Positional Dependence of DNA Hole Transfer Efficiency in Nucleosome Core Particles

Sun, Huabing; Zheng, Liwei; Yang, Kun; Greenberg, Marc M.

doi:10.1021/jacs.9b03686

Cited by 13 publications

(23 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The spectrum in Figure 1A shows a large central doublet due to an isotropic β-proton HFCC value of H2′ at 51.5 G, a triplet from an axially symmetric anisotropic aminyl 14 N (spin = 1) HFCC (A zz (A ∥ ) = 40.5 G, A ⊥ = A xx = A yy = 0 G), along with g ∥ = 2.0020 and g ⊥ = 2.0043 (see also Figure 2A and Table 1). The anisotropic 14 N HFCC and the g values agree with those of aminyl radicals reported in the literature. 7−9,17−29 Based on these results, the green spectrum in Figure 1A is assigned to U(C2′)-14 ND•.…”

Section: ■ Resultssupporting

confidence: 87%

Site of Azido Substitution in the Sugar Moiety of Azidopyrimidine Nucleosides Influences the Reactivity of Aminyl Radicals Formed by Dissociative Electron Attachment

et al. 2020

View full text Add to dashboard Cite

In this work, electron-induced site-specific formation of neutral π-type aminyl radicals (RNH·) and their reactions with pyrimidine nucleoside analogs azidolabeled at various positions in the sugar moiety, e.g., at 2′-, 3′-, 4′-, and 5′- sites along with a model compound 3-azido-1-propanol (3AZPrOH), were investigated. Electron paramagnetic resonance (EPR) studies confirmed the site and mechanism of RNH· formation via dissociative electron attachment-mediated loss of N2 and subsequent facile protonation from the solvent employing the 15N-labeled azido group, deuterations at specific sites in the sugar and base, and changing the solvent from H2O to D2O. Reactions of RNH· were investigated employing EPR by warming these samples from 77 K to ca. 170 K. RNH· at a primary carbon site (5′-azido-2′,5′-dideoxyuridine, 3AZPrOH) facilely converted to a σ-type iminyl radical (RN·) via a bimolecular H-atom abstraction forming an α-azidoalkyl radical. RNH· when at a secondary carbon site (e.g., 2′-azido-2′-deoxyuridine) underwent bimolecular electrophilic addition to the C5C6 double bond of a proximate pyrimidine base. Finally, RNH· at tertiary alkyl carbon (4′-azidocytidine) underwent little reaction. These results show the influence of the stereochemical and electronic environment on RNH· reactivity and allow the selection of those azidonucleosides that would be most effective in augmenting cellular radiation damage.

show abstract

Section: ■ Resultssupporting

confidence: 87%

Site of Azido Substitution in the Sugar Moiety of Azidopyrimidine Nucleosides Influences the Reactivity of Aminyl Radicals Formed by Dissociative Electron Attachment

et al. 2020

View full text Add to dashboard Cite

show abstract

“…After formation of the “hole” (i.e., the unpaired spin) via direct-type effect, the hole is localized on the guanine base via base-to-base and backbone-to-base hole transfer processes [30,31,38,39,43,44,45,46,66]. Reactions of the localized hole on the guanine base in DNA are schematically shown as well [29,30,31,43,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,69]. For successful formation of a neutral sugar radical, a rapid deprotonation must occur from the one-electron oxidized sugar–phosphate backbone before a competitive backbone-to-base hole transfer takes place [30,31,43,45,46].…”

Section: Figures Schemes and Tablementioning

confidence: 99%

“…A substantial volume of work has been focused on radiation-induced hole-mediated damage in DNA via the oxidation pathway, as this pathway may lead to cellular death [29,30,31,38,39,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68]. A fast base-to-base hole transfer process [29,30,31,38,39,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72] and backbone-to-base hole transfer process [30,31,38,39,43,…”

Section: Introductionmentioning

confidence: 99%

“…are the most stable hole localization sites after long range hole transfer [29,30,31,38,39,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72]. Previous laser spectroscopic measurements or the use of one-electron oxidants (SO 4 •− ), which had often been used to model the pathways involved in DNA damage via the direct effect, were not able to probe these dynamics immediately following the ionizing radiation [29,30,31,38,39,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

Denisov

Adhikary

et al. 2019

IJMS

View full text Add to dashboard Cite

Among the radicals (hydroxyl radical (•OH), hydrogen atom (H•), and solvated electron (esol−)) that are generated via water radiolysis, •OH has been shown to be the main transient species responsible for radiation damage to DNA via the indirect effect. Reactions of these radicals with DNA-model systems (bases, nucleosides, nucleotides, polynucleotides of defined sequences, single stranded (ss) and double stranded (ds) highly polymeric DNA, nucleohistones) were extensively investigated. The timescale of the reactions of these radicals with DNA-models range from nanoseconds (ns) to microseconds (µs) at ambient temperature and are controlled by diffusion or activation. However, those studies carried out in dilute solutions that model radiation damage to DNA via indirect action do not turn out to be valid in dense biological medium, where solute and water molecules are in close contact (e.g., in cellular environment). In that case, the initial species formed from water radiolysis are two radicals that are ultrashort-lived and charged: the water cation radical (H2O•+) and prethermalized electron. These species are captured by target biomolecules (e.g., DNA, proteins, etc.) in competition with their inherent pathways of proton transfer and relaxation occurring in less than 1 picosecond. In addition, the direct-type effects of radiation, i.e., ionization of macromolecule plus excitations proximate to ionizations, become important. The holes (i.e., unpaired spin or cation radical sites) created by ionization undergo fast spin transfer across DNA subunits. The exploration of the above-mentioned ultrafast processes is crucial to elucidate our understanding of the mechanisms that are involved in causing DNA damage via direct-type effects of radiation. Only recently, investigations of these ultrafast processes have been attempted by studying concentrated solutions of nucleosides/tides under ambient conditions. Recent advancements of laser-driven picosecond electron accelerators have provided an opportunity to address some long-term puzzling questions in the context of direct-type and indirect effects of DNA damage. In this review, we have presented key findings that are important to elucidate mechanisms of complex processes including excess electron-mediated bond breakage and hole transfer, occurring at the single nucleoside/tide level.

show abstract

“…In recent years, DNA ET studies have also attempted to elucidate how electrons travel through DNA in a living cell. 40,41 Our results on ET efficiency using cp G under crowded conditions indicate the possibility that DNA-mediated ET can work effectively inside living cells, especially in condensed liquid crystalline form.…”

mentioning

confidence: 80%

Evaluation of DNA-mediated electron transfer using a hole-trapping nucleobase under crowded conditions

et al. 2022

View full text Add to dashboard Cite

show abstract

Positional Dependence of DNA Hole Transfer Efficiency in Nucleosome Core Particles

Cited by 13 publications

References 53 publications

Site of Azido Substitution in the Sugar Moiety of Azidopyrimidine Nucleosides Influences the Reactivity of Aminyl Radicals Formed by Dissociative Electron Attachment

Site of Azido Substitution in the Sugar Moiety of Azidopyrimidine Nucleosides Influences the Reactivity of Aminyl Radicals Formed by Dissociative Electron Attachment

Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

Evaluation of DNA-mediated electron transfer using a hole-trapping nucleobase under crowded conditions

Contact Info

Product

Resources

About