Citation: Wang Yinghui, Jie Jialong, Zhao Hongmei, Bai Yu, Qin Peixuan, Song Di. Deprotonation of Guanine Radical Cation in G-Quadruplex: A Combined Experimental and Theoretical Study[J]. Acta Chimica Sinica, ;2018, 76(6): 475-482. doi: 10.6023/A17120557 shu

Deprotonation of Guanine Radical Cation in G-Quadruplex: A Combined Experimental and Theoretical Study

Wang Yinghui ^a,b ,
Jie Jialong ^a,b ,
Zhao Hongmei ^a,b ,
Bai Yu ^a ,
Qin Peixuan ^c ,
Song Di ^a,b,,

a.
Beijing National Laboratory for Molecular Science(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190
b.
University of Chinese Academy of Sciences, Beijing 100049
c.
Beijing Sanfan Middle School, Beijing 100088

Corresponding author: Song Di, songdi@iccas.ac.cn
Received Date: 27 December 2017
Available Online: 20 June 2018
Fund Project: the National Natural Science Foundation of China 91441108the National Natural Science Foundation of China 21773257Project supported by the National Natural Science Foundation of China (Nos. 21773257, 21373233 and 91441108)the National Natural Science Foundation of China 21373233

Figures(4)

G-Quadruplex can be a promising candidate as molecular electronic device due to the ability of transferring hole. Extensive studies have reported that fast deprotonation of guanine radical cation (G^·+) to form a neutral radical G(-H)^· is the most important reaction in competition with hole transfer in DNA, hindering potential applications of DNA in molecular electronics. We thus carry out joint experimental and theoretical studies on deprotonation of G^·+ in human telomere G-quadruplex AG₃(T₂AG₃)₃by using nanosecond laser flash photolysis and quantum chemical calculations. Upon 355 nm laser photolysis of Na₂S₂O₈, instantaneously generated SO₄^·- radical oxidizes G base in the G-quadruplex to G^·+. In the time-resolved absorption spectra that record the reaction of G-quadruplex with SO₄^·- at different temperatures, the transient absorptions of G(N(2)-H)^· featured by absorption band at 640 nm are observed. It turns out that the G-quadruplex deprotonation product is G(N(2)-H)^· and the deprotonation site is thereby validated to be amino proton. To obtain the activation energy of the G^·+ deprotonation in G-quadruplex, the N(2)-H deprotonation rate constants at different temperatures varying from 280 to 300 K in steps 5 K are measured at a high G-quadruplex concentration, where the deprotonation has been proved to be the rate-limiting step in our previous work. Based upon Arrhenius equation, the deprotonation activation energy of G^·+ in G-quadruplex is determined to be 20.0±1.0 kJ/mol. Further, the potential energy profile for the G^·+ deprotonation in G-quadruplex is calculated at M062X/6-31G(d) level by carefully taking into account hydration environment of G^·+ in G-quadruplex. The calculated energy barrier of 26.4 kJ/mol matches with the measured activation energy value, indicating the calculated potential energy profile can describe the deprotonation process of G^·+ in the G-quadruplex. These theoretical and experimental results provide valuable dynamics information and mechanistic insights for potential applications of DNA structures in electronic device.
- G-quadruplex,
- guanine radical cation,
- deprotonation reaction,
- activation energy,
- potential energy profile
1. [1]
  Hall, D. B.; Holmlin, R. E.; Barton, J. K. Nature 1996, 382, 731. doi: 10.1038/382731a0
2. [2]
  Wang, X. X.; Gu, Y.; Chen, D. X.; Fang, Y. F.; Huang, Y. P. Acta Chim. Sinica 2010, 68, 2463.
3. [3]
  Lu, Y. M.; Ou, Z. B.; Hu, W.; Le, X. Y. Acta Chim. Sinica 2012, 70, 973. doi: 10.3969/j.issn.0253-2409.2012.08.011
4. [4]
  Shao, B.; Mao, L.; Qu, N.; Wang, Y.-F.; Gao, H.-Y.; Li, F.; Qin, L.; Shao, J.; Huang, C.-H.; Xu, D.; Xie, L.-N.; Shen, C.; Zhou, X.; Zhu, B.-Z. Free Radical Biol. Med. 2017, 104 (Suppl. C), 54.
5. [5]
  Kawai, K.; Majima, T. Acc. Chem. Res. 2013, 46, 2616. doi: 10.1021/ar400079s
6. [6]
  Endres, R. G.; Cox, D. L.; Singh, R. R. P. Rev. Mod. Phys. 2004, 76, 195. doi: 10.1103/RevModPhys.76.195
7. [7]
  Okamoto, A.; Tanaka, K.; Saito, I. J. Am. Chem. Soc. 2003, 125, 5066. doi: 10.1021/ja0294008
8. [8]
  Barnett, R. N.; Cleveland, C. L.; Joy, A.; Landman, U.; Schuster, G. B. Science 2001, 294, 567. doi: 10.1126/science.1062864
9. [9]
  Giese, B. Acc. Chem. Res. 2000, 33, 631. doi: 10.1021/ar990040b
10. [10]
  Faraggi, M.; Broitman, F.; Trent, J. B.; Klapper, M. H. J. Phys. Chem. 1996, 100, 14751. doi: 10.1021/jp960590g
11. [11]
  Cleveland, C. L.; Barnett, R. N.; Bongiorno, A.; Joseph, J.; Liu, C. S.; Schuster, G. B.; Landman, U. J. Am. Chem. Soc. 2007, 129, 8408. doi: 10.1021/ja071893z
12. [12]
  Kawai, K.; Osakada, Y.; Majima, T. ChemPhysChem 2009, 10, 1766 doi: 10.1002/cphc.v10:11
13. [13]
  Kobayashi, K.; Yamagami, R.; Tagawa, S. J. Phys. Chem. B 2008, 112, 10752. doi: 10.1021/jp804005t
14. [14]
  Wu, L. D.; Liu, K. H.; Jie, J. L.; Song, D.; Su, H. M. J. Am. Chem. Soc. 2015, 137, 259. doi: 10.1021/ja510285t
15. [15]
  Candeias, L. P.; Steenken, S. J. Am. Chem. Soc. 1989, 111, 1094. doi: 10.1021/ja00185a046
16. [16]
  Candeias, L. P.; Steenken, S. J. Am. Chem. Soc. 1992, 114, 699. doi: 10.1021/ja00028a043
17. [17]
  Kobayashi, K.; Tagawa, S. J. Am. Chem. Soc. 2003, 125, 10213. doi: 10.1021/ja036211w
18. [18]
  Steenken, S.; Reynisson, J. Phys. Chem. Chem. Phys. 2010, 12, 9088. doi: 10.1039/c002528c
19. [19]
  Cerón-Carrasco, J. P.; Requena, A.; Perpète, E. A.; Michaux, C.; Jacquemin, D. J. Phys. Chem. B 2010, 114, 13439. doi: 10.1021/jp101711z
20. [20]
  Takada, T.; Kawai, K.; Fujitsuka, M.; Majima, T. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 14002. doi: 10.1073/pnas.0402756101
21. [21]
  Choi, J.; Park, J.; Tanaka, A.; Park, M. J.; Jang, Y. J.; Fujitsuka, M.; Kim, S. K.; Majima, T. Angew. Chem., Int. Ed. 2013, 52, 1134. doi: 10.1002/anie.201208149
22. [22]
  Delaney, S.; Barton, J. K. Biochemistry 2003, 42, 14159. doi: 10.1021/bi0351965
23. [23]
  Szalai, V. A.; Thorp, H. H. J. Am. Chem. Soc. 2000, 122, 4524. doi: 10.1021/ja0001355
24. [24]
  Song, D.; Yang, W.; Qin, T.; Wu, L.; Liu, K.; Su, H. J. Phys. Chem. Lett. 2014, 5, 2259. doi: 10.1021/jz501040a
25. [25]
  Wolter, M.; Elstner, M.; Kubař, T. J. Chem. Phys. 2013, 139, 125102. doi: 10.1063/1.4821594
26. [26]
  Barnett, R. N.; Bongiorno, A.; Cleveland, C. L.; Joy, A.; Landman, U.; Schuster, G. B. J. Am. Chem. Soc. 2006, 128, 10795. doi: 10.1021/ja061795y
27. [27]
  Rokhlenko, Y.; Geacintov, N. E.; Shafirovich, V. J. Am. Chem. Soc. 2012, 134, 4955. doi: 10.1021/ja212186w
28. [28]
  Rokhlenko, Y.; Cadet, J.; Geacintov, N. E.; Shafirovich, V. J. Am. Chem. Soc. 2014, 136, 5956. doi: 10.1021/ja412471u
29. [29]
  Saintome, C.; Amrane, S.; Mergny, J. L.; Alberti, P. Nucleic Acids Res. 2016, 44, 2926. doi: 10.1093/nar/gkw003
30. [30]
  Wu, L. D.; Jie, J. L.; Liu, K. H.; Su, H. M. Acta Chim. Sinica 2014, 72, 1182.
31. [31]
  Morikawa, M.; Kino, K.; Oyoshi, T.; Suzuki, M.; Kobayashi, T.; Miyazawa, H. Bioorg. Med. Chem. Lett. 2015, 25, 3359. doi: 10.1016/j.bmcl.2015.05.050
32. [32]
  Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2008, 112, 1095.
33. [33]
  Galano, A.; Alvarez-Idaboy, J. R. Phys. Chem. Chem. Phys. 2012, 14, 12476. doi: 10.1039/c2cp40799j
34. [34]
  Li, J.; Fu, K.-X.; Li, X.-Y. J. Mol. Struct.:THEOCHEM. 2007, 819, 32. doi: 10.1016/j.theochem.2007.05.031
35. [35]
  Li, X.; Cai, Z.; Sevilla, M. D. J. Phys. Chem. B 2001, 105, 10115. doi: 10.1021/jp012364z
36. [36]
  Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2009, 113, 11359. doi: 10.1021/jp903403d
37. [37]
  Horvath, M. P.; Schultz, S. C. J. Mol. Biol. 2001, 310, 367. doi: 10.1006/jmbi.2001.4766
38. [38]
  Parkinson, G. N.; Lee, M. P. H.; Neidle, S. Nature 2002, 417, 876. doi: 10.1038/nature755
39. [39]
  Marx, D.; Tuckerman, M. E.; Hutter, J.; Parrinello, M. Nature 1999, 397, 601. doi: 10.1038/17579
40. [40]
  Berkelbach, T. C.; Lee, H. S.; Tuckerman, M. E. Phys. Rev. Lett. 2009, 238302.
41. [41]
  Frisch, M. J. ; Trucks, G. W. ; Schlegel, H. B. ; Scuseria, G. E. ; Robb, M. A. ; Cheeseman, J. R. ; Montgomery, J. A. ; Vreven, T. ; Kudin, K. N. ; Burant, J. C. ; Millam, J. M. ; Iyengar, S. S. ; Tomasi, J. ; Barone, V. ; Mennucci, B. ; Cossi, M. ; Scalmani, G. ; Rega, N. ; Petersson, G. A. ; Nakatsuji, H. ; Hada, M. ; Ehara, M. ; Toyota, K. ; Fukuda, R. ; Ha-segawa, J. ; Ishida, M. ; Nakajima, T. ; Honda, Y. ; Kitao, O. ; Nakai, H. ; Klene, M. ; Li, X. ; Knox, J. E. ; Hratchian, H. P. ; Cross, J. B. ; Bakken, V. ; Adamo, C. ; Jaramillo, J. ; Gomperts, R. ; Stratmann, R. E. ; Yazyev, O. ; Austin, A. J. ; Cammi, R. ; Pomelli, C. ; Ochterski, J. W. ; Ayala, P. Y. ; Morokuma, K. ; Voth, G. A. ; Salvador, P. ; Dannen-berg, J. J. ; Zakrzewski, V. G. ; Dapprich, S. ; Daniels, A. D. ; Strain, M. C. ; Farkas, O. ; Malick, D. K. ; Rabuck, A. D. ; Raghavachari, K. ; Foresman, J. B. ; Ortiz, J. V. ; Cui, Q. ; Baboul, A. G. ; Clifford, S. ; Cioslowski, J. ; Stefanov, B. B. ; Liu, G. ; Liashenko, A. ; Piskorz, P. ; Komaromi, I. ; Martin, R. L. ; Fox, D. J. ; Keith, T. ; Al-Laham, M. A. ; Peng, C. Y. ; Nanayakkara, A. ; Challacombe, M. ; Gill, P. M. W. ; Johnson, B. ; Chen, W. ; Wong, M. W. ; Gonzalez, C. ; Pople, J. A. Gaussian 09, Revision A. 01, Gaussian, Inc., Wallingford, CT, 2009.
1. [1]
  Jia Zhou . Constructing Potential Energy Surface of Water Molecule by Quantum Chemistry and Machine Learning: Introduction to a Comprehensive Computational Chemistry Experiment. University Chemistry, 2024, 39(3): 351-358. doi: 10.3866/PKU.DXHX202309060
2. [2]
  Min LIU , Huapeng RUAN , Zhongtao FENG , Xue DONG , Haiyan CUI , Xinping WANG . Neutral boron-containing radical dimers. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 123-130. doi: 10.11862/CJIC.20240362
3. [3]
  .
  CCS Chemistry | 超分子活化底物为自由基促进高效选择性光催化氧化
  . CCS Chemistry, 2025, 7(10.31635/ccschem.025.202405229): -.
4. [4]
  Danqing Wu , Jiajun Liu , Tianyu Li , Dazhen Xu , Zhiwei Miao . Research Progress on the Simultaneous Construction of C—O and C—X Bonds via 1,2-Difunctionalization of Olefins through Radical Pathways. University Chemistry, 2024, 39(11): 146-157. doi: 10.12461/PKU.DXHX202403087
5. [5]
  Baitong Wei , Jinxin Guo , Xigong Liu , Rongxiu Zhu , Lei Liu . Theoretical Study on the Structure, Stability of Hydrocarbon Free Radicals and Selectivity of Alkane Chlorination Reaction. University Chemistry, 2025, 40(3): 402-407. doi: 10.12461/PKU.DXHX202406003
6. [6]
  Lei Shi . Nucleophilicity and Electrophilicity of Radicals. University Chemistry, 2024, 39(11): 131-135. doi: 10.3866/PKU.DXHX202402018
7. [7]
  Guangming YIN , Huaiyao WANG , Jianhua ZHENG , Xinyue DONG , Jian LI , Yi'nan SUN , Yiming GAO , Bingbing WANG . Preparation and photocatalytic degradation performance of Ag/protonated g-C₃N₄ nanorod materials. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1491-1500. doi: 10.11862/CJIC.20240086
8. [8]
  Jiajia Li , Xiangyu Zhang , Zhihan Yuan , Zhengyang Qian , Jian Zhu . 3D Printing Based on Photo-Induced Reversible Addition-Fragmentation Chain Transfer Polymerization. University Chemistry, 2024, 39(5): 11-19. doi: 10.3866/PKU.DXHX202309073
9. [9]
  Zijian Zhao , Yanxin Shi , Shicheng Li , Wenhong Ruan , Fang Zhu , Jijun Jiang . A New Exploration of the Preparation of Polyacrylic Acid by Free Radical Polymerization Based on the Concept of Green Chemistry. University Chemistry, 2024, 39(5): 315-324. doi: 10.3866/PKU.DXHX202311094
10. [10]
  Jiaxuan Zuo , Kun Zhang , Jing Wang , Xifei Li . 锂离子电池Ni-Co-Mn基正极材料前驱体的形核调控及机制. Acta Physico-Chimica Sinica, 2025, 41(1): 2404042-. doi: 10.3866/PKU.WHXB202404042
11. [11]
  Jianjun LI , Mingjie REN , Lili ZHANG , Lingling ZENG , Huiling WANG , Xiangwu MENG . UV-assisted degradation of tetracycline hydrochloride by MnFe₂O₄@activated carbon activated persulfate. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1869-1880. doi: 10.11862/CJIC.20240187
12. [12]
  Yuan GAO , Yiming LIU , Chunhui WANG , Zhe HAN , Chaoyue FAN , Jie QIU . A hexanuclear cerium oxo cluster stabilized by furoate: Synthesis, structure, and remarkable ability to scavenge hydroxyl radicals. Chinese Journal of Inorganic Chemistry, 2025, 41(3): 491-498. doi: 10.11862/CJIC.20240271
13. [13]
  Qiqi Li , Su Zhang , Yuting Jiang , Linna Zhu , Nannan Guo , Jing Zhang , Yutong Li , Tong Wei , Zhuangjun Fan . 前驱体机械压实制备高密度活性炭及其致密电容储能性能. Acta Physico-Chimica Sinica, 2025, 41(3): 2406009-. doi: 10.3866/PKU.WHXB202406009
14. [14]
  Wendian XIE , Yuehua LONG , Jianyang XIE , Liqun XING , Shixiong SHE , Yan YANG , Zhihao HUANG . Preparation and ion separation performance of oligoether chains enriched covalent organic framework membrane. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1528-1536. doi: 10.11862/CJIC.20240050
15. [15]
  Yuanyin Cui , Jinfeng Zhang , Hailiang Chu , Lixian Sun , Kai Dai . Rational Design of Bismuth Based Photocatalysts for Solar Energy Conversion. Acta Physico-Chimica Sinica, 2024, 40(12): 2405016-. doi: 10.3866/PKU.WHXB202405016
16. [16]
  Gonglan Ye , Xia Yin , Feng Xu , Peng Yang , Yingpeng Wu , Huilong Fei . Innovations in “Four-in-One” Inorganic Chemistry Education. University Chemistry, 2024, 39(8): 136-141. doi: 10.3866/PKU.DXHX202401071
17. [17]
  Jiaqi AN , Yunle LIU , Jianxuan SHANG , Yan GUO , Ce LIU , Fanlong ZENG , Anyang LI , Wenyuan WANG . Reactivity of extremely bulky silylaminogermylene chloride and bonding analysis of a cubic tetragermylene. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1511-1518. doi: 10.11862/CJIC.20240072
18. [18]
  Yixuan Gao , Lingxing Zan , Wenlin Zhang , Qingbo Wei . Comprehensive Innovation Experiment: Preparation and Characterization of Carbon-based Perovskite Solar Cells. University Chemistry, 2024, 39(4): 178-183. doi: 10.3866/PKU.DXHX202311091
19. [19]
  Honglian Liang , Xiaozhe Kuang , Fuping Wang , Yu Chen . Exploration and Practice of Integrating Ideological and Political Education into Physical Chemistry: a Case on Surface Tension and Gibbs Free Energy. University Chemistry, 2024, 39(10): 433-440. doi: 10.12461/PKU.DXHX202405073
20. [20]
  Feiya Cao , Qixin Wang , Pu Li , Zhirong Xing , Ziyu Song , Heng Zhang , Zhibin Zhou , Wenfang Feng . Magnesium-Ion Conducting Electrolyte Based on Grignard Reaction: Synthesis and Properties. University Chemistry, 2024, 39(3): 359-368. doi: 10.3866/PKU.DXHX202308094

Get Citation

PDF

XML

Metrics

PDF Downloads(6)
Abstract views(2010)
HTML views(294)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142