气相中碱基与核苷自由基的产生与结构研究

寇敏; 徐诗音; 焦鲁杨; 杜梦颖; 李树奇; 孔祥蕾

doi:10.7538/zpxb.2023.0125

气相中碱基与核苷自由基的产生与结构研究

1. 南开大学化学学院, 元素有机化学国家重点实验室, 天津 300071;
2. 南开大学有机新物质创造前沿科学中心, 天津 300071;
3. 南开大学化学学院, 天津市生物传感与分子识别重点实验室, 天津 300071

基金项目:

国家自然科学基金（22174076）

详细信息

中图分类号: O657.63
计量
- 文章访问数: 726
- HTML全文浏览量: 2
- PDF下载量: 17
出版历程
- 收稿日期: 2023-11-04
- 修回日期: 2023-12-17
- 网络出版日期: 2024-01-22

Production and Structure Study of Free Radicals of Bases and Nucleosides in Gas Phase

1. State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China;
2. Frontiers Science Center for New Organic Matte, Nankai University, Tianjin 300071, China;
3. Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China

摘要

摘要: 核苷自由基在生物体内扮演着关键角色，特别是在DNA损伤过程中。为深入研究这些自由基的性质、反应机制以及与其他生物分子的相互作用，确定其结构至关重要。质谱通过提供高真空环境，为自由基离子创造了惰性的研究环境，在核苷自由基和碱基自由基的气相研究中展示了不可替代的作用。此外，结合串联质谱和理论计算，能够更准确地分析自由基结构。本文总结了近20年来基于质谱技术的气相中碱基与核苷自由基的研究，详细介绍了自由基离子的产生方法、研究手段以及结构分析的最新成果，提出了对于高活性自由基中间体的结构研究，以及自由基异构体的选择性产生仍然面临挑战，亟需发展新的实验方法和技术手段。
- 质谱 /
- 核苷 /
- 自由基阳离子 /
- 气相结构 /
- 光解离光谱
Abstract: Nucleoside free radicals have important functions in organisms and play a crucial role in DNA damage. Accurately understanding the structure of nucleoside free radicals is crucial for studying their properties, reaction mechanisms, and interactions with other biomolecules. The high vacuum in the mass spectrometer provides an inert environment for free radicals. Further tandem mass spectrometry combined with theoretical calculation is crucial for achieving their structural informations. This article reviewed gas phase studies of base and nucleoside radicals based on mass spectrometry in the past two decades, and provided a detailed introduction and comparison of their production methods, structural research methods and progress. Different methods were developed for the generation of the free radical ions, including collision induced dissociation of precursor ions of ternary transition metal complexes or those introducing free radical initiators, electron transfer dissociation of precursor ions charge-tagged, and UV photodissociation of precursor ions including C-I bonds. Besides, the methods for studying the structure of free radical ions in gas phase have gradually enriched, including commonly used tandem mass spectrometry, UV-visible and IR photodissociation spectroscopy. Based on the above methods, many different base and nucleoside free radical ions were generated and structurally determined in gas phase. On the other hand, the research of the highly active free radical intermediates and the selective generation of free radical isomers still pose challenges, and there is an urgent need to develop new experimental method.
- mass spectrometry /
- nucleosides /
- radical cations /
- gas phase structure /
- photodissociation spectroscopy

HTML全文

参考文献(54)

[1]	ZHENG L, GREENBERG M M. DNA damage emanating from a neutral purine radical reveals the sequence dependent convergence of the direct and indirect effects of γ-radiolysis[J]. Journal of the American Chemical Society, 2017, 139(49):17751-17754.
[2]	LUNDAHL M N, SARKSIAN R, YANG H, JODTS R J, PAGNIER A, SMITH D F, MOSQUERA M A, van der DONK W A, HOFFMAN B M, BRODERICK W E, BRODERICK J B. Mechanism of radical S-adenosyl-l-methionine adenosylation:radical intermediates and the catalytic competence of the 5'-deoxyadenosyl radical[J]. Journal of the American Chemical Society, 2022, 144(11):5087-5098.
[3]	ZHENG L, GREENBERG M M. Traceless tandem lesion formation in DNA from a nitrogen-centered purine radical[J]. Journal of the American Chemical Society, 2018, 140(20):6400-6407.
[4]	CHEN X, SYRSTAD E A, NGUYEN M T, GERBAUX P, TURECEK F. Adenine radicals in the gas phase:an experimental and computational study of hydrogen atom adducts to adenine[J]. The Journal of Physical Chemistry A, 2005, 109(36):8121-8132.
[5]	CANDEIAS L P, STEENKEN S. Reaction of HO* with guanine derivatives in aqueous solution:formation of two different redox-active OH-adduct radicals and their unimolecular transformation reactions. Properties of G (-H)[J]. Chemistry, 2000, 6(3):475-484.
[6]	ROKHLENKO Y, CADET J, GEACINTOV N E, SHAFIROVICH V. Mechanistic aspects of hydration of guanine radical cations in DNA[J]. Journal of the American Chemical Society, 2014, 136(16):5956-5962.
[7]	SANTIAGO J, de FARIA J C, SAN-MIGUEL M, BERNAL M A. A TD-DFT-based study on the attack of the OH·radical on a guanine nucleotide[J]. International Journal of Molecular Sciences, 2022, 23(17):10007.
[8]	CHOI J, YANG C, FUJITSUKA M, TOJO S, IHEE H, MAJIMA T. Proton transfer of guanine radical cations studied by time-resolved resonance Raman spectroscopy combined with pulse radiolysis[J]. The Journal of Physical Chemistry Letters, 2015, 6(24):5045-5050.
[9]	WU L, LIU K, JIE J, SONG D, SU H. Direct observation of guanine radical cation deprotonation in G-quadruplex DNA[J]. Journal of the American Chemical Society, 2015, 137(1):259-266.
[10]	JIE J, LIU K, WU L, ZHAO H, SONG D, SU H. Capturing the radical ion-pair intermediate in DNA guanine oxidation[J]. Science Advances, 2017, 3(6):e1700171.
[11]	SHI Y, DU M, REN J, ZHANG K, XU Y, KONG X. Application of infrared multiple photon dissociation (IRMPD) spectroscopy in chiral analysis[J]. Molecules, 2020, 25(21):5152.
[12]	MA L, REN J, FENG R, ZHANG K, KONG X. Structural characterizations of protonated homodimers of amino acids:revealed by infrared multiple photon dissociation (IRMPD) spectroscopy and theoretical calculations[J]. Chinese Chemical Letters, 2018, 29(9):1333-1339.
[13]	FENN J B, MANN M, MENG C K, WONG S F, WHITEHOUSE C M. Electrospray ionization for mass spectrometry of large biomolecules[J]. Science, 1989, 246(4926):64-71.
[14]	SLENO L, VOLMER D A. Ion activation methods for tandem mass spectrometry[J]. Journal of Mass Spectrometry, 2004, 39(10):1091-1112.
[15]	BAYAT P, LESAGE D, COLE R B. Tutorial:ion activation in tandem mass spectrometry using ultra-high resolution instrumentation[J]. Mass Spectrometry Reviews, 2020, 39(5/6):680-702.
[16]	HUSH N S, CHEUNG A S. Ionization potentials and donor properties of nucleic acid bases and related compounds[J]. Chemical Physics Letters, 1975, 34(1):11-13.
[17]	LIN J, YU C, PENG S, AKIYAMA I, LI K, LEE L K, LeBRETON P R. Ultraviolet photoelectron studies of the ground-state electronic structure and gas-phase tautomerism of purine and adenine[J]. Journal of the American Chemical Society, 1980, 102(14):4627-4631.
[18]	YU C, PENG S, AKIYAMA I, LIN J, LeBRETON P R. Ultraviolet photoelectron studies of biological pyrimidines. The valence electronic structure of cytosine[J]. Journal of the American Chemical Society, 1978, 100(8):2303-2307.
[19]	RICE J M, DUDEK G O, BARBER M. Mass spectra of nucleic acid derivatives. Pyrimidines[J]. Journal of the American Chemical Society, 1965, 87(20):4569-4576.
[20]	RICE J M, DUDEK G O. Mass spectra of nucleic acid derivatives. Ⅱ. Guanine, adenine, and related compounds[J]. Journal of the American Chemical Society, 1967, 89(11):2719-2725.
[21]	WEE S, O'HAIR R A J, McFADYEN W D. Can radical cations of the constituents of nucleic acids be formed in the gas phase using ternary transition metal complexes? [J]. Rapid Communications in Mass Spectrometry:RCM, 2005, 19(13):1797-1805.
[22]	FEKETEOVÁ L, CHAN B, KHAIRALLAH G N, STEINMETZ V, MAITRE P, RADOM L, O'HAIR R A J. Watson-crick base pair radical cation as a model for oxidative damage in DNA[J]. The Journal of Physical Chemistry Letters, 2017, 8(13):3159-3165.
[23]	LESSLIE M, LAWLER J T, DANG A, KORN J A, BÍM D, STEINMETZ V, MAÎTRE P, TUREČEK F, RYZHOV V. Cytosine radical cations:a gas-phase study combining IRMPD spectroscopy, UVPD spectroscopy, ion-molecule reactions, and theoretical calculations[J]. Chemphyschem:a European Journal of Chemical Physics and Physical Chemistry, 2017, 18(10):1293-1301.
[24]	DANG A, NGUYEN H T H, RUIZ H, PIACENTINO E, RYZHOV V, TUREČEK F. Experimental evidence for noncanonical thymine cation radicals in the gas phase[J]. The Journal of Physical Chemistry B, 2018, 122(1):86-97.
[25]	HUANG S R, DANG A, TUREČEK F. Ground and excited states of gas-phase DNA nucleobase cation-radicals. A UV-vis photodisociation action spectroscopy and computational study of adenine and 9-methyladenine[J]. Journal of the American Society for Mass Spectrometry, 2020, 31(6):1271-1281.
[26]	ZIMA V, LIU Y, TUREČEK F. Radical cascade dissociation pathways to unusual nucleobase cation radicals[J]. Journal of the American Society for Mass Spectrometry, 2022, 33(6):1038-1047.
[27]	LIU Y, DANG A, URBAN J, TUREČEK F. Charge-tagged DNA radicals in the gas phase characterized by UV/vis photodissociation action spectroscopy[J]. Angewandte Chemie (International Ed in English), 2020, 59(20):7772-7777.
[28]	LIU Y, MA C, NOVÁKOVÁ G, MAREK A, TUREČEK F. Charge-tagged nucleosides in the[HJ] gas phase:UV-vis action spectroscopy and structures of cytidine cations, dications, and cation radicals[J]. The Journal of Physical Chemistry A, 2021, 125(28):6096-6108.
[29]	LIU Y, MA C, LEONEN C J A, CHATTERJEE C, NOVÁKOVÁ G, MAREK A, TUREČEK F. Tackling a curious case:generation of charge-tagged guanosine radicals by gas-phase electron transfer and their characterization by UV-vis photodissociation action spectroscopy and theory[J]. Journal of the American Society for Mass Spectrometry, 2021, 32(3):772-785.
[30]	LIU Y, KORN J A, DANG A, TUREČEK F. Hydrogen-rich cation radicals of DNA dinucleotides:generation and structure elucidation by UV-vis action spectroscopy[J]. The Journal of Physical Chemistry B, 2018, 122(42):9665-9680.
[31]	HUANG S R, LIU Y, TUREČEK F. UV-vis photodissociation action spectroscopy reveals cytosine-guanine hydrogen transfer in DNA tetranucleotide cation radicals upon one-electron reduction[J]. The Journal of Physical Chemistry B, 2020, 124(17):3505-3517.
[32]	LIU Y, HUANG S R, TUREČEK F. Guanine-adenine interactions in DNA tetranucleotide cation radicals revealed by UV/vis photodissociation action spectroscopy and theory[J]. Physical Chemistry Chemical Physics:PCCP, 2020, 22(29):16831-16842.
[33]	KHANDURI D, COLLINS S, KUMAR A, ADHIKARY A, SEVILLA M D. Formation of sugar radicals in RNA model systems and oligomers via excitation of guanine cation radical[J]. The Journal of Physical Chemistry B, 2008, 112(7):2168-2178.
[34]	BANYASZ A, KETOLA T M, MUÑOZ-LOSA A, RISHI S, ADHIKARY A, SEVILLA M D, MARTINEZ-FERNANDEZ L, IMPROTA R, MARKOVITSI D. UV-induced adenine radicals induced in DNA a-tracts:spectral and dynamical characterization[J]. The Journal of Physical Chemistry Letters, 2016, 7(19):3949-3953.
[35]	ZHANG K, SHI Y, DU M, XU Y, WANG Y, KONG X. Versatile double-beam confocal laser system combined with a Fourier transform ion cyclotron resonance mass spectrometer for photodissociation mass spectrometry and spectroscopy[J]. Analytical Chemistry, 2021, 93(26):9056-9063.
[36]	KOU M, JIAO L, XU S, DU M, HOU Y, KONG X. Structural characterization of the metalized radical cations of adenosine ([Ade+Li-H] ^·+ and [Ade+Na-H] ^·+) by infrared multiphoton dissociation spectroscopy and theoretical studies[J]. International Journal of Molecular Sciences, 2023, 24(20):15385.
[37]	WOLKEN J K, SYRSTAD E A, VIVEKANANDA S, TURECEK F. Uracil radicals in the gas phase:specific generation and energetics[J]. Journal of the American Chemical Society, 2001, 123(24):5804-5805.
[38]	YAO C, CUADRADO-PEINADO M L, POLÁSEK M, TURECEK F. Specific generation of 1-methylcytosine radicals in the gas phase[J]. Angewandte Chemie (International Ed in English), 2005, 44(41):6708-6711.
[39]	YUAN Q, FENG W, CAO W, ZHOU Y, CHENG L, WANG X B. Sodium cationization enables exotic deprotonation sites on gaseous mononucleotides[J]. The Journal of Physical Chemistry Letters, 2022, 13(42):9975-9982.
[40]	HOULE F A, BEAUCHAMP J L. Detection and investigation of allyl and benzyl radicals by photoelectron spectroscopy[J]. Journal of the American Chemical Society, 1978, 100(11):3290-3294.
[41]	SCHVßLER T, DEYERL H J, D'UMMLER S, FISCHER I, ALCARAZ C, ELHANINE M. The vacuum ultraviolet photochemistry of the allyl radical investigated using synchrotron radiation[J]. The Journal of Chemical Physics, 2003, 118(20):9077-9080.
[42]	WANG X B, WOO H K, WANG L S, MINOFAR B, JUNGWIRTH P. Determination of the electron affinity of the acetyloxyl radical (CH₃COO) by low-temperature anion photoelectron spectroscopy and AB initio calculations[J]. The Journal of Physical Chemistry A, 2006, 110(15):5047-5050.
[43]	HOSSAIN E, DENG S M, GOZEM S, KRYLOV A I, WANG X B, WENTHOLD P G. Photoelectron spectroscopy study of quinonimides[J]. Journal of the American Chemical Society, 2017, 139(32):11138-11148.
[44]	HRODMARSSON H R, GARCIA G A, NAHON L, GANS B, LOISON J C. Threshold photoelectron spectrum of the anilino radical[J]. The Journal of Physical Chemistry A, 2019, 123(42):9193-9198.
[45]	FISCHER I, PRATT S T. Photoelectron spectroscopy in molecular physical chemistry[J]. Physical Chemistry Chemical Physics, 2022, 24(4):1944-1959.
[46]	RUOTOLO B T, HYUNG S J, ROBINSON P M, GILES K, BATEMAN R H, ROBINSON C V. Ion mobility-mass spectrometry reveals long-lived, unfolded intermediates in the dissociation of protein complexes[J]. Angewandte Chemie (International Ed in English), 2007, 46(42):8001-8004.
[47]	MOSS C L, CHAMOT-ROOKE J, NICOL E, BROWN J, CAMPUZANO I, RICHARDSON K, WILLIAMS J P, BUSH M F, BYTHELL B, PAIZS B, TURECEK F. Assigning structures to gas-phase peptide cations and cation-radicals. An infrared multiphoton dissociation, ion mobility, electron transfer, and computational study of a histidine peptide ion[J]. The Journal of Physical Chemistry B, 2012, 116(10):3445-3456.
[48]	PLATT S P, ATTAH I K, AZIZ S, EL-SHALL M S. Communication:Ion mobility of the radical cation dimers:(Naphthalene)2(+·) and naphthalene(+·)-benzene:evidence for stacked sandwich and T-shape structures[J]. The Journal of Chemical Physics, 2015, 142(19):191102.
[49]	ZIMA V, VLK M, WAN J, CVAČKA J, TUREČEK F. Tracking isomerizations[HJ] of high-energy adenine cation radicals by UV-vis action spectroscopy and cyclic ion mobility mass spectrometry[J]. The Journal of Physical Chemistry A, 2023, 127(28):5899-5913.
[50]	GOZZO T A, BUSH M F. Effects of charge on protein ion structure:lessons from cation-to-anion, proton-transfer reactions[J]. Mass Spectrometry Reviews, 2023:1-26.
[51]	NAYLOR C N, SCHAEFER C, KIRK A T, ZIMMERMANN S. The origin of isomerization of aniline revealed by high kinetic energy ion mobility spectrometry (HiKE-IMS)[J]. Physical Chemistry Chemical Physics, 2023, 25(2):1139-1152.
[52]	DANG A, KORN J A, GLADDEN J, MOZZONE B, TUREČEK F. UV-vis photodissociation[HJ] action spectroscopy on thermo LTQ-XL ETD and Bruker AmaZon ion trap mass spectrometers:a practical guide[J]. Journal of the American Society for Mass Spectrometry, 2019, 30(9):1558-1564.
[53]	EVANGELISTA F A, SCHAEFER H F. Hydrogen atom and hydride anion addition to adenine:structures and energetics[J]. Chemphyschem:a European Journal of Chemical Physics and Physical Chemistry, 2006, 7(7):1471-1480.
[54]	HEBERT S P, SCHLEGEL H B. Computational study of the pH-dependent competition between carbonate and thymine addition to the guanine radical[J]. Chemical Research in Toxicology, 2019, 32(1):195-210.

施引文献

资源附件(0)

计量

文章访问数: 726
HTML全文浏览量: 2
PDF下载量: 17
被引次数: 0

气相中碱基与核苷自由基的产生与结构研究

计量

出版历程

Production and Structure Study of Free Radicals of Bases and Nucleosides in Gas Phase

计量

出版历程

目录