed that pyrene ( Py dU, Ered* = -2.2 V vs NHE) [6] only enables a superexchange mechanism, whereas phenothiazine (PTZ, Ered* = -2.7 V vs SCE) [7] allowed to trigger the system into an electron hopping mechanism with a transport that spreads over longer distances.[5] A photoexcitable dimethyl amino-pyrenyl donor attached to a deoxyuracil ( AP dU, Ered* = -2.2 V vs NHE) [8] that exhibits suitable redox properties for long range charge transfer experiments was successfully used by Bätzner et. al. to inject an electron in hydroquinoline base surrogates. [9] In this study, we investigated the EET through DNA containing phenanthrenyl base surrogates with different reduction potentials and LUMO energy levels. It is believed that the electron transfer within DNA can be modulated by the installation of a potential energy gradient.[10] The predicted advantage of such a redox/LUMO gradient was envisioned to be the unidirectionality of the electron transfer and therefore a gain in efficiency. The installation of the different reduction potentials was deemed to be possible by the introduction of electron withdrawing (CN) and donating (NH2) groups at the 7-position of the phenanthrene (phen). The synthesis of the NH2 phen and phen phosphoramidites applicable for automated DNA synthesis was performed according to published procedures.[11] The introduction of a cyano group required a palladium catalyzed substitution of the intermediate 9 with copper-(I)-cyanide. Tritiylation and phosphiti...

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Direct Measurement of the Dynamics of Excess Electron Transfer through Consecutive Thymine Sequence in DNA

Cited by 69 publications

References 41 publications

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

Charge separation and charge delocalization identified in long-living states of photoexcited DNA

Excess‐Electron Injection and Transfer in Terthiophene‐Modified DNA: Terthiophene as a Photosensitizing Electron Donor for Thymine, Cytosine, and Adenine

Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates

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