A Hole and One.
Ontology highlight
ABSTRACT:
SUBMITTER: Suliman A
PROVIDER: S-EPMC8712989 | biostudies-literature | 2021 Dec
REPOSITORIES: biostudies-literature
Publications
A Hole and One.
Suliman Asem A Al-Mousawy Saif S Safajou Nesar N Salehian Omid O
CASE (Philadelphia, Pa.) 20210909 6
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Project description:The distance of hole migration through DNA determines the degree to which radiation-induced lesions are clustered. It is the degree of clustering that confers to ionizing radiation its high toxicity. The migration distance is governed by a competition between hole transfer and irreversible trapping reactions. An important type of trapping is reactions that lead to the formation of deoxyribose radicals, which are precursors to free base release (fbr). Using HPLC, fbr was measured in X-irradiated films of d(CGCGCGCGCG)(2) and d(CGCGAATTCGCG)(2) as well as three genomic DNAs: M. luteus, calf thymus, and C. perfringens. The level of DNA hydration was varied from Gamma = 2.5 to 22 mol waters/mol nucleotide. The chemical yields of each base, G(base), were measured and used to calculate the modification factor, M(base). This factor compensates for differences in the GC/AT ratio, providing a measure of the degree to which a given base influences its own release. In the DNA oligomers, M(Gua) > M(Cyt), a result ascribed to the previously observed end effect in short oligomers. In the highly polymerized genomic DNA, we found that M(Cyt) > M(Gua) and that M(Thy) is consistently the smallest of the M factors. For these same DNA films, the yields of total DNA trapped radicals, G(tot)(fr), were measured using EPR spectroscopy. The yield of deoxyribose radicals was calculated using G(dRib)(fr) = approximately 0.11 x G(tot)(fr). Comparing G(dRib)(fr) with total fbr, we found that only about half of the fbr is accounted for by deoxyribose radical intermediates. We conclude that for a hole on cytosine, Cyt(*+), base-to-base hole transfer competes with irreversible trapping by the deoxyribose. In the case of a hole on thymine, Thy(*+), base-to-base hole transfer competes with irreversible trapping by methyl deprotonation. Close proximity of Gua protects the deoxyribose of Cyt but sensitizes the deoxyribose of Thy.
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Project description:The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S- )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G.+ -P(S- )=S. The ionization potential of G-P(S- )=S was calculated to be slightly lower than that of guanine in 5'-dGMP. Subsequent thermally activated hole transfer from G.+ to P(S- )=S led to dithiyl radical (P-2S. ) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S- )=S concentrations showed a bimolecular conversion of P-2S. to the σ2 -σ*1 -bonded dimer anion radical [-P-2S -. 2S-P-]- [ΔG (150 K, DFT)=-7.2 kcal mol-1 ]. However, [-P-2S -. 2S-P-]- formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=-1.4 kcal mol-1 ]. Neither P-2S. nor [-P-2S -. 2S-P-]- oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.
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Project description:Low dimensional semiconducting structures with strong spin-orbit interaction (SOI) and induced superconductivity attracted great interest in the search for topological superconductors. Both the strong SOI and hard superconducting gap are directly related to the topological protection of the predicted Majorana bound states. Here we explore the one-dimensional hole gas in germanium silicon (Ge-Si) core-shell nanowires (NWs) as a new material candidate for creating a topological superconductor. Fitting multiple Andreev reflection measurements shows that the NW has two transport channels only, underlining its one-dimensionality. Furthermore, we find anisotropy of the Landé g-factor that, combined with band structure calculations, provides us qualitative evidence for the direct Rashba SOI and a strong orbital effect of the magnetic field. Finally, a hard superconducting gap is found in the tunneling regime and the open regime, where we use the Kondo peak as a new tool to gauge the quality of the superconducting gap.
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Project description:The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.
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Project description:We investigate the relationships between open-shell character and longitudinal static second hyperpolarizabilities γ for one-hole-doped diradicaloids using the strong-correlated ab initio molecular orbital methods and simple one-dimensional (1D) three-site two-electron (3s-2e) models. As examples of one-hole-doped diradicaloids, we examine H3 +, methyl radical trimer cation ((CH3)3 +), silyl radical trimer cation ((SiH3)3 +), and 1,2,3,5-dithiadizolyl trimer cation (DTDA3 +). For H3 +, the static γ exhibits negative values and shows a monotonic increase in amplitude with an increase in the open-shell character defined by a neighbor-site interaction (y S). On the other hand, it is found for (CH3)3 +, (SiH3)3 +, and DTDA3 + that the static γ value exhibits similar behavior to that for H3 + up to an intermediate y S value, while it takes the negative maximum at a large y S value, followed by a decrease in γ amplitude, and subsequently, γ changes to positive values with a drastic increase for larger y S values. For example, in DTDA3 +, the negative/positive γ values, -69 × 105/700 × 105 au at y S = 0.75/0.87, exhibit significant enhancements in amplitude, 2.4/24 times as large as that (-29 × 105 au) at intermediate y S = 0.59 as is often the case in DTDA2. Using the 1D 3s-2e valence-bond configuration interaction model, these sign inversions and drastic increase in the amplitude of γ are found to originate in the differences in Coulomb interactions between valence electrons, between valence and core electrons, and between valence electrons and nuclei. These results contribute to pave the way for the construction of novel control guidelines for the amplitude and sign of γ for one-hole-doped diradicaloids.
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Project description:The increasing efficiency of the inorganic-organic hybrid halides has revolutionised photovoltaic research. Despite this rapid progress, the significant issues of poor stability and toxicity have yet to be suitably overcome. In this article, we use Density Functional Theory to examine (Pb2I6) · (H2DPNDI) · (H2O) · (NMP), an alternative lead-based hybrid inorganic-organic solar absorber based on a photoactive organic cation. Our results demonstrate that optical properties suitable for photovoltaic applications, in addition to spatial electron-hole separation, are possible but efficient charge transport may be a limiting factor.
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Project description:BackgroundEpithelia act as physical barriers protecting living organisms and their organs from the surrounding environment. Simple epithelial tissues have the capacity to efficiently repair wounds through a resealing mechanism. The known molecular mechanisms underlying this process appear to be conserved in both vertebrates and invertebrates, namely the involvement of the transcription factors Grainy head (Grh) and Fos. In Drosophila, Grh and Fos lead to the activation of wound response genes required for epithelial repair. ERK is upstream of this pathway and known to be one of the first kinases to be activated upon wounding. However, it is still unclear how ERK activation contributes to a proper wound response and which molecular mechanisms regulate its activation.Methodology/principal findingsIn a previous screen, we isolated mutants with defects in wound healing. Here, we describe the role of one of these genes, hole-in-one (holn1), in the wound healing process. Holn1 is a GYF domain containing protein that we found to be required for the activation of several Grh and Fos regulated wound response genes at the wound site. We also provide evidence suggesting that Holn1 may be involved in the Ras/ERK signaling pathway, by acting downstream of ERK. Finally, we show that wound healing requires the function of EGFR and ERK signaling.Conclusions/significanceBased on these data, we conclude that holn1 is a novel gene required for a proper wound healing response. We further propose and discuss a model whereby Holn1 acts downstream of EGFR and ERK signaling in the Grh/Fos mediated wound closure pathway.
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