Controlling Electron Rebound within Four‐Base π‐Stacks in Z‐DNA by Changing the Sugar Moiety from Deoxy‐ to Ribonucleotide

Sannohe, Yuta; Kizaki, Seiichiro; Kanesato, Shuhei; Fujiwara, Ayaka; Li, Yue; Morinaga, Hironobu; Tashiro, Ryu; Sugiyama, Hiroshi

doi:10.1002/chem.201303930

Cited by 3 publications

(2 citation statements)

References 20 publications

(12 reference statements)

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“…8a). CGrepeated sequence-containing RNA can adopt a Z-form structure (55,56). In this structure, the uracil radical abstracts the C2 0 aH of ribose, resulting in the formation of the keto product (Fig.…”

Section: Formation Of the Ribose Residuementioning

confidence: 99%

Photoreaction of DNA Containing 5‐Halouracil and its Products^†

Tashiro

Sugiyama

2021

Photochem & Photobiology

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5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structuredependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groovebinder/DNA and protein/DNA complexes using a 5bromouracil-based electron transfer system is also described.

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Section: Formation Of the Ribose Residuementioning

confidence: 99%

Photoreaction of DNA Containing 5‐Halouracil and its Products^†

Tashiro

Sugiyama

2021

Photochem & Photobiology

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“…Ketone photochemistry, specifically the Norrish type I photoreaction, has most frequently been used to generate carbon π-radicals in these studies. This strategy has been expanded to nitrogen nucleobase radical generation via β-fragmentation of a photochemically generated carbon radical. − More often, aminyl and carbon σ-radicals are generated directly via one-electron reduction of alkyl azides and vinyl halides, respectively, as well as UV-photolysis of the latter. − Such precursors are also of interest as radiosensitizing agents for hypoxic cells. , Reduced O 2 levels in hypoxic cells enable the precursors to capture solvated electrons produced from ionizing radiation. In contrast to carbon π-type radicals, nitrogen and carbon σ-type radicals directly abstract hydrogen atoms from the 2′-deoxyribose backbone and/or add to nucleobase π-bonds to generate DNA-strand breaks and interstrand cross-links, respectively. ,,, A 2′-deoxycytidin- N 4-yl radical (dC·) is a nitrogen-centered σ-type iminyl radical produced as a result of oxidative stress in DNA. − Herein, we describe the use of oxime esters to generate dC· photochemically and via single electron transfer.…”

Section: Introductionmentioning

confidence: 99%

Photochemical and Single Electron Transfer Generation of 2′-Deoxycytidin-N4-yl Radical from Oxime Esters

Peng,

Vu,

Retes

et al. 2023

J. Org. Chem.

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A 2′-deoxycytidin-N4-yl radical (dC•), a strong oxidant that also abstracts hydrogen atoms from carbon−hydrogen bonds, is produced in a variety of DNA damaging processes. We describe here the independent generation of dC• from oxime esters under UV-irradiation or single electron transfer conditions. Support for this σ-type iminyl radical generation is provided by product studies carried out under aerobic and anaerobic conditions, as well as electron spin resonance (ESR) characterization of dC• in a homogeneous glassy solution at low temperature. Density functional theory (DFT) calculations also support fragmentation of the corresponding radical anions of oxime esters 2d and 2e to dC• and subsequent hydrogen atom abstraction from organic solvents. The corresponding 2′-deoxynucleotide triphosphate (dNTP) of isopropyl oxime ester 2c (5) is incorporated opposite 2′-deoxyadenosine and 2′-deoxyguanosine by a DNA polymerase with approximately equal efficiency. Photolysis experiments of DNA containing 2c support dC• generation and indicate that the radical produces tandem lesions when flanked on the 5′-side by 5′-d(GGT). These experiments suggest that oxime esters are reliable sources of nitrogen radicals in nucleic acids that will be useful mechanistic tools and possibly radiosensitizing agents when incorporated in DNA.

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Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids

Pandian¹,

Sugiyama²

2016

Bulletin of the Chemical Society of Japan

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In the natural cellular environment, nucleic acid biomolecules like DNA have biological implications via structural modifications and through precise coordination with other biomolecules in the local environment. Here, we detail the design of nature-inspired smart biomaterials that are based on the chemical biology of nucleic acids. N-Methylpyrrole (P) and N-methylimidazole (I) polyamides (PIPs), sequence-specific DNA-binding molecules have been, developed to image specific DNA sequences and to alter gene expression inside the living cells. The self-assembling feature of DNA was harnessed to achieve the programmed assembly of nanostructures with different dimensions. Also, the advanced DNA architectures with well-defined properties allowed the real-time visualization of the complicated single-molecule interactions, which in-turn provided vital intracellular mechanistic information. The molecular recognition properties of DNA were exploited to design biologically inspired hybrid catalysts for sustainable organic synthesis. Our review could serve as a guidebook for researchers who aim to develop nucleic acid-based synthetic biomaterials.

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Controlling Electron Rebound within Four‐Base π‐Stacks in Z‐DNA by Changing the Sugar Moiety from Deoxy‐ to Ribonucleotide

Cited by 3 publications

References 20 publications

Photoreaction of DNA Containing 5‐Halouracil and its Products^†

Photoreaction of DNA Containing 5‐Halouracil and its Products^†

Photochemical and Single Electron Transfer Generation of 2′-Deoxycytidin-N4-yl Radical from Oxime Esters

Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids

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Controlling Electron Rebound within Four‐Base π‐Stacks in Z‐DNA by Changing the Sugar Moiety from Deoxy‐ to Ribonucleotide

Cited by 3 publications

References 20 publications

Photoreaction of DNA Containing 5‐Halouracil and its Products†

Photoreaction of DNA Containing 5‐Halouracil and its Products†

Photochemical and Single Electron Transfer Generation of 2′-Deoxycytidin-N4-yl Radical from Oxime Esters

Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids

Contact Info

Product

Resources

About

Photoreaction of DNA Containing 5‐Halouracil and its Products^†

Photoreaction of DNA Containing 5‐Halouracil and its Products^†