Citation: Xinfu Zhang, Lu Wang, Ning Li, Yi Xiao. Assessing chromatin condensation for epigenetics with a DNA-targeting sensor by FRET and FLIM techniques[J]. Chinese Chemical Letters, ;2021, 32(8): 2395-2399. doi: 10.1016/j.cclet.2021.02.031 shu

Assessing chromatin condensation for epigenetics with a DNA-targeting sensor by FRET and FLIM techniques

State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China

xiaoyi@dlut.edu.cn

Received Date: 17 December 2020
Revised Date: 16 February 2021
Accepted Date: 17 February 2021
Available Online: 19 February 2021

Figures(5)

Here we propose a fluorescent sensor, Chroma-V, consisted of a Hoechst ligand (Hoe) to target chromatin DNA and a BODIPY rotor (BDP) to sense the local viscosity that reflects chromatin condensation state. Within Chroma-V, efficient FRET process from Hoe to BDP facilitated a single-excitation ratiometric imaging of nucleus DNA under fluorescence confocal microscope, which utilized the ratio of two channels to enable an intuitive visualization of chromatin condensation state. And fluorescence lifetime imaging (FLIM) based on fluorescent signal from BDP proved to be a more accurate method to quantify the changes of chromatin condensation state under different epigenetic states, including histone acetylation regulated by deacetylase inhibitors, cell apoptosis induced by DNA-bining drugs, and the epithelial-mesenchymal transition of HUVEC cells induced by TGF-β.
- Ratio imaging,
- Fluorescence lifetime imaging,
- Epigenetic,
- Chromatin,
- BODIPY rotor,
- Hoechst
1. [1]
  R. Feil, M.F. Fraga, Nat. Rev. Genet. 13 (2012) 97-109 doi: 10.1038/nrg3142
2. [2]
  A.P. Wolffe, M.A. Matzke, Science 286 (1999) 481-486 doi: 10.1126/science.286.5439.481
3. [3]
  B.D. Strahl, C.D. Allis, Nature 403 (2000) 41-45 doi: 10.1038/47412
4. [4]
  B.M. Turner, BioEssays 22 (2000) 836-845 doi: 10.1002/1521-1878(200009)22:9<836::AID-BIES9>3.0.CO;2-X
5. [5]
  X. Wang, J.J. Hayes, Mol. Cell Biol. 28 (2008) 227-236 doi: 10.1128/MCB.01245-07
6. [6]
  D.Y. Lee, J.J. Hayes, D. Pruss, A.P. Wolffe, Cell 72 (1993) 73-84 doi: 10.1016/0092-8674(93)90051-Q
7. [7]
  P.J. Hamilton, E.J. Nestler, Curr. Opin. Neurobiol. 59 (2019) 128-136 doi: 10.1016/j.conb.2019.05.005
8. [8]
  S. Dhawan, R. Natarajan, Curr. Diabetes Rep. 19 (2019) 47 doi: 10.1007/s11892-019-1168-8
9. [9]
  D. Chen, C. Kerr, Trends Cell Biol. 29 (2019) 563-568 doi: 10.1016/j.tcb.2019.03.006
10. [10]
  K.D. Jarrell, L.M. Lennon, G.J. Jacot, Diseases 7 (2019) 52 doi: 10.3390/diseases7030052
11. [11]
  T.B. Toh, J.J. Lim, E.K.H. Chow, Clin. Transl. Med. 8 (2019) 13
12. [12]
  L.S. VandenBosch, T.A. Reh, Semin. Cell Dev. Biol. 97 (2020) 63-73 doi: 10.1016/j.semcdb.2019.04.001
13. [13]
  S.A. Belinsky, K.J. Nikula, S.B. Baylin, J.P. Issa, Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 4045 doi: 10.1073/pnas.93.9.4045
14. [14]
  S.L. Liu, Y. Han, Y. Zhang, et al., Target. Oncol. 7 (2012) 135-143 doi: 10.1007/s11523-012-0215-z
15. [15]
  K. Prakash, D. Fournier, S. Redl, et al., Proc. Natl. Acad. Sci. U. S. A. 112 (2015) 14635-14640 doi: 10.1073/pnas.1516928112
16. [16]
  M.A. Ricci, C. Manzo, M.F. García-Parajo, M. Lakadamyali, M.P. Cosma, Cell 160 (2015) 1145-1158 doi: 10.1016/j.cell.2015.01.054
17. [17]
  J. Xu, H. Ma, J. Jin, et al., Cell Rep. 24 (2018) 873-882 doi: 10.1016/j.celrep.2018.06.085
18. [18]
  M. Figueroa, J. Vandenameele, E. Goormaghtigh, et al., Data in Brief 8 (2016) 1221-1226 doi: 10.1016/j.dib.2016.07.036
19. [19]
  J.R. Daban, Micron 42 (2011) 733-750 doi: 10.1016/j.micron.2011.05.002
20. [20]
  R. Cortini, M. Barbi, B.R. Caré, et al., Rev. Mod. Phys. 88 (2016) 025002 doi: 10.1103/RevModPhys.88.025002
21. [21]
  S. Pelicci, A. Diaspro, L. Lanzanò, J. Biophotonics 12 (2019) e201900164
22. [22]
  E. Abdollahi, G. Taucher-Scholz, B. Jakob, Int. J. Mol. Sci. 19 (2018) 2399 doi: 10.3390/ijms19082399
23. [23]
  S.T. Spagnol, K.N. Dahl, PloS One 11 (2016) e0146244 doi: 10.1371/journal.pone.0146244
24. [24]
  A. Colom, E. Derivery, S. Soleimanpour, et al., Nat. Chem. 10 (2018) 1118-1125 doi: 10.1038/s41557-018-0127-3
25. [25]
  N. Audugé, S. Padilla-Parra, M. Tramier, N. Borghi, M. Coppey-Moisan, Nucleic Acids Res. 47 (2019) 6184-6194 doi: 10.1093/nar/gkz373
26. [26]
  H. Xiong, L. He, Y. Zhang, et al., Chin. Chem. Lett. 30 (2019) 1075-1077 doi: 10.1016/j.cclet.2019.02.008
27. [27]
  S. Long, Q. Qiao, L. Miao, Z. Xu, Chin. Chem. Lett. 30 (2019) 573-576 doi: 10.1016/j.cclet.2018.11.031
28. [28]
  M. Di Bona, M.A. Mancini, D. Mazza, et al., Biophys. J. 116 (2019) 987-999 doi: 10.1016/j.bpj.2019.02.003
29. [29]
  H. Sparks, H. Kondo, S. Hooper, et al., Nat. Commun. 9 (2018) 2662 doi: 10.1038/s41467-018-04820-6
30. [30]
  L. Wang, Y. Xiao, W. Tian, L. Deng, J. Am. Chem. Soc. 135 (2013) 2903-2906 doi: 10.1021/ja311688g
31. [31]
  Z. Yang, Y. He, J.H. Lee, et al., J. Am. Chem. Soc. 135 (2013) 9181-9185 doi: 10.1021/ja403851p
32. [32]
  M.K. Kuimova, G. Yahioglu, J.A. Levitt, K. Suhling, J. Am. Chem. Soc. 130 (2008) 6672-6673 doi: 10.1021/ja800570d
33. [33]
  A. Nakamura, K. Takigawa, Y. Kurishita, et al., Chem. Commun. 50 (2014) 6149-6152 doi: 10.1039/C4CC01753F
34. [34]
  Y. Yasueda, T. Tamura, I. Hamachi, Chem. Lett. 45 (2015) 265-267
35. [35]
  F. Yang, C. Wang, L. Wang, et al., Chin. Chem. Lett. 28 (2017) 2019-2022
36. [36]
  A. Nakamura, S. Tsukiji, Bioorg. Med. Chem. Lett. 27 (2017) 3127-3130 doi: 10.1016/j.bmcl.2017.05.036
37. [37]
  D. Hara, Y. Umehara, A. Son, et al., ChemBioChem 19 (2018) 956-962 doi: 10.1002/cbic.201700685
38. [38]
  X. Zhang, Z. Ye, X. Zhang, et al., Chem. Commun. 55 (2019) 1951-1954 doi: 10.1039/c8cc08575g
39. [39]
  C.K. Spahn, M. Glaesmann, J.B. Grimm, et al., Sci. Rep. 8 (2018) 14768 doi: 10.1038/s41598-018-33052-3
40. [40]
  G. Lukinavičius, C. Blaukopf, E. Pershagen, et al., Nat. Commun. 6 (2015) 8497 doi: 10.1038/ncomms9497
41. [41]
  Y. He, J. Shin, W. Gong, et al., Chem. Commun. 55 (2019) 2453-2456 doi: 10.1039/c9cc00300b
42. [42]
  X. Song, N. Li, C. Wang, Y. Xiao, J. Mater. Chem. B 5 (2017) 360-368 doi: 10.1039/C6TB02524B
43. [43]
  C. Wang, X. Song, L. Chen, Y. Xiao, Biosens. Bioelectron. 91 (2017) 313-320 doi: 10.1016/j.bios.2016.11.018
44. [44]
  H. Lee, Z. Yang, Y. Wi, et al., Bioconjugate Chem. 26 (2015) 2474-2480 doi: 10.1021/acs.bioconjchem.5b00508
45. [45]
  J.E. Chambers, M. Kubánková, R.G. Huber, et al., ACS Nano 12 (2018) 4398-4407 doi: 10.1021/acsnano.8b00177
46. [46]
  X. Zhang, Y. Xiao, X. Qian, Org. Lett. 10 (2008) 29-32 doi: 10.1021/ol702381j
47. [47]
  K.J. Embrey, M.S. Searle, D.J. Craik, Eur. J. Biochem. 211 (1993) 437-447 doi: 10.1111/j.1432-1033.1993.tb17569.x
48. [48]
  K. Suhling, P.M.W. French, D. Phillips, Photochem. Photobiol. Sci. 4 (2005) 13-22 doi: 10.1039/b412924p
49. [49]
  Y. Tsubakihara, A. Moustakas, Int. J. Mol. Sci. 19 (2018) 3672 doi: 10.3390/ijms19113672
50. [50]
  L. Sun, J. Fang, Cell Mol. Life Sci. 73 (2016) 4493-4515 doi: 10.1007/s00018-016-2303-1
1. [1]
  Gongcheng Ma , Qihang Ding , Yuding Zhang , Yue Wang , Jingjing Xiang , Mingle Li , Qi Zhao , Saipeng Huang , Ping Gong , Jong Seung Kim . Palladium-free chemoselective probe for in vivo fluorescence imaging of carbon monoxide. Chinese Chemical Letters, 2024, 35(9): 109293-. doi: 10.1016/j.cclet.2023.109293
2. [2]
  Leichen Wang , Anqing Mei , Na Li , Xiaohong Ruan , Xu Sun , Yu Cai , Jinjun Shao , Xiaochen Dong . Aza-BODIPY dye with unexpected bromination and high singlet oxygen quantum yield for photoacoustic imaging-guided synergetic photodynamic/photothermal therapy. Chinese Chemical Letters, 2024, 35(6): 108974-. doi: 10.1016/j.cclet.2023.108974
3. [3]
  Yiling Li , Zekun Gao , Xiuxiu Yue , Minhuan Lan , Xiuli Zheng , Benhua Wang , Shuang Zhao , Xiangzhi Song . FRET-based two-photon benzo[a] phenothiazinium photosensitizer for fluorescence imaging-guided photodynamic therapy. Chinese Chemical Letters, 2024, 35(7): 109133-. doi: 10.1016/j.cclet.2023.109133
4. [4]
  Peide Zhu , Yangjia Liu , Yaoyao Tang , Siqi Zhu , Xinyang Liu , Lei Yin , Quan Liu , Zhiqiang Yu , Quan Xu , Dixian Luo , Juncheng Wang . Bi-doped carbon quantum dots functionalized liposomes with fluorescence visualization imaging for tumor diagnosis and treatment. Chinese Chemical Letters, 2024, 35(4): 108689-. doi: 10.1016/j.cclet.2023.108689
5. [5]
  Kangmin Wang , Liqiu Wan , Jingyu Wang , Chunlin Zhou , Ke Yang , Liang Zhou , Bijin Li . Multifunctional 2-(2′-hydroxyphenyl)benzoxazoles: Ready synthesis, mechanochromism, fluorescence imaging, and OLEDs. Chinese Chemical Letters, 2024, 35(10): 109554-. doi: 10.1016/j.cclet.2024.109554
6. [6]
  Biao Huang , Tao Tang , Fushou Liu , Shi-Hui Chen , Zhi-Ling Zhang , Mingxi Zhang , Ran Cui . Quantum dots boost large-view NIR-Ⅱ imaging with high fidelity for fluorescence-guided tumor surgery. Chinese Chemical Letters, 2024, 35(12): 109694-. doi: 10.1016/j.cclet.2024.109694
7. [7]
  Du Liu , Yuyan Li , Hankun Zhang , Benhua Wang , Chaoyi Yao , Minhuan Lan , Zhanhong Yang , Xiangzhi Song . Three-in-one erlotinib-modified NIR photosensitizer for fluorescence imaging and synergistic chemo-photodynamic therapy. Chinese Chemical Letters, 2025, 36(2): 109910-. doi: 10.1016/j.cclet.2024.109910
8. [8]
  Jing-Jing Zhang , Lujun Lou , Rui Lv , Jiahui Chen , Yinlong Li , Guangwei Wu , Lingchao Cai , Steven H. Liang , Zhen Chen . Recent advances in photochemistry for positron emission tomography imaging. Chinese Chemical Letters, 2024, 35(8): 109342-. doi: 10.1016/j.cclet.2023.109342
9. [9]
  Shihong Wu , Ronghui Zhou , Hang Zhao , Peng Wu . Sonoafterglow luminescence for in vivo deep-tissue imaging. Chinese Chemical Letters, 2024, 35(10): 110026-. doi: 10.1016/j.cclet.2024.110026
10. [10]
  Xiaohong Wen , Mei Yang , Lie Li , Mingmin Huang , Wei Cui , Suping Li , Haiyan Chen , Chen Li , Qiuping Guo . Enzymatically controlled DNA tetrahedron nanoprobes for specific imaging of ATP in tumor. Chinese Chemical Letters, 2024, 35(8): 109291-. doi: 10.1016/j.cclet.2023.109291
11. [11]
  Zhihui Zhang , Ru Sun , Chong Bian , Hongbo Wang , Zhen Zhao , Panpan Lv , Jianzhong Lu , Haixin Zhang , Hulie Zeng , Yuanyuan Chen , Zhijuan Cao . A dual-protease-triggered chemiluminescent probe for precise tumor imaging. Chinese Chemical Letters, 2025, 36(2): 109784-. doi: 10.1016/j.cclet.2024.109784
12. [12]
  Botao QU , Qian WANG , Xiaogang NING , Yuxin ZHOU , Ruiping ZHANG . Deeply penetrating photoacoustic imaging in tumor tissues based on dual-targeted melanin nanoparticle. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 1025-1032. doi: 10.11862/CJIC.20230416
13. [13]
  Peng Jia , Yunna Guo , Dongliang Chen , Xuedong Zhang , Jingming Yao , Jianguo Lu , Liqiang Zhang . In-situ imaging electrocatalysis in a solid-state Li-O₂ battery with CuSe nanosheets as air cathode. Chinese Chemical Letters, 2024, 35(5): 108624-. doi: 10.1016/j.cclet.2023.108624
14. [14]
  Boran Cheng , Lei Cao , Chen Li , Fang-Yi Huo , Qian-Fang Meng , Ganglin Tong , Xuan Wu , Lin-Lin Bu , Lang Rao , Shubin Wang . Fluorine-doped carbon quantum dots with deep-red emission for hypochlorite determination and cancer cell imaging. Chinese Chemical Letters, 2024, 35(6): 108969-. doi: 10.1016/j.cclet.2023.108969
15. [15]
  Hui-Juan Wang , Wen-Wen Xing , Zhen-Hai Yu , Yong-Xue Li , Heng-Yi Zhang , Qilin Yu , Hongjie Zhu , Yao-Yao Wang , Yu Liu . Cucurbit[7]uril confined phenothiazine bridged bis(bromophenyl pyridine) activated NIR luminescence for lysosome imaging. Chinese Chemical Letters, 2024, 35(6): 109183-. doi: 10.1016/j.cclet.2023.109183
16. [16]
  Jingqi Xin , Shupeng Han , Meichen Zheng , Chenfeng Xu , Zhongxi Huang , Bin Wang , Changmin Yu , Feifei An , Yu Ren . A nitroreductase-responsive nanoprobe with homogeneous composition and high loading for preoperative non-invasive tumor imaging and intraoperative guidance. Chinese Chemical Letters, 2024, 35(7): 109165-. doi: 10.1016/j.cclet.2023.109165
17. [17]
  Lijia Xu , Tong Zhong , Wei Zhao , Bing Yao , Lin Ding , Huangxian Ju . Chemoselective labeling-based spermatozoa glycan imaging reveals abnormal glycosylation in oligoasthenotspermia. Chinese Chemical Letters, 2024, 35(4): 108760-. doi: 10.1016/j.cclet.2023.108760
18. [18]
  Ling-Ling Wu , Xiangchuan Meng , Qingyang Zhang , Xiaowan Han , Feiya Yang , Qinghua Wang , Hai-Yu Hu , Nianzeng Xing . Heavy-atom engineered hypoxia-responsive probes for precisive photoacoustic imaging and cancer therapy. Chinese Chemical Letters, 2024, 35(4): 108663-. doi: 10.1016/j.cclet.2023.108663
19. [19]
  Jinyu Guo , Yandai Lin , Shaohua He , Yueqing Chen , Fenglu Li , Renjie Ruan , Gaoxing Pan , Hexin Nan , Jibin Song , Jin Zhang . Utilizing dual-responsive iridium(Ⅲ) complex for hepatocellular carcinoma: Integrating photoacoustic imaging with chemotherapy and photodynamic therapy. Chinese Chemical Letters, 2024, 35(9): 109537-. doi: 10.1016/j.cclet.2024.109537
20. [20]
  Zhixue Liu , Haiqi Chen , Lijuan Guo , Xinyao Sun , Zhi-Yuan Zhang , Junyi Chen , Ming Dong , Chunju Li . Luminescent terphen[3]arene sulfate-activated FRET assemblies for cell imaging. Chinese Chemical Letters, 2024, 35(9): 109666-. doi: 10.1016/j.cclet.2024.109666

Get Citation

PDF

XML

Metrics

PDF Downloads(12)
Abstract views(645)
HTML views(62)

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