Radical Intermediates during Reductive Electron Transfer through DNA

Varghese, Reji; Wagenknecht, Hans‐Achim

doi:10.1002/9780470526279.ch8

Cited by 3 publications

(5 citation statements)

References 94 publications

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“…The spin density plot of the fully optimized T-6H 2 O •– obtained using the B3LYP/6-31++G** method is shown in Figure , while the spin density plot for other optimized systems before and after electron transfer are also shown in Figure S2 in the Supporting Information. The optimized result for T-6H 2 O •– (Figure ) appears in direct contrast with the experimental fact that all DNA bases react at diffusion controlled rates with e aq – . − ,− ,− The unpaired electron spin distribution shown in Figure appears anomalous since the stable position for the electron is actually on the thymine, not in the water cavity as shown in the figure. However, this metastable state converts to the stable molecular arrangement when molecular dynamics induces the electron transfer as described below.…”

Section: Resultsmentioning

confidence: 75%

“…In a recent report, Abel and co-workers used the VDE (3.3 eV) for e aq – to interpret the binding of e aq – with nucleobases. − On the basis of the VDE, they concluded that e aq – should not bind with nucleobases (see Figures 4, 5, and 13 in refs– as nucleobases have electron affinities in the range of ca. 1.7–2.2 eV. , Their interpretation concerning the reactivity of e aq – with nucleobases is incorrect since it ignores the well-established experimental fact that the solvated electron, e aq – , efficiently adds to all the nucleobases. − ,,, These include many works using pulse radiolysis that report near diffusion-controlled reaction rates (3.8 × 10 9 M –1 s –1 to 1.8 × 10 10 M –1 s –1 ; see Table 10.6 in ref ) of e aq – with DNA/RNA components. , Moreover, as emphasized in this work, the addition of e aq – to the nucleobases should follow its AEA and not its VDE.…”

Section: Introductionmentioning

confidence: 99%

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Do Solvated Electrons (e_aq^–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study

et al. 2016

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The solvated electron (e-aq) is a primary intermediate after an ionization event that produces reductive DNA damage. Accurate determination of standard redox potentials (E°) of nucleobases and of e-aq determine the extent of reaction of e-aq with nucleobases. In this work, E° of e-aq and of nucleobases have been calculated employing the accurate ab initio Gaussian-4 theory including the polarizable continuum model (PCM). The Gaussian-4-calculated E° of e-aq (-2.86 V) is in excellent agreement with the experimental one (-2.87 V). The Gaussian-4-calculated E° of nucleobases in dimethylformamide (DMF) lie in the range (-2.36 V to -2.86 V); they are in reasonable agreement with the experimental E° in DMF and have a mean unsigned error (MUE) = 0.22 V. However, inclusion of specific water molecules reduces this error significantly (MUE= 0.07). Employing a model of e-aq-nucleobase complex with 6 water molecules, reaction of e-aq with the adjacent nucleobase is investigated using approximate ab initio molecular dynamics (MD) simulations including PCM. Our MD simulations show that e-aq transfers to uracil, thymine, cytosine and adenine, within 10 to 120 fs and e-aq reacts with guanine only when a water molecule forms a hydrogen bond to O6 of guanine which stabilizes the anion radical.

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Section: Resultsmentioning

confidence: 75%

Section: Introductionmentioning

confidence: 99%

Do Solvated Electrons (e_aq^–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study

et al. 2016

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“…The different quenching effects observed for the fluorescence of the 5-aza-7-deazaguanine and 7-deazaguanine pyrene conjugates most probably result from charge separation between the pyrene residues and the nucleobases (intramolecular electron transfer or hole transfer). It is reported that 7-deazapurine conjugates form a charge separated state with a nucleobase radical cation and a radical anion of pyrene. , A similar behavior is expected for 5-aza-7-deazapurine pyrene conjugates. The higher quantum yields of the 5-aza-7-deazapurine pyrene conjugates might result from a higher oxidation potential of the 5-aza-7-deazaguanine to 7-deazaguanine.…”

Section: Resultsmentioning

confidence: 99%

Nucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2′-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties

et al. 2019

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The special nucleobase recognition pattern of 5-aza-7-deazaguanine nucleosides makes them valuable for construction of homo purine DNA, silver-mediated base pairs, and expansion of the four letter genetic coding system. To widen the utility of 5-aza-7-deazaguanine nucleosides, side chains were introduced at position-7 of the nucleobase. As key compounds, 7-iodo nucleosides were synthesized. Nucleobase anion glycosylation of the iodo derivative of isobutyrylated 5-aza-7-deazaguanine with the bromo sugar of 2,3,5-tri-O-benzoyl-1-O-acetyl-d-ribofuranose gave the pure β-D anomeric N-9 glycosylation product (67%), whereas one-pot Vorbrüggen conditions gave only 42% of the iodinated nucleoside. The noniodinated nucleoside was formed in 84%. For the synthesis of 2′-deoxyribonucleosides, anion glycosylation performed with Hoffer’s 2′-deoxyhalogenose yielded an anomeric mixture (α-D = 33% and β-D = 39%) of 2′-deoxyribonucleosides. Various side chain derivatives were prepared from nonprotected nucleosides by Pd-assisted Sonogashira or Suzuki–Miyaura cross-coupling. Among the functionalized ribonucleosides and anomeric 2′-deoxyribonucleosides, some of them showed strong fluorescence. Benzofuran and pyrene derivatives display high quantum yields in non-aqueous solvents and solvatochromism. Single-crystal X-ray analysis of 7-iodo-5-aza-7-deaza-2′-deoxyguanosine displayed intermolecular iodo–oxygen interactions in the crystal and channels filled with solvent molecules.

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“…The suggestion that DNA might be a molecular wire 3 spurred applications of fast-detection optical methods to further advance our understanding of charge separation (CS) in DNA. 4 But advances in understanding EET have lagged that of hT, 4a, b, 5 in part because the quantum yield for EE obtained by photochemical injection is very small, ~10 −3 6 due, in part, to charge recombination with the electron donor. This problem does not arise in EPR studies of trapped EE, where a covalently bound electron donor does not supply the attached electron.…”

Section: Introductionmentioning

confidence: 99%

“…4b, 5 Anderson and Wright studied CT using the reaction of aqueous electrons generated by pulse radiolysis at RT. They determined transfer distances of ≤ 3–7 bp which are governed by a free energy of activation of ≥ 26 kJ mol −1 .…”

Section: Introductionmentioning

confidence: 99%

Excess Electron Trapping in Duplex DNA: Long Range Transfer via Stacked Adenines

Black

Bernhard

2012

J. Phys. Chem. B

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An understanding of charge transfer (CT) in DNA lies at the root of assessing the risks and benefits of exposure to ionizing radiation. Energy deposition by high-energy photons and fast charged particles creates holes and excess electrons (EE) in DNA and the subsequent reactions determine the complexity of DNA damage and ultimately the risk of disease. Further interest in CT comes from the possibility that hole transfer and/or excess electron transfer (EET) in DNA might be used to develop nanoscale circuits. In order to study EET in DNA, EPR spectroscopy was used to determine the distribution of EE trapping by oligodeoxynucleotides irradiated and observed at 4K. Our results indicate that stretches of consecutive adenine bases on the same strand serve as an ideal conduit for intrastrand EET in duplex DNA at 4K. Specifically, we show that A is an efficient trap for EE at 4K if, and only if, the A strand of the duplex does not contain one of the other three bases. If there is a T, C, or G on the A strand, trapping occurs at T or C instead of A. This holds true for stretches up to 32 A’s. While T competes effectively against A for the EE, it does not compete effectively against C. Long stretches of T pass the majority of EE to C. Our results show that AT stretches channel EE to cytosine, an endpoint with significance to both radiation damage and the photochemical repair of pyrimidine dimers.

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Radical Intermediates during Reductive Electron Transfer through DNA

Cited by 3 publications

References 94 publications

Do Solvated Electrons (e_aq^–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study

Do Solvated Electrons (e_aq^–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study

Nucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2′-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties

Excess Electron Trapping in Duplex DNA: Long Range Transfer via Stacked Adenines

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Radical Intermediates during Reductive Electron Transfer through DNA

Cited by 3 publications

References 94 publications

Do Solvated Electrons (eaq–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study

Do Solvated Electrons (eaq–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study

Nucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2′-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties

Excess Electron Trapping in Duplex DNA: Long Range Transfer via Stacked Adenines

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Do Solvated Electrons (e_aq^–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study

Do Solvated Electrons (e_aq^–) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study