Degradation of Cytosine Radical Cations in 2′-Deoxycytidine and in i-Motif DNA: Hydrogen-Bonding Guided Pathways

Wang, Yinghui; Zhao, Hongmei; Yang, Chunfan; Jie, Jialong; Dai, Xiaolin; Zhou, Qian; Liu, Kunhui; Song, Dong Joo; Su, Hongmei

doi:10.1021/jacs.8b10743

Cited by 23 publications

(30 citation statements)

References 50 publications

(125 reference statements)

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“…Ou et al studied the influence of X-ray on DNA chemical structure using SERS [79,106]. Various radiation doses (6,10,15, and 20 Gy) and cell incubation times following radiation (0, 24, 48, and 72 h) were applied, to determine the chemical modifications of DNA following X-ray exposure. For SERS enhancement, DNA isolated from the nasopharyngeal carcinoma cell line (CNE2) was mixed with Ag nanoparticles.…”

Section: Sersmentioning

confidence: 99%

“…In addition to the molecule conformation, the structure in general defines the susceptibility to DNA damage formation. Therefore, studies of DNA damage should involve various DNA forms including double helical DNA as well as the physiologically relevant four-stranded DNA structures like G-quadruplexes or i-Motifs (iM) [8][9][10]. DNA conformation plays a significant role in the susceptibility to DNA damage and repair processes [6,7].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Spectroscopic Markers of DNA Damage

Sofińska¹,

Wilkosz²,

Szymoński³

et al. 2020

Molecules

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Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of each eukaryotic cell, is stored in the DNA. In this review, we describe spectroscopic markers of DNA damage, which can be detected by infrared, Raman, surface-enhanced Raman, and tip-enhanced Raman spectroscopies, using data acquired from DNA solutions and mammalian cells. Various physical and chemical DNA damaging factors are taken into consideration, including ionizing and non-ionizing radiation, chemicals, and chemotherapeutic compounds. All major spectral markers of DNA damage are presented in several tables, to give the reader a possibility of fast identification of the spectral signature related to a particular type of DNA damage.

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Section: Sersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular Spectroscopic Markers of DNA Damage

Sofińska¹,

Wilkosz²,

Szymoński³

et al. 2020

Molecules

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show abstract

“…Methods. 1 H and 13 C NMR spectra were recorded on a Bruker Avance II spectrometer at 300 and 75 MHz, respectively, at 25 °C. Experiments with tandem mass and photodissociation action spectra were performed on a modified amaZon speed 3D ion trap tandem mass spectrometer (Bruker Daltonik, Bremen, Germany) equipped with an EKSPLA NL301G Nd-YAG laser (Altos Photonics, Bozeman, MT, USA) working at 20 Hz frequency and 3 to 6 ns pulse width, as described in detail previously.…”

Section: ■ Introductionmentioning

confidence: 99%

The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine

et al. 2020

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Noncanonical nucleobases and nucleosides represent newly discovered species of relevance for DNA ionization. We report a targeted synthesis of gas-phase 9-methylene(1H)adenine cation radical (2 +• ) as a low-energy isomer of ionized 9methyladenine. Ion 2 +• showed unique collision-induced dissociation and UV−vis photodissociation action spectra that distinguished it from other cation radical isomers. Ab initio energy calculations with coupled cluster theory extrapolated to the complete basis set limit, CCSD(T)/CBS, identified cation radical 2 +• as the global energy minimum of the adenine-related C 6 H 7 N 5 +• isomers. The action spectrum of 2 +• was assigned on the basis of vibronic absorption spectra that were calculated with timedependent density functional theory for multiple vibrational configurations of thermal ions. The major dissociation of 2 +• proceeded by hydrogen loss that was elucidated by deuterium labeling at the exchangeable N-1 and NH 2 positions and C-8 position and by kinetic analysis. The dissociation involved a reversible rearrangement to intermediate dihydropteridine structures, yielding a protonated aminopteridine as the product, which was identified by multistep UV−vis action spectroscopy. We also report a computational study of related noncanonical isomers of 2′-deoxyadenosine cation radical having the radical defect at C-1′ that were found to be thermodynamically more stable than the canonical isomer in both the gas phase and aqueous solution. The noncanonical isomers were calculated to have extremely low ion−electron recombination energies of 4.42−5.10 eV that would make them dead-end hole traps if produced by DNA ionization.

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“…Here phase transformation between the perforated nanovesicle and nanovesicle was achieved through changes in the system temperature. Supramolecular nanoaggregates that are driven by hydrogen bonding interactions have also attracted much attention 40–44 . The hydrogen bonding force is influenced by temperature, pH and solvent polarity; therefore, stimuli‐responsive supramolecular nanostructures can be prepared by employing molecules with hydrogen bonds, with potential applications in various materials, such as memory and self‐healing materials 45–49 …”

Section: Introductionmentioning

confidence: 99%

Construction of nanoaggregates from amphiphilic supramolecules containing barbiturate and Hamilton wedge units

Lü

Deng

Zhong

et al. 2021

Polymer International

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The study of supramolecular morphology is gaining significant attention. This may be attributed to the fact that nanostructures of aggregates have been found to significantly influence the photoelectronic properties of supramolecular materials. In this study, the self‐assembling behaviour of rod–coil molecules with barbiturate (Ba) or Hamilton wedge (Hw) units and the supramolecule Ba‐Hw was investigated. In chloroform solution, molecule Hw consisted of an oligo‐ethylene chain with degree of polymerization of 17 as well as biphenyl, phenyl and Hw units. Ba molecules incorporated octyloxy, biphenyl, phenyl and Ba groups that self‐organized into nanofibres with different diameters. Supramolecular amphiphile Hw‐Ba self‐aggregated into different sizes of nanosheet‐like aggregates. In a dimethylsulfoxide/H2O (1:19 v/v) mixed polar solvent, molecules Hw and Ba aggregated into twist‐shaped and nanosheet aggregates, while the supramolecular Hw‐Ba aggregated into larger‐size microtubes. Experimental results obtained for these molecular assemblies suggest that combining Ba and Hw units by employing hydrogen bonds is an effective strategy for forming amphiphilic supramolecules. Compared with the individual rod–coil molecules Ba and Hw, supramolecule Hw‐Ba has stronger π–π intermolecular forces due to the presence of more planar Hw‐Ba building blocks, which form various supramolecular assemblies with less curvature than the rigid and flexible surfaces of the original molecules. © 2021 Society of Industrial Chemistry.

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Degradation of Cytosine Radical Cations in 2′-Deoxycytidine and in i-Motif DNA: Hydrogen-Bonding Guided Pathways

Cited by 23 publications

References 50 publications

Molecular Spectroscopic Markers of DNA Damage

Molecular Spectroscopic Markers of DNA Damage

The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine

Construction of nanoaggregates from amphiphilic supramolecules containing barbiturate and Hamilton wedge units

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