1
|
Metto M, Tesfaye A, Atlabachew M, Abebe A, Fentahun T, Munshea A. A Novel Poly(cytosine)-Based Electrochemical Biosensor for Sensitive and Selective Determination of Guanine in Biological Samples. ACS OMEGA 2024; 9:26222-26234. [PMID: 38911807 PMCID: PMC11191103 DOI: 10.1021/acsomega.4c01939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/16/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024]
Abstract
The novel poly(cytosine)-modified glassy carbon electrode-based electrochemical sensor was fabricated potentiodynamically for the detection of Guanine (G) in clinical and biological samples. The surface of the electrode was successfully activated by electropolymerization, and about a 7.5-fold current improvement due to modification was achieved. From the analysis of the dependence of peak current and peak potential on a scan rate, a higher R 2 for the peak current on the square root of scan rate (R 2 = 0.999) than the dependence of peak current on scan rate (R 2 = 0.982) indicated that the oxidation of G at poly(cytosine)/GCE was predominantly diffusion controlled. The oxidative peak response of the electrode revealed a high linear range of G concentration (0.1-200 μM) under optimized conditions. The detection limit and limit of quantification were 6.10 and 20.13 nM, respectively, associated with the %RSD of under 1%. The validation of the developed electrochemical sensor for the determination of G was investigated by analyzing human urine DNA and serum samples with spike recovery results in the range of 98.20-103.70% with the interferent recovery percentage in the range of 97.86-103.10% containing 50-300% of potential interferents. The newly designed sensor demonstrated the highest level of performance for the G detection in real samples.
Collapse
Affiliation(s)
- Melaku Metto
- Department
of Chemistry, College of Science, Bahir
Dar University, Bahir
Dar 6000, Ethiopia
- Department
of Chemistry, College of Natural and Computational Sciences, Injibara University, Injibara 6400, Ethiopia
| | - Alemu Tesfaye
- Department
of Chemistry, College of Science, Bahir
Dar University, Bahir
Dar 6000, Ethiopia
| | - Minaleshewa Atlabachew
- Department
of Chemistry, College of Science, Bahir
Dar University, Bahir
Dar 6000, Ethiopia
| | - Atakilt Abebe
- Department
of Chemistry, College of Science, Bahir
Dar University, Bahir
Dar 6000, Ethiopia
| | - Tihunie Fentahun
- Department
of Chemistry, College of Science, Bahir
Dar University, Bahir
Dar 6000, Ethiopia
| | - Abaineh Munshea
- Department
of Chemistry, College of Science, Bahir
Dar University, Bahir
Dar 6000, Ethiopia
| |
Collapse
|
2
|
Wang Y, Liu L, Gao Y, Zhao J, Liu C, Gong L, Yang Z. Development of a QM/MM(ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX(8-oxo-G) tetrad. Phys Chem Chem Phys 2023; 26:504-516. [PMID: 38084041 DOI: 10.1039/d3cp04357f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The rapid deprotonation of G˙+ in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G˙+ in the G-tetrad makes it a more suitable carrier for hole conduction. The QM/MM(ABEEM) combined method, which involves the integration of QM and the ABEEM polarizable force field (ABEEM PFF), was developed to investigate the deprotonation of neutral and cation free radicals in the G-tetrad and GGX(8-oxo-G) tetrad (xanthine and 8-oxoguanine dual substituted G-tetrad). By incorporating valence-state electronegativity piecewise functions χ*(r) and implementing charge local conservation conditions, QM/MM(ABEEM) possesses the advantage of accurately simulating charge transfer and polarization effect during deprotonation. The activation energy calculated by the QM method of X˙ is the lowest among other bases in the GGX(8-oxo-G) tetrad, which is supported by the computation of the average electronegativity calculated by ABEEM PFF. By utilizing QM/MM(ABEEM) with a two-way free energy perturbation method, the deprotonation activation energy of X˙ in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol-1, while that of G˙+ in the G-tetrad is 20.7 ± 0.6 kJ mol-1, consistent with the experimental measurement of 20 ± 1.0 kJ mol-1. These results manifest that X˙ in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G˙+ in the G-tetrad, suggesting that the GGX(8-oxo-G) tetrad may serve as a more favorable hole transport carrier. Furthermore, the unequal average electronegativities of bases in the GGX(8-oxo-G) tetrad impede the deprotonation rate. This study provides a potential foundation for investigating the microscopic mechanism of DNA electronic devices.
Collapse
Affiliation(s)
- Yue Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Linlin Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yue Gao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Jiayue Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Zhongzhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| |
Collapse
|
3
|
Masi A, Capobianco A, Bobrowski K, Peluso A, Chatgilialoglu C. Hydroxyl Radical vs. One-Electron Oxidation Reactivities in an Alternating GC Double-Stranded Oligonucleotide: A New Type Electron Hole Stabilization. Biomolecules 2023; 13:1493. [PMID: 37892175 PMCID: PMC10605094 DOI: 10.3390/biom13101493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
We examined the reaction of hydroxyl radicals (HO•) and sulfate radical anions (SO4•-), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO• to the G:C pair moiety, affording the [8-HO-G:C]• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H+):C]• after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.
Collapse
Affiliation(s)
- Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
- Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
| |
Collapse
|
4
|
Jin P, Wang JN, Wang X, Jia M, Pan H, Mei Y, Chen J. Tracking the Early Stage of Triplet-Induced Photodamage in a DNA Dimer and Oligomer Containing 5-Methylcytosine. J Phys Chem B 2023; 127:6878-6886. [PMID: 37490365 DOI: 10.1021/acs.jpcb.3c02454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Methylation at the C5 position of cytosine, a naturally occurring epigenetic modification on DNA, shows a high correlation with mutational hotspots in disease such as skin cancer. Due to its essential biological relevance, numerous studies were devoted to confirming that the methylated sites favor the formation of the cyclobutane pyrimidine dimer (CPD), a well-known UV-induced lesion. However, photophysical and photochemical properties of dinucleotides and polynucleotides containing 5-methylcytosine (5mC) remain elusive. Herein, a charge transfer (CT) triplet state, generated via intersystem crossing (ISC) from a CT singlet state that enhanced after methylation on cytosine, is directly observed by using femtosecond transient absorption (TA) and time-resolved mid-infrared (TRIR) spectroscopy together with quantum chemical calculations for the first time in the T5mC dimer. Such an ISC process is quenched due to limitations of the ground-state geometries in 5mC-containing single-strand oligomer d(T5mC)9. This mechanistic information is important for understanding the early stage of triplet state-induced CPD formation in 5mC containing DNA.
Collapse
Affiliation(s)
- Peipei Jin
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| |
Collapse
|
5
|
Improta R. Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations. Int J Mol Sci 2023; 24:12614. [PMID: 37628797 PMCID: PMC10454157 DOI: 10.3390/ijms241612614] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical-physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.
Collapse
Affiliation(s)
- Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
| |
Collapse
|
6
|
Peng H, Vu S, Retes P, Ward S, Kumar A, Sevilla MD, Adhikary A, Greenberg MM. Photochemical and Single Electron Transfer Generation of 2'-Deoxycytidin- N4-yl Radical from Oxime Esters. J Org Chem 2023; 88:7381-7390. [PMID: 37220149 PMCID: PMC10308854 DOI: 10.1021/acs.joc.3c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
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.
Collapse
Affiliation(s)
- Haihui Peng
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Son Vu
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Parker Retes
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| |
Collapse
|
7
|
Yang C, Yi K, Zhu M, Yang J, Wei Y, Shang Y, Xu X. Photosensitive damage of dipeptides: mechanism and influence of structure. Phys Chem Chem Phys 2023; 25:4923-4928. [PMID: 36722384 DOI: 10.1039/d2cp05047a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We illustrate the influence of the dipeptide structure on photosensitive damage and the kinetic mechanism was investigated using acenaphthenequinone (ACQ) as a triplet photosensitizer. With tyrosine (Tyr) serving as the core structure, two classic dipeptides with double (trptophan-tyrosine, Trp-Tyr) and single (tyrosine-alanine, Tyr-Ala and Ala-Tyr) active reaction sites were constructed, and the underlying photodamage mechanisms were investigated carefully. According to the experimental results, the proton-coupled electron transfer processes between ACQ and numerous Trp-Tyr reaction sites have independent reaction properties. The bimolecular quenching rate (kq) value is roughly equivalent to the sum of the rates of two amino acid monomers, and a novel intramolecular dynamic channel between Trp/N˙-Tyr and Trp-Tyr/O˙ was observed. The ACQ/Tyr-Ala system demonstrated the key role of steric hindrance on the kq in bimolecular reactions.
Collapse
Affiliation(s)
- Cheng Yang
- Anhui Province Key Laboratory of Optoelectric Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu 241002, China.
| | - Kai Yi
- Anhui Province Key Laboratory of Optoelectric Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu 241002, China.
| | - Meirou Zhu
- Anhui Province Key Laboratory of Optoelectric Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu 241002, China.
| | - Jiangxue Yang
- Anhui Province Key Laboratory of Optoelectric Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu 241002, China.
| | - Yaxiong Wei
- Anhui Province Key Laboratory of Optoelectric Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu 241002, China.
| | - Yongjia Shang
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
| | - Xinsheng Xu
- Anhui Province Key Laboratory of Optoelectric Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu 241002, China.
| |
Collapse
|
8
|
Wei S, He Q, Duan J, Zheng H, Ma L, Wang Y. An Exploration of the Transformation of the 8-Oxo-7,8-Dihydroguanine Radical Cation to Protonated 2-Amino-5-Hydroxy-7,9-Dihydropurine-6,8-Dione in a Base Pair. Chemphyschem 2023; 24:e202200625. [PMID: 36175389 DOI: 10.1002/cphc.202200625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Indexed: 02/04/2023]
Abstract
A theoretical investigation was performed to disclose the transformation mechanism of 8-oxo-7,8-dihydroguanine radical cation (8-oxoG⋅+ ) to protonated 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-8-oxoG) in base pair. The energy profiles for three possible pathways of the events were mapped. It is shown that direct loss of H7 from base paired 8-oxoG⋅+ is the only energetically favorable pathway to generate neutral radical, 8-oxoG(-H7)⋅. Further oxidation of 8-oxoG(-H7)⋅ : C to 8-oxoG(-H7)+ : C is exothermic. However, the 8-oxoG(-H7)+ : C deprotonation from all possible active sites is infeasible, indicating the inaccessible second proton loss and the lack of essential intermediate 2-amino-7,9-dihydropurine-6,8-dione (8-oxoGOX ). This makes 8-oxoG(-H7)+ act as the precursor of hydration leading to the generation of protonated 5-HO-8-oxoG by stepwise fashion in base pair, which would initiate the step down guanidinohydantoin (Gh) pathway. These results clearly specify the structure-dependent transformation for 8-oxoG⋅+ and verify the emergence of protonated 5-HO-8-oxoG in base pair.
Collapse
Affiliation(s)
- Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang, 712083, China
| | - Qihao He
- Institution Shaanxi Transportation Holding Group Co., Ltd., Xi'an, 710065, China
| | - Jinwei Duan
- College of Science, Chang'an University, Xi'an, 710064, China
| | - Huayu Zheng
- College of Science, Chang'an University, Xi'an, 710064, China
| | - Lei Ma
- College of Science, Chang'an University, Xi'an, 710064, China
| | - Yinghui Wang
- College of Science, Chang'an University, Xi'an, 710064, China
| |
Collapse
|
9
|
Zheng M, Li Y, Wei Y, Chen L, Zhou X, Liu S. Determining the Energy Gap between the S 1 and T 1 States of Thermally Activated Delayed Fluorescence Molecular Systems Using Transient Fluorescence Spectroscopy. J Phys Chem Lett 2022; 13:2507-2515. [PMID: 35274961 DOI: 10.1021/acs.jpclett.2c00428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The energy gap (ΔES-T) between the lowest single and triple excited states is a crucial parameter for thermally activated delayed fluorescence (TADF) molecular systems with high quantum yield. However, a reliable experimental approach to precisely determine this value is challenging. Here, we introduce a new, simple, and efficient strategy to accurately obtain the ΔES-T in TADF systems from time-resolved fluorescence spectroscopy using a recently reported TADF molecule, DMACPDO, as a representative. By introducing an explicit model to describe the corresponding singlet-triplet coupling system, elusive intersystem crossing and reverse intersystem crossing rates can be extracted by fitting the kinetics of the observed fluorescence. The ΔES-T value can then be determined. Moreover, our modeling accurately explained the opposite trend in fluorescence intensity of DMACPDO with solvent polarity under air-saturated and deoxygenated conditions. Additionally, the validity of this approach has been demonstrated in another well-known TADF molecule, 4CzIPN. We demonstrate how this approach of determining ΔES-T sheds light on a deeper understanding of energy-loss mechanisms involved in related photoconversion processes.
Collapse
Affiliation(s)
- Min Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuanming Li
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yaxiong Wei
- School of Physics and Electronic Information, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Lin Chen
- School of Physics and Materials Engineering, Hefei Normal University, Hefei, Anhui 230601, China
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| |
Collapse
|
10
|
Lu J, Deng Y, Zhong K, Huang Z, Jin LY. Construction of nanoaggregates from amphiphilic supramolecules containing barbiturate and
Hamilton
wedge units. POLYM INT 2021. [DOI: 10.1002/pi.6318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jie Lu
- Department of Chemistry, National Demonstration Centre for Experimental Chemistry Education Yanbian University Yanji China
| | - Yingying Deng
- Department of Chemistry, National Demonstration Centre for Experimental Chemistry Education Yanbian University Yanji China
| | - Keli Zhong
- College of Chemistry, Chemical Engineering and Food Safety, Bohai University Jinzhou China
| | - Zhegang Huang
- School of Chemistry, Sun Yat Sen University Guangzhou China
| | - Long Yi Jin
- Department of Chemistry, National Demonstration Centre for Experimental Chemistry Education Yanbian University Yanji China
| |
Collapse
|
11
|
Peng H, Jie J, Mortimer IP, Ma Z, Su H, Greenberg MM. Reactivity and DNA Damage by Independently Generated 2'-Deoxycytidin- N4-yl Radical. J Am Chem Soc 2021; 143:14738-14747. [PMID: 34467764 DOI: 10.1021/jacs.1c06425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Oxidative stress produces a variety of radicals in DNA, including pyrimidine nucleobase radicals. The nitrogen-centered DNA radical 2'-deoxycytidin-N4-yl radical (dC·) plays a role in DNA damage mediated by one electron oxidants, such as HOCl and ionizing radiation. However, the reactivity of dC· is not well understood. To reduce this knowledge gap, we photochemically generated dC· from a nitrophenyl oxime nucleoside and within chemically synthesized oligonucleotides from the same precursor. dC· formation is confirmed by transient UV-absorption spectroscopy in laser flash photolysis (LFP) experiments. LFP and duplex DNA cleavage experiments indicate that dC· oxidizes dG. Transient formation of the dG radical cation (dG+•) is observed in LFP experiments. Oxidation of the opposing dG in DNA results in hole transfer when the opposing dG is part of a dGGG sequence. The sequence dependence is attributed to a competition between rapid proton transfer from dG+• to the opposing dC anion formed and hole transfer. Enhanced hole transfer when less acidic O6-methyl-2'-deoxyguanosine is opposite dC· supports this proposal. dC· produces tandem lesions in sequences containing thymidine at the 5'-position by abstracting a hydrogen atom from the thymine methyl group. The corresponding thymidine peroxyl radical completes tandem lesion formation by reacting with the 5'-adjacent nucleotide. As dC· is reduced to dC, its role in the process is traceless and is only detectable because of the ability to independently generate it from a stable precursor. These experiments reveal that dC· oxidizes neighboring nucleotides, resulting in deleterious tandem lesions and hole transfer in appropriate sequences.
Collapse
Affiliation(s)
- Haihui Peng
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ifor P Mortimer
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Zehan Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| |
Collapse
|
12
|
Zou B, Xue J, Zhao Y, Zheng X. Effect of the weak intermolecular C-H···O=C hydrogen bonding, solvent polarity and concentration on the frequency of the C=O stretch mode of 2-thiophenecarboxaldehyde. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 255:119651. [PMID: 33765534 DOI: 10.1016/j.saa.2021.119651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/21/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The vibrational frequency shift in the C=O stretch mode of 2-thiophenecarboxaldehyde (2TC) in the condensed phase is still not fully understood. In this paper, the vibrational spectra of 2TC were investigated using the FT-Raman, FT-IR and resonance Raman spectroscopies in conjunction with the density functional theory calculation. The pure compound (in the neat liquid) exhibits three vibrational bands 1658, 1672 and 1687 cm-1 in the νC=O spectral region. It differs from the band pair 1672 and 1682 cm-1 for 2-cyclohexene-1-one (CHO) and the single band 1700 cm-1 for benzaldehyde. The relative intensities of observed bands vary with the polarity of aprotic solvents and the compound's concentration. In a diluted solution, the strongest band in the resonance Raman spectra of 2TC appears the C=O stretch mode at 1690 cm-1 in cyclohexane and 1674/1675 cm-1 in acetonitrile. The imparting factors that shift the C=O stretch mode frequency in the neat liquid and solvents with different polarities were examined. The spectral sources of the vibrational bands at 1658 and 1672 cm-1 in the neat liquid and a dilute solution were determined, and the resonance Raman spectra were assigned. It is concluded that tetramers and monomer are the major sources of the bands at 1658 and 1672 cm-1 in the neat liquid, respectively, while the monomer is the main source of the bands at 1674/1675 cm-1 in acetonitrile and the band at 1690 cm-1 in cyclohexane with a dilute concentration. The band's source at 1662/1663 cm-1 in acetonitrile (a dilute concentration) can be either the dimers or 2TC-CH3CN clusters. The C=O bond's electronic charge density is the main factor that shifts the vibrational frequency of the C=O stretch mode of 2TC monomer when an aprotic solvent is used. The larger the polarity of an aprotic solvent, the more negative the electronic charge-density of the C=O bond for the monomer, the lower the frequency of the C=O stretch mode.
Collapse
Affiliation(s)
- Bangkun Zou
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Jiadan Xue
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, PR China.
| | - Yanying Zhao
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xuming Zheng
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| |
Collapse
|
13
|
Kohl FR, Zhang Y, Charnay AP, Martínez-Fernández L, Kohler B. Ultrafast excited state dynamics of silver ion-mediated cytosine-cytosine base pairs in metallo-DNA. J Chem Phys 2021; 153:105104. [PMID: 32933288 DOI: 10.1063/5.0020463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To better understand the nexus between structure and photophysics in metallo-DNA assemblies, the parallel-stranded duplex formed by the all-cytosine oligonucleotide, dC20, and silver nitrate was studied by circular dichroism (CD), femtosecond transient absorption spectroscopy, and time-dependent-density functional theory calculations. Silver(I) ions mediate Cytosine-Cytosine (CC) base pairs by coordinating to the N3 atoms of two cytosines. Although these silver(I) mediated CC base pairs resemble the proton-mediated CC base pairs found in i-motif DNA at first glance, a comparison of experimental and calculated CD spectra reveals that silver ion-mediated i-motif structures do not form. Instead, the parallel-stranded duplex formed between dC20 and silver ions is proposed to contain consecutive silver-mediated base pairs with high propeller twist-like ones seen in a recent crystal structure of an emissive, DNA-templated silver cluster. Femtosecond transient absorption measurements with broadband probing from the near UV to the near IR reveal an unusually long-lived (>10 ns) excited state in the dC20 silver ion complex that is not seen in dC20 in single-stranded or i-motif forms. This state is also absent in a concentrated solution of cytosine-silver ion complexes that are thought to assemble into planar ribbons or sheets that lack stacked silver(I) mediated CC base pairs. The large propeller twist angle present in metal-mediated base pairs may promote the formation of long-lived charged separated or triplet states in this metallo-DNA.
Collapse
Affiliation(s)
- Forrest R Kohl
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Aaron P Charnay
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Bern Kohler
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| |
Collapse
|
14
|
Ye Z, Du Y, Pan X, Zheng X, Xue J. Electron transfer from guanosine to the lowest triplet excited state of 4-nitroindole through hydrogen-bonded complex. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
15
|
Wang M, Shi Y, Guo Y, Chen Y, Zhao C, Zhou Y, Xiao Y, Wang Y, Zhang S, Jin B, Wu Z, Zhao G. Nonadiabatic dynamics Mechanisms of natural UV Photoprotection ompounds chlorogenic acid and isochlorogenic acid a: Double conjugated structures but single photoexcited channel. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114725] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
16
|
Wei S, Zhang Z, Liu S, Wang Y. Theoretical insight into 7,8-dihydrogen-8-oxoguanine radical cation deprotonation. NEW J CHEM 2021. [DOI: 10.1039/d1nj01653a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The pKa values of reactive protons in 8-oxoG˙+ and potential energy profiles for 8-oxoG radical cation deprotonation reaction (N1–H and N7–H) were firstly calculated.
Collapse
Affiliation(s)
- Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Zhenhua Zhang
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Shijun Liu
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Yinghui Wang
- College of Science
- Chang’an University
- Xi’an 710064
- China
| |
Collapse
|
17
|
Huang SR, Nováková G, Marek A, Tureček F. The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine. J Phys Chem A 2020; 125:338-348. [DOI: 10.1021/acs.jpca.0c10293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| |
Collapse
|
18
|
Zhang X, Jie J, Song D, Su H. Deprotonation of Guanine Radical Cation G •+ Mediated by the Protonated Water Cluster. J Phys Chem A 2020; 124:6076-6083. [PMID: 32585092 DOI: 10.1021/acs.jpca.0c03748] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H2O-PCM, 4H2O-PCM, 5H2O-PCM, and 7H2O-PCM models are used to calculate deprotonation potential energy profile, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G•+.
Collapse
Affiliation(s)
- Xianwang Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100048, P. R. China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| |
Collapse
|
19
|
Shi L, Cao F, Zhang L, Tian Y. I-motif Formed at Physiological pH Triggered by Spatial Confinement of Nanochannels: An Electrochemical Platform for pH Monitoring in Brain Microdialysates. Anal Chem 2020; 92:4535-4540. [PMID: 32052626 DOI: 10.1021/acs.analchem.9b05732] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The development of switches responding to specific pH changes was particularly useful in wide application fields. Owing to flexible switches simulated by pH, i-motif DNAs are widely used as a pH sensor. But its character of structure transition strongly dependent on acidic pH severely hampers the application of i-motif DNA in physiological media. Herein, we report the stable i-motif structure formed at a physiological pH triggered by spatial confinement of silica nanochannels. Three classic DNA chains containing 21-mer i-motif domain base-pairs and a single-stranded multiply (T)n spacer, 5'-COOH-(T)n-CCCTAACCCTAACCCTAACCC-3', were employed to evaluate the enhanced stability of i-motif structure. Compared to their free states in a dilute solution, the transition pH of all i-motif DNAs decorated in nanochannels remarkably shifts toward a neutral pH. Moreover, the transition midpoint can be tuned sensitively over the physiologically relevant pH range through slightly varying the length of T base spacer. Density functional theory (DFT) calculations validate that the increased proton density in a nanochannel triggers the formation of an i-motif structure under a neutral pH. Finally, this i-motif DNA based nanochannels electrode was successfully employed to monitor pH in brain microdialysates followed by cerebral ischemia. The present approach is not limited by fundamental investigation for DNA conformation but may extend toward the manipulation of i-motif based structures for artificial molecular machines and signaling systems.
Collapse
Affiliation(s)
- Lu Shi
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Feifei Cao
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Limin Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Tian
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| |
Collapse
|
20
|
Sofińska K, Wilkosz N, Szymoński M, Lipiec E. Molecular Spectroscopic Markers of DNA Damage. Molecules 2020; 25:E561. [PMID: 32012927 PMCID: PMC7037412 DOI: 10.3390/molecules25030561] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
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.
Collapse
Affiliation(s)
| | | | | | - Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland; (K.S.); (N.W.); or (M.S.)
| |
Collapse
|
21
|
Hou M, Li Q, Scheiner S. The ability of a tetrel bond to transition a neutral amino acid into a zwitterion. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
22
|
Wang Y, Zhao H, Zhou Q, Dai X, Liu K, Song D, Su H. Monitoring the Structure-Dependent Reaction Pathways of Guanine Radical Cations in Triplex DNA: Deprotonation Versus Hydration. J Phys Chem B 2019; 123:2853-2863. [PMID: 30834754 DOI: 10.1021/acs.jpcb.9b00608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exposure of DNA to one-electron oxidants leads initially to the formation of guanine radical cations (G•+), which may degrade by deprotonation or hydration and ultimately cause strand breaks or 8-oxoG lesions. As the structure is dramatically changed by binding of the third strand in the major groove of the target duplex, it makes the triplex an interesting DNA structure to be examined and compared with the duplex on the G•+ degradation pathways. Here, we report for the first time the time-resolved spectroscopy study on the G•+ reaction dynamics in triplex DNA together with the Fourier transform infrared characterization of steady-state products, from which structural effects on the reactivity of G•+ are unraveled. For an antiparallel triplex-containing GGC motif, G•+ mainly suffers from fast deprotonation (9.8 ± 0.2) × 106 s-1, featuring release of both N1-H and N2-H of G in the third strand directly into bulk water. The much faster and distinct deprotonation behavior compared to the duplex should be related to long-resident water spines in the third strand. The G•+ hydration product 8-oxoG is negligible for an antiparallel triplex; instead, the 5-HOO-(G-H) hydroperoxide formed after G•+ deprotonation is identified by its vibrational marker band. In contrast, in a parallel triplex (C+GC), the deprotonation of G•+ occurs slowly (6.0 ± 0.3) × 105 s-1 with the release of N1-H, while G•+ hydration becomes the major pathway with yields of 8-oxoG larger than in the duplex. The increased positive charge brought by the third strand makes the G radical in the parallel triplex sustain more cation character and prone for hydration. These results indicate that non-B DNA (triplex) plays an important role in DNA damage formation and provide mechanistic insights to rationalize why triplex structures might become hot spots for mutagenesis.
Collapse
Affiliation(s)
- Yinghui Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Qian Zhou
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Xiaojuan Dai
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Kunhui Liu
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Di Song
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Hongmei Su
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| |
Collapse
|