Competitive Electron Scavenging by Chemically Modified Pyrimidine Bases in Bromine-Doped DNA:  Relative Efficiencies and Relevance to Intrastrand Electron Migration Distances

Razskazovskii, Y.V.; Swarts, Steven G; Falcone, Joseph M.; Taylor, and Craig; Sevilla, Michael D.

doi:10.1021/jp9630941

Cited by 82 publications

(78 citation statements)

References 63 publications

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“…78 Here, it is also worth emphasizing that both the AEA E (0.49 and 2.27 eV) calculated in the gas phase and in solution and the gas-phase VDE (1.02 eV) for BrU (see Table 2) remain in good agreement with those obtained at the B3LYP/6-31+G(d) level by Li et al, who estimated these values to be 0.51, 2.44, and 1.21 eV, respectively. 48 The small discrepancy between our values and the ones in the literature may be due to differences in the BrU structures compared: our calculations refer to 5-bromo-1-methyluracil, while Li et al reported data for unsubstituted BrU.…”

Section: Resultsmentioning

confidence: 99%

Electron-Induced Elimination of the Bromide Anion from Brominated Nucleobases. A Computational Study

2012

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The enhancement of radiodamage to DNA labeled with halonucleobases is attributed to the reactive radical produced from a halonucleobase by the attachment of an electron. We examined at the B3LYP/6-31++G** level electron capture by four brominated nucleobases (BrNBs): 8-bromo-9-methyladenine, 8-bromo-9-methylguanine, 5-bromo-1-methylcytosine, and 5-bromo-1-methyluracil followed by the release of the bromide anion and a nucleobase radical. We demonstrate that neutral BrNBs in both gas and aqueous phases are better electron acceptors than unsubstituted NBs and that resulting anion radicals, BrNBs(•-), can easily transform into the product complex of the bromide anion and the nucleobase radical ([Br(-)···NB(•)]). The overall thermodynamic stimulus for the process starting with the neutral BrNB and ending with the isolated bromide anion and the NB(•) radical is similar in the case of all four BrNBs studied, which suggests their comparable radiosensitizing capabilities.

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Section: Resultsmentioning

confidence: 99%

Electron-Induced Elimination of the Bromide Anion from Brominated Nucleobases. A Computational Study

2012

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“…It has long been known that electrons and holes created by ionizing radiation can have a range of many base pairs (2). Recent results suggest that these carriers migrate over distances greater than 30 bases at room temperature (3). However, these results were apparently not considered evidence that electrons and holes introduced by other means could migrate relatively freely over the base-pair stack.…”

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confidence: 99%

Polarons in DNA

Conwell

Rakhmanova²

2000

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

327

258

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Many experiments have been done to determine how far and how freely holes can move along the stack of base pairs in DNA. The results of these experiments are usually described in terms of a parameter ␤ under the assumption that it describes an exponential decay with distance. The reported values range from ␤ < 0.2͞Å to ␤ > 1.4͞Å. For the larger values of ␤, the transport can be accounted for as single step superexchange-mediated hole transfer. To account for the smaller values, hopping models have been proposed, the simplest being nearest-neighbor hopping. This model assumes that, between hops, the hole is localized on a single base with no overlap to neighbors. Noting that an electron or hole added to a DNA stack, as to other essentially one-dimensional entities, should distort its structure to form a polaron, Schuster and coworkers It is generally, although perhaps not universally, believed that DNA has no free carriers in its thermal equilibrium state because of the gap of many eV (1 eV ϭ 1.602 ϫ 10 Ϫ19 J) between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Electrons (radical anions) or holes (radical cations) may be introduced by ionizing radiation, injection from contacts, photoinduced electron transfer involving an impurity, etc. Of particular interest has been the transport of electrons and holes along the stack of base pairs. The process is important, because radical migration through DNA may play a crucial role in mutagenesis and carcinogenesis. The suggestion that the -interaction between the base pairs could support extended transport was made almost 40 years ago (1). It has long been known that electrons and holes created by ionizing radiation can have a range of many base pairs (2). Recent results suggest that these carriers migrate over distances greater than 30 bases at room temperature (3). However, these results were apparently not considered evidence that electrons and holes introduced by other means could migrate relatively freely over the base-pair stack.Particularly in the last decade, many different experiments have been carried out to determine the range of a hole on the base-pair stack. In a frequently used technique, photoexcitation of an acceptor associated with the stack in some fashion, sometimes intercalated, allows transfer of an electron, usually from a guanine (G) base, leaving a hole on the stack. In some experiments, the migrating hole is trapped at a GG step on the stack, and its range is determined by observing strand cleavage at the trap site (4, 5). In other experiments, the range is determined by observation of fluorescence quenching of a donor intercalated in the stack (6-8).On the expectation of the electron or hole transfer decreasing exponentially with distance R according to exp(Ϫ␤R), as predicted by Marcus theory, the observed penetration distance for the hole was described in terms of a parameter ␤. ␤ values ranging from greater than 1.4 Å Ϫ1 to less than 0.1 Å Ϫ1 have been reported. Values from 1.2 Å Ϫ1 to 1.6 Å Ϫ1

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“…Избыточные электроны (анион-радикалы) или дырки (катион-радикалы) могут вноситься в ДНК либо в результате фотовозбуждения при облучении молекулы в ультрафиолетовой области, либо в результате химических реакций или введения специального типа примесей [1][2][3][6][7][8]. Рассматривается также возможность переноса протонов в ДНК [9].…”

Section: ключевые слова: днк акцептор донор дырка моделирование unclassified

Dynamics of Charge Transfer in Ordered and Chaotic Nucleotide Sequences

Fialko¹

2006

Math.Biol.Bioinf.

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Аннотация. Исследуется перенос заряда в системах, состоящих из донора, акцептора и мостиковых сайтов -(АТ) нуклеотидных пар. Для мостика из 180 (АТ) пар рассматриваются три случая: однородный, когда все нуклеотиды в каждой нити ДНК одинаковы; регулярный, когда через равное число (АТ) пар встречаются (ТА) пары, и нерегулярный -когда мостик состоит из случайно разбросанных (АТ) и (ТА) пар. Показано, что во всех случаях есть перенос с донора на акцептор. При одинаковых условиях перенос наиболее эффективен в случае однородного полинуклеотида, затем по убыванию -для регулярной и неупорядоченной цепочки. Результаты расчетов согласуются с экспериментальными данными по переносу заряда в ДНК на большие расстояния. Ключевые слова: ДНК, акцептор, донор, дырка, моделирование, уравнение Шредингера.Проблема переноса заряда в биомакромолекулах, в частности, в ДНК, в настоящее время входит в число наиболее важных задач молекулярной биофизики и биохимии, и ей посвящено множество как теоретических, так и экспериментальных работ [1−9].Идея о том, что ДНК обладает проводящими свойствами, была выдвинута давно. Вскоре после определения структуры ДНК -двойной спирали -было предположено, что, благодаря упорядоченному расположению нуклеотидов в стопке, ДНК может проводить заряд [10]. Две нити ДНК можно рассматривать как цепочки, состоящие из нуклеотидных оснований: аденина (А), гуанина (G), цитозина (C) и тимина (T), с разными энергиями ионизации и интегралами перекрытия соседних оснований.Сейчас считается уже установленным, что молекула ДНК в равновесном состоянии не имеет свободных переносчиков заряда. Избыточные электроны (анион-радикалы) или дырки (катион-радикалы) могут вноситься в ДНК либо в результате фотовозбуждения при облучении молекулы в ультрафиолетовой области, либо в результате химических реакций или введения специального типа примесей [1][2][3][6][7][8]. Рассматривается также возможность переноса протонов в ДНК [9]. Однако особый интерес для исследований представляет перенос электронов и дырок вдоль цепи пар оснований, потому что передвижение радикалов сквозь молекулу ДНК, возможно, играет решающую роль в процессах мутагенеза и канцерогенеза. Кроме того, понимание механизма переноса заряда необходимо для развития новой области -молекулярных компьютеров на основе ДНК.Возможность экспериментального изучения переноса заряда по фрагментам ДНК появилась сравнительно недавно, что связано, с одной стороны, с разработкой нано-и фемтосекундной техники, и с другой -с развитием биохимических методов * fialka@impb.psn.ru ** lak@impb.psn.ru

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Competitive Electron Scavenging by Chemically Modified Pyrimidine Bases in Bromine-Doped DNA: Relative Efficiencies and Relevance to Intrastrand Electron Migration Distances

Cited by 82 publications

References 63 publications

Electron-Induced Elimination of the Bromide Anion from Brominated Nucleobases. A Computational Study

Electron-Induced Elimination of the Bromide Anion from Brominated Nucleobases. A Computational Study

Polarons in DNA

Dynamics of Charge Transfer in Ordered and Chaotic Nucleotide Sequences

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