Solvent Effects on the Suppression of Oxidative Decomposition of Guanines by Phenyl Group Attachment in Deoxyribonucleic Acid (DNA)

Yokojima, Satoshi; Yanoi, Wataru; Yoshiki, Norifumi; Kurita, Noriyuki; Tanaka, Shigenori; Nakatani, Kazuhiko; Okada, Akira

doi:10.1021/jp037845s

Cited by 4 publications

(15 citation statements)

References 69 publications

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“…Thus, it is considered that this free energy reduction is due to the removal of the solvent molecules. ( 22 ) This result agrees with the experimental one( 18 ) that the damage to guanines near the phenylated guanine is suppressed as follows. The phenyl group attachment to a guanine reduces the free energy of the hole on it, and thus, the hole is trapped there; therefore, the guanines near the phenylated guanine are less damaged.…”

Section: Introductionsupporting

confidence: 90%

“…( 42 ) These optimized parameters are expected to produce better results than the default ones implemented in the software;( 43 ) this expectation was confirmed in the case of the IP of the nucleosides. ( 22 ) We calculated the IP as the difference between the total energies after and before one electron is removed. For these calculations, we used the unrestricted HF (UHF) method.…”

Section: Methodsmentioning

confidence: 99%

“…This removal was found to reduce the free energy of the hole on the guanine. ( 22 ) This might sound paradoxical. That is, since a polar solvent usually reduces the free energies of ions, the removal of nearby solvent molecules might be expected to increase the free energy of the hole.…”

Section: Introductionmentioning

confidence: 99%

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Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent

et al. 2009

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We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explains this unexpected stabilization of a hole as follows. When some water molecules are removed, the attractive electrostatic interaction stabilizing the hole increases, and thus, the hole is stabilized. In order to design the hole energetics by a chemical modification of DNA, this mechanism has to be taken into account and can be used.

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Section: Introductionsupporting

confidence: 90%

Section: Methodsmentioning

confidence: 99%

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Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent

et al. 2009

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“…͑1͒ describes the mean field electron-electron ͑e-e͒ interaction, which is screened in the solvent by the polarizable and/or counterion surroundings that are crucial for the stability of DNA molecules. 3,21,22 Even under the dry condition there are still some counterions from the synthesizing procedure. So we adopt the screened Coulomb potential ͑SCP͒ continuum solvent model 23 PHYSICAL REVIEW B 72, 064304 ͑2005͒…”

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confidence: 99%

Trapping and hopping of bipolarons in DNA: Su-Schrieffer-Heeger model calculations

et al. 2005

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With the Su-Schrieffer-Heeger model involving the effects of solvent polarization and external electric field, we show that a bipolaron maybe more stable than two polarons when a dication is induced into a DNA stack. Under the high electric field, the dication can move quite a long distance through the DNA by a series of hopping process, partially losing its configuration instantaneously due to the nonadiabatic effects. DOI: 10.1103/PhysRevB.72.064304 PACS number͑s͒: 72.80.Le, 71.38.Ϫk, 87.14.Gg, 87.15.He Long-range charge transport in duplex DNA is of great importance for its relevance to both the blueprint of life 1,2 and the potential applications in molecular electronics. 3,4 It is found experimentally that a radical cation ͑hole͒ introduced into a duplex DNA oligomer in solution can migrate over distance before being trapped by reactions with water and/or molecular oxygen. [5][6][7] To explain the long-range charge transport in DNA, a phonon-assisted polaronlike hopping mechanism was put forward. 8 In that view, the radical cation is stabilized with a distortion of the DNA and its environment ͑water molecules and counterions͒.9 This model is supported by the detailed electrical transport measurements through DNA molecules, 10 in which the conduction is due to the thermal motion of small polarons. Ab initio calculations have also provided clear evidence for the formation of a small polaron involving the change of chemical bonds in each base pair as well as the positions of hydrogen and oxygen.11 With a Su-Schrieffer-Heeger ͑SSH͒ model similar to that used for conjugated polymers, 12,13 Conwell and Rakhmanova have showed that large polarons extended over 5-7 base pairs may exist in DNA.14 They have also found that the time required for polaron formation is of the order of picoseconds. 15 Bishop et al. recently studied the normal modes of polaron solutions to the Peyrard-Bishop-Holstein ͑PBH͒ model for DNA polymers. 16 What will happen when there is more than one charge, such as two cations or a dication, introduced into a duplex DNA oligomer? It has been argued that, as a result of the strong electron-lattice interaction, two polarons on a -conjugated chain coalesce into a bipolaron, which is a pair of like charges with an associated strong local geometry deformation.17 Whether a DNA double strand structure supports a bipolaron or two polarons needs theoretical clarification because it is an essential question directly relevant to experiments and applications.In this paper, we investigate the dication ͑two holes͒ trapping and hopping properties in a DNA molecule. We shall exploit the celebrated SSH model to incorporate the doublechain interaction in order to describe the DNA double strands of Watson-Crick ͑W-C͒ base pairs, G/C, C/G, A/T, and T/A. The SSH model has shown remarkable success in the study of the electronic conductivity and optical phenomena in systems. To include the effects of solvent polarization and external electric field on the DNA charge transfer, we modify the standard SSH model with t...

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“…͑1͒ describes the mean-field electron-electron ͑e-e͒ interaction, which is screened in the solvent by the polarizable and/or counterion surroundings that are crucial for the stability of DNA molecules. 3,38,39 So we adopt the screened Coulomb potential ͑SCP͒ continuum solvent model, 40…”

Section: Model and Methodsmentioning

confidence: 99%

Pathways of polaron and bipolaron transport in DNA double strands

Wei

Liu

Berakdar

et al. 2008

The Journal of Chemical Physics

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We investigate the pathways of polaron and bipolaron transports in DNA double strands with an extended Su-Schrieffer-Heeger model involving the effects of solvent polarization. We find that the long-range transport of polaron/bipolaron under high electric field at low temperature is the field-facilitated sequential tunneling through spatial-disordered potential barriers via multiple intrastrand and interstrand pathways. Although the interstrand pathways may be very active and effective in some DNA sequences, the intrastrand ones always dominate the charge transfer when the excess charge moves close to the final acceptor.

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Solvent Effects on the Suppression of Oxidative Decomposition of Guanines by Phenyl Group Attachment in Deoxyribonucleic Acid (DNA)

Cited by 4 publications

References 69 publications

Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent

Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent

Trapping and hopping of bipolarons in DNA: Su-Schrieffer-Heeger model calculations

Pathways of polaron and bipolaron transport in DNA double strands

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