A DNA nanomachine that maps spatial and temporal pH changes inside living cells

Nature Nanotechnology

Volumn 4, Issue 5, 2009, Pages 325-330

  Modi, Souvik ^a   Swetha, M G ^a   Goswami, Debanjan ^a   Gupta, Gagan D ^a   Mayor, Satyajit ^a   Krishnan, Yamuna ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SYSTEMS; DNA; ENERGY TRANSFER; FORSTER RESONANCE ENERGY TRANSFER; NANOTECHNOLOGY; PH SENSORS;

DNA NANOMACHINE; FLUORESCENCE RESONANCE ENERGY TRANSFER; HIGH DYNAMIC RANGE; LIVING CELL; LIVING SYSTEMS; MOLECULAR CONFORMATION; NANO-DEVICES; NANOMACHINES;

MOLECULAR DYNAMICS;

DNA;

ANIMAL CELL; ARTICLE; CELL PH; DNA CONFORMATION; ENDOSOME; FLUORESCENCE RESONANCE ENERGY TRANSFER; NANODEVICE; NONHUMAN; PH MEASUREMENT; PRIORITY JOURNAL; ANIMAL; CELL CULTURE; CHEMISTRY; EQUIPMENT DESIGN; GENETIC PROCEDURES; HUMAN; INSTRUMENTATION; NANOTECHNOLOGY; PH; ULTRASTRUCTURE;

ANIMALS; BIOSENSING TECHNIQUES; CELLS, CULTURED; DNA; EQUIPMENT DESIGN; HUMANS; HYDROGEN-ION CONCENTRATION; MOLECULAR PROBE TECHNIQUES; NANOTECHNOLOGY;

EID: 67049154133     PISSN: 17483387     EISSN: 17483395     Source Type: Journal    
DOI: 10.1038/nnano.2009.83     Document Type: Article

References (33)

1. Bath, J. & Turberfield, A. J. DNA nanomachines. Nature Nanotech. 2, 275-284 (2007).
2. Shih, W. Biomolecular self-assembly: Dynamic DNA. Nature Mater. 7, 98-100 (2008).
3. Yurke, B., Turberfield, A. J., Mills, A. P. Jr, Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605-608 (2000).
4. Liu, J. & Lu, Y. A colorimetric lead biosensor using DNA enzyme-directed assembly of gold nanoparticles. J. Am. Chem. Soc. 125, 6642-6643 (2003).
5. Alberti, P. & Mergny, J.-L. DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc. Natl Acad. Sci. USA. 100, 1569-1573 (2003).
6. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R. & Shapiro, E. An autonomous molecular computer for logical control of gene expression. Nature 429, 423-428 (2004).
7. Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. A. Programming biomolecular self-assembly pathways. Nature 451, 318-322 (2008).
8. Beyer, S. & Simmel, F. C. A modular DNA signal translator for the controlled release of a protein by an aptamer. Nucleic Acids Res. 34, 1581-1587 (2006).
9. Mao, C., Sun, W., Shen, Z. & Seeman, N. C. A nanomechanical device based on the B-Z transition of DNA. Nature 397, 144-146 (1999).
10. Allan, V. J. & Schroer, T. A. Membrane motors. Curr. Opin. Cell Biol. 11, 476-482 (1999).
11. Griesbeck, O. Fluorescent proteins as sensors for cellular functions, Curr. Opin. Neurobiol. 14, 636-641 (2004).
12. Ai1, H. W., Hazelwood, K. L., Davidson, M. W. & Campbell, R. E. Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors. Nature Methods 5, 401-403 (2008).
13. Gehring, K., Leroy, J.-L. & Gueron, M. A tetrameric DNA structure with protonated cytidine-cytidine base pairs. Nature 363, 561-565 (1993).
14. Mukherjee, S. Ghosh, R. N. & Maxfield, F. R. Endocytosis. Physiol. Rev. 77, 759-803 (1997).
15. Montesano, R., Roth, J., Robert, A. & Orci, L. Non-coated membrane invaginations are involved in binding and internalization of cholera and tetanus toxins. Nature 296, 651-653 (1982).
16. Stryer, L. & Haugland, R. P. Energy transfer: a spectroscopic ruler. Proc. Natl Acad. Sci. USA 58, 719-726 (1967).
17. Liu, D. & Balasubramanian, S. A proton-fuelled DNA nanomachine. Angew Chem. Int. Ed. 42, 5734-5736 (2003).
18. Liedl, T. & Simmel, F. C. Switching the conformation of a DNA molecule with a chemical oscillator. Nano Lett. 5, 1894-1898 (2005).
19. Ohkuma, S. & Poole, B. Fluorescence probe measurement of the intralysosomal pH in living cells and the perturbation of pH by various agents. Proc. Natl Acad. Sci. USA 75, 3327-3331 (1978).
20. Overly, C. C., Lee, K. D., Berthiaumet, E. & Hollenbeck, P. J. Quantitative measurement of intraorganelle pH in the endosomal-lysosomal pathway in neurons by using ratiometric imaging with pyranine. Proc. Natl Acad. Sci. USA 92, 3156-3160 (1995).
21. Guha, A., Sriram, V., Krishnan, K. S. & Mayor, S. Shibire mutations reveal distinct dynamin-independent and -dependent endocytic pathways in primary cultures of Drosophila hemocytes. J. Cell Sci. 116, 3373-3386 (2003).
22. Miesenbock, G., De Angelis, D. A. & Rothman, J. E. Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins Nature 394, 192-195 (1998).
23. Yamashiro, D. J. & Maxfield, F. R. Acidification of morphologically distinct endosomes in mutant and wild-type Chinese hamster ovary cells. J. Cell Biol. 105, 2723-2733 (1987).
24. Sipe, D. M. & Murphy, R. F. High-resolution kinetics of transferrin acidification in BALB/3T3 cells exposed to pH 6 followed by temperature sensitive alkalinization during recycling. Proc. Natl Acad. Sci. USA 84, 7119-7123 (1987).
25. Thomas, J. A., Buschbaum, R. N., Zimniak, A. & Racker, E. Intracellular pH measurements in Ehrlich ascites tumor cells utilizing spectroscopic probes generated in situ. Biochemistry 18, 2210-2218 (1979).
26. Murphy, R. F., Powers, S. & Cantor, C. R. Endosome pH measured in single cells by dual fluorescence flow cytometry: rapid acidification of insulin to pH 6. J. Cell Biol. 98, 1757-1762 (1984).
27. Roberta, L. G. & Acosta, D. Ratiometric measurement of intracellular pH of cultured cells with BCECF in a fluorescence multi-well plate reader. In Vitro Cell. Devel. Biol. Animal 33, 256-260 (1997).
28. Koo, M. K., Oh, C. H., Holme, A. L. & Pervaiz, S. Simultaneous analysis of steady-state intracellular pH and cell morphology by automated laser scanning cytometry. Cytometry A 71A, 87-93 (2007).
29. Disbrow, G. L., Hanover, J. A. & Schlegel, R. Endoplasmic reticulum-localized human papillomavirus type 16 E5 protein alters endosomal pH but not trans-Golgi pH. J. Virol. 79, 5839-5846 (2005).
30. Downey, G. P. et al. Phagosomal maturation, acidification, and inhibition of bacterial growth in nonphagocytic cells transfected with FcgRIIA Receptors J. Biol. Chem. 274, 28436-28444 (1999).
31. Simchowitz, L. & Cragoe, E. J. Jr Regulation ofhuman neutrophil chemotaxis by intracellular pH. J. Biol. Chem. 261, 6492-6500 (1986).
32. Matsuyama, S. & Reed, J. C. Mitochondria-dependent apoptosis and cellular pH regulation. Cell Death Diff. 7, 1155-1165 (2000).
33. Altan, N., Chen, Y., Schindler, M. & Simon, S. M. Defective acidification in human breast tumor cells and implications for chemotherapy. J. Exp. Med. 187, 1583-1598 (1998).