In situ simultaneous monitoring of ATP and GTP using a graphene oxide nanosheet-based sensing platform in living cells

Nature Protocols

Volumn 9, Issue 8, 2014, Pages 1944-1955

  Wang, Ying ^a   Tang, Longhua ^a   Li, Zhaohui ^b   Lin, Yuehe ^b,c   Li, Jinghong ^a  

^a TSINGHUA UNIVERSITY   (China)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c Washington State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; APTAMER; GRAPHENE OXIDE; GRAPHENE OXIDE NANOSHEET; GUANOSINE TRIPHOSPHATE; NANOMATERIAL; UNCLASSIFIED DRUG; DEOXYRIBONUCLEASE; GRAPHITE;

ARTICLE; BINDING AFFINITY; CELL VIABILITY ASSAY; COMPLEX FORMATION; CONFOCAL MICROSCOPY; CONTROLLED STUDY; FLUORESCENCE ANALYSIS; FLUORESCENCE IMAGING; FLUORESCENCE MICROSCOPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; HUMAN CELL; IN VITRO STUDY; MCF 7 CELL LINE; MOLECULAR IMAGING; MOLECULAR INTERACTION; MOLECULAR PROBE; MOLECULAR STABILITY; PRIORITY JOURNAL; CELL VIABILITY; ENDOCYTOSIS; NANOTECHNOLOGY; PROCEDURES;

ADENOSINE TRIPHOSPHATE; GRAPHITE; GUANOSINE TRIPHOSPHATE; MCF-7 CELLS; MICROSCOPY, FLUORESCENCE; NANOSTRUCTURES; NANOTECHNOLOGY;

EID: 84905040722     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.126     Document Type: Article

References (49)

1. Herschman, H.R. Molecular imaging: Looking at problems, seeing solutions. Science 302, 605-608 (2003
2. Baker, M. Cellular imaging: Taking a long, hard look. Nature 466, 1137-1140 (2010
3. Massoud, T.F. & Gambhir, S.S. Molecular imaging in living subjects: Seeing fundamental biological processes in a new light. Genes Dev. 17, 545-580 (2003
4. Imamura, H. et al. Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators. Proc. Natl. Acad. Sci. USA 106, 15651-15656 (2009
5. Tsuboi, T., Lippiat, J.D., Ashcroft, F.M. & Rutter, G.A. ATP-dependent interaction of the cytosolic domains of the inwardly rectifying K+ channel Kir6.2 revealed by fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 101, 76-81 (2004
6. Berg, J., Hung, Y.P. & Yellen, G. A genetically encoded fluorescent reporter of ATP: ADP ratio. Nat. Methods 6, 161-166 (2009
7. Wang, W.U., Chen, C., Lin, K.H., Fang, Y. & Lieber, C.M. Label-free detection of small-molecule-protein interactions by using nanowire nanosensors. Proc. Natl. Acad. Sci. USA 102, 3208-3212 (2005
8. Bell, C.J., Manfredi, G., Griffiths, E.J. & Rutter, G.A. Luciferase expression for ATP imaging: Application to cardiac myocytes. Methods Cell Biol. 80, 341-352 (2007
9. Jose, D.A. et al. Colorimetric sensor for ATP in aqueous solution. Org. Lett. 9, 1979-1982 (2007
10. Lee, D.H., Kim, S.Y. & Hong, J.I. A fluorescent pyrophosphate sensor with high selectivity over ATP in water. Angew. Chem. Int. Ed. 43, 4777-4780 (2004
11. Sancenón, F., Descalzo, A.B., Martínez-Mánñz, R., Miranda, M.A. & Soto, J. A colorimetric ATP sensor based on 1, 3, 5-Triarylpent-2-en-1, 5-diones. Angew. Chem. Int. Ed. 40, 2640-2643 (2001
12. Mizukami, S., Nagano, T., Urano, Y., Odani, A. & Kikuchi, K. A fluorescent anion sensor that works in neutral aqueous solution for bioanalytical application. J. Am. Chem. Soc. 124, 3920-3925 (2002
13. Schneider, S.E., O'Neil, S.N. & Anslyn, E.V. Coupling rational design with libraries leads to the production of an ATP selective chemosensor. J. Am. Chem. Soc. 122, 542-543 (2000
14. Wang, S.L. & Chang, Y.T. Combinatorial synthesis of benzimidazolium dyes and its diversity directed application toward GTP-selective fluorescent chemosensors. J. Am. Chem. Soc. 128, 10380-10381 (2006
15. McCleskey, S.C., Griffin, M.J., Schneider, S.E., McDevitt, J.T. & Anslyn, E.V. Differential receptors create patterns diagnostic for ATP and GTP. J. Am. Chem. Soc. 125, 1114-1115 (2003
16. Kwon, J.Y. et al. Fluorescent GTP-sensing in aqueous solution of physiological pH. J. Am. Chem. Soc. 126, 8892-8893 (2004
17. Neelakandan, P.P., Hariharan, M. & Ramaiah, D. A supramolecular ON-OFF-ON fluorescence assay for selective recognition of GTP. J. Am. Chem. Soc. 128, 11334-11335 (2006
18. Xu, Z. et al. Unique sandwich stacking of pyrene-Adenine-pyrene for selective and ratiometric fluorescent sensing of ATP at physiological pH. J. Am. Chem. Soc. 131, 15528-15533 (2009
19. Ojida, A. et al. Bis(Dpa-Zn-II) appended xanthone: Excitation ratiometric chemosensor for phosphate anions. Angew. Chem. Int. Ed. 45, 5518-5521 (2006
20. Li, C., Numata, M., Takeuchi, M. & Shinkai, S. A sensitive colorimetric and fluorescent probe based on a polythiophene derivative for the detection of ATP. Angew. Chem. Int. Ed. 44, 6371-6374 (2005
21. Nutiu, R. & Li, Y.F. Structure-switching signalling aptamers. J. Am. Chem. Soc. 125, 4771-4778 (2003
22. Nutiu, R. & Li, Y.F. In vitro selection of structure-switching signaling aptamers. Angew. Chem. Int. Ed. 117, 1085-1089 (2005
23. Li, N. & Ho, C.-M. Aptamer-based optical probes with separated molecular recognition and signal transduction modules. J. Am. Chem. Soc. 130, 2380-2381 (2008
24. Liu, J. & Lu, Y. Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew. Chem. Int. Ed. 45, 90-94 (2006
25. Zayats, M., Huang, Y., Gill, R., Ma, C. & Willner, I. Label-free and reagentless aptamer-based sensors for small molecules. J. Am. Chem. Soc. 128, 13666-13667 (2006
26. Geim, A.K. Graphene: Status and prospects. Science 324, 1530-1534 (2009
27. Liu, X.Q., Aizen, R., Freeman, R., Yehezkeli, O. & Willner, I. Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: Application for logic gate operations. ACS Nano 6, 3553-3563 (2012
28. Liu, B.W., Sun, Z.Y., Zhang, X. & Liu, J.W. Mechanisms of DNA sensing on graphene oxide. Anal. Chem. 85, 7987-7993 (2013
29. Huang, P.J. & Liu, J.W. Molecular beacon lighting up on graphene oxide. Anal. Chem. 84, 4192-4198 (2012
30. Chen, D., Feng, H. & Li, J. Graphene oxide: Preparation, functionalization, and electrochemical applications. Chem. Rev. 112, 6027-6053 (2012
31. Wang, Y., Li, Z.H., Wang, J., Li, J.H. & Lin, Y.H. Graphene and graphene oxide: Biofunctionalization and applications in biotechnology. Trends Biotechnol. 29, 205-212 (2011
32. Wang, Y., Lu, J., Tang, L.H., Chang, H.X. & Li, J.H. Graphene oxide amplified electrogenerated chemiluminescence of quantum dots and its selective sensing for glutathione from thiol-containing compounds. Anal. Chem. 81, 9710-9715 (2009
33. Liu, Z., Robinson, J.T., Sun, X.M. & Dai, H.J. PEGylated nanographene oxide for delivery of water-insoluble cancer drugs. J. Am. Chem. Soc. 130, 10876-10877 (2008
34. Lu, C.H. et al. Using graphene to protect DNA from cleavage during cellular delivery. Chem. Commun. 46, 3116-3118 (2010
35. Chang, H.X., Tang, L.H., Wang, Y., Jiang, J.H. & Li, J.H. Graphene fluorescence resonance energy transfer aptasensor for the thrombin detection. Anal. Chem. 82, 2341-2346 (2010
36. Wang, Y. et al. Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells, . J. Am. Chem. Soc. 132, 9274-9276 (2010
37. Nel, A.E. et al. Understanding biophysicochemical interactions at the nano-bio interface. Nat. Mat. 8, 543-557 (2009
38. Wang, Y. et al. In situ live cell sensing of multiple nucleotides exploiting DNA/RNA aptamers and graphene oxide nanosheets. Anal. Chem. 85, 6775-6782 (2013
39. Liu, J., Cao, Z. & Lu, Y. Functional nucleic acid sensors. Chem. Rev. 109, 1948-1998 (2009
40. Fang, X. & Tan, W. Aptamers generated from cell-SELEX for molecular medicine: A chemical biology approach. Acc. Chem. Res. 43, 48-57 (2010
41. Huizenga, D.E. & Szostak, J.W. A DNA aptamer that binds adenosine and ATP. Biochemistry 34, 656-665 (1995
42. Carothers, J.M., Oestreich, S.C. & Szostak, J.W. Aptamers selected for higher-Affinity binding are not more specific for the target ligand. J. Am. Chem. Soc. 128, 7929-7937 (2006
43. Davis, J.H. & Szostak, J.W. Isolation of high-Affinity GTP aptamers from partially structured RNA libraries. Proc. Natl. Acad. Sci. USA 99, 11616-11621 (2002
44. Carothers, J.M., Oestreich, S.C., Davis, J.H. & Szostak, J.W. Informational complexity and functional activity of RNA structures. J. Am. Chem. Soc. 126, 5130-5137 (2004
45. Carothers, J.M., Davis, J.H., Chou, J.J. & Szostak, J.W. Solution structure of an informationally complex high-Affinity RNA aptamer to GTP. RNA 12, 567-579 (2006
46. Li, Q. & Chang, Y.T. A protocol for preparing, characterizing and using three RNA-specific, live cell imaging probes: E36, E144 and F22. Nat. Protoc. 1, 2922-2932 (2006
47. Pittet, M.J., Swirski, F.K., Reynolds, F., Josephson, L. & Weisslede, R. Labeling of immune cells for in vivo imaging using magnetofluorescent nanoparticles. Nat. Protoc. 1, 74-79 (2006
48. Zrazhevskiy, P., True, L.D. & Gao, X.H. Multicolor multicycle molecular profiling with quantum dots for single-cell analysis. Nat. Protoc. 8, 1852-1869 (2013
49. Robinson, K.M., Janes, M.S. & Beckman, J.S. The selective detection of mitochondrial superoxide by live-cell imaging. Nat. Protoc. 3, 941-947 (2008