Dynamics and Energetics of Single-Step Hole Transport in DNA Hairpins

Lewis, Frederick D.; Liu, Jian‐Qin; Zuo, Xiaobing; Hayes, Rachel M.; Wasielewski, Michael R.

doi:10.1021/ja029390a

Cited by 124 publications

(179 citation statements)

References 79 publications

(157 reference statements)

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“…Considering that the ionization potential of A is lower than that of T, the hole transfer for G-A-G sequence is expected to be faster than that for G-T-G sequence. Our results are in good agreement with the prediction, and similar results were reported in other photoinduced electron-transfer systems (26). In contrast, delocalization of a hole over several nucleobases may affect the holetransfer process (45).…”

Section: Direct Observation Of Hole-transfer Process Through Double-hsupporting

confidence: 93%

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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.

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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Section: Direct Observation Of Hole-transfer Process Through Double-hsupporting

confidence: 93%

“…Lewis et al (15) and Wasielewski and coworkers (26) reported the kinetic study of single-step hole transfer in DNA by means of time-resolved transient absorption measurements. They determined the hole-transfer rate from G to GG by monitoring the decay of stilbene radical anion.…”

mentioning

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.

161

177

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“…It is clear from these data that a radical cation injected into the DNA condensate leads to the formation of lesions at nearby guanines that are detected as strand cleavage. Moreover, the GG steps that are closer to the AQ react more frequently than those located farther away, which is characteristic of those cases where hopping of the radical cation from one GG step to the next (k hop ) is slower than its trapping at a GG step by reaction with H 2 O or O 2 (k trap ) (22,(28)(29)(30). For the condensates, this distance dependence is rather steep, falling Ϸ10-fold over a distance of 70 Å.…”

Section: Resultsmentioning

confidence: 98%

Effect of condensate formation on long-distance radical cation migration in DNA

Das

Schuster

2005

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

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Long-distance radical cation transport was studied in DNA condensates. Linearized pUC19 plasmid was ligated to an oligomer containing a covalently linked anthraquinone group and six regularly spaced GG steps, which serve as traps for the migrating radical cation. Treatment of the linear, ligated plasmid with spermidine results in formation of condensates that were detected by light scattering and observed by transmission electron microscopy. Irradiation of the anthraquinone group in the condensate causes long-distance charge migration, which is detected by reaction at the remote guanines. The efficiency of charge migration in the condensate is significantly less than it is for the corresponding oligomer in solution. This result is attributed to a lower mobility for the migrating radical cation in the condensate, which is caused by inhibited formation of charge-transfer-effective states.charge transfer ͉ oxidative damage I t is well known that DNA is damaged by reactive chemical species. Extensive studies have shown that the one-electron oxidation of an oligonucleotide in solution creates a nucleobase radical cation (electron ''hole'') that may migrate hundreds of angstroms through duplex DNA before it is irreversibly trapped by reaction with H 2 O or O 2 (1-3). Trapping occurs most commonly at a guanine, because it is the base with the lowest ionization potential (4), and this reaction leads to mutagenic products such as 8-oxoguanine (5-8). DNA within cells is tightly packed and does not closely resemble oligonucleotides in solution. An examination of radical-cation hopping through DNA in loosely organized nucleosome core particles showed that histone binding does not affect the pattern and extent of oxidation (9). However, it is not known how the long-distance radical-cation migration that is observed in oligonucleotides is affected by conversion of the DNA to a well ordered structure. We began the systematic investigation of this question by examining the reactions of radical cations that were specifically introduced into DNA condensates.Multivalent cations like spermine or spermidine and proteins such as polylysine initiate DNA condensation (10-14). DNA condensates are nanometer-scale particles formed by the collapse of extended DNA chains into compact, ordered structures containing a small number of molecules (15, 16). These structures are recognized as models that are useful for studying gene packing in viruses, bacteria, and eukaryotic cells (17).We prepared condensates formed from the linearized pUC19 plasmid (which contains 2,686 bp) that had been ligated to an oligonucleotide containing a covalently linked anthraquinone (AQ) group (for photoinitiated introduction of a radical cation) and a series of regularly spaced GG steps (as traps for the radical cation) (Fig. 1) (18). Dynamic light-scattering results and examination by transmission electron microscopy (TEM) shows that the ligated DNA sample is converted into condensates by the addition of spermidine. The condensates were irradiated with UV light (t...

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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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Dynamics and Energetics of Single-Step Hole Transport in DNA Hairpins

Cited by 124 publications

References 79 publications

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

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

Effect of condensate formation on long-distance radical cation migration in DNA

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

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