The physics of life: One molecule at a time

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 368, Issue 1611, 2013, Pages

  Leake, Mark C ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Bionanomedicine; Bionanotechnology; Molecular machine; Single molecule biophysics; Super resolution; Systems and synthetic biology

Indexed keywords

BIOPHYSICS; BIOTECHNOLOGY; MOLECULAR ANALYSIS; POLYMER; QUANTUM MECHANICS; RESOLUTION;

EID: 84871694264     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2012.0248     Document Type: Article

References (62)

1. Feynman RP. (1960). There's plenty of room at the bottom. Engineering and Science, 23, 22-36.
2. Taniguchi N. (1974). On the basic concept of 'nano-technology'. In Proc. Intl. Conf. Prod. Eng. Tokyo, 2, 18-23. Japan Society of Precision Engineering.
3. Leake MC. (2012). Singe-molecule cellular biophysics, 1st edn. Cambridge, UK: Cambridge University Press.
4. Harriman OLJ, Leake MC. (2011). Single molecule experimentation in biological physics: exploring the living component of soft condensed matter one molecule at a time. J. Phys. Condens. Matter. 23, 503101. (doi:10.1088/0953-8984/23/50/503101)
5. Van Holde KE, Johnson C, Shing Ho P. (2005). Principles of physical biochemistry, 1st edn. Upper Saddle River, NJ: Pearson Education.
6. Nölting B. (2009). Methods in modern biophysics, 2nd edn. Berlin, Germany: Springer.
7. Lenn T, Leake MC. (2012). Experimental approaches for addressing fundamental biological questions in living, functioning cells with single molecule precision. Open Biol. 2, 120090. (doi:10.1098/rsob. 120090)
8. Hall CE. (1956). Method for the observation of macromolecules with the electron microscope illustrated with micrographs of DNA. Biophys. Biochem. Cytol. 2, 625-628. (doi:10.1083/jcb.2.5.625)
9. Wineland D, Ekstrom P, Dehmelt H. (1973). Monoelectron oscillator. Phys. Rev. Lett. 31, 1279-1282. (doi:10.1103/PhysRevLett.31.1279)
10. Nagourney W, Sandberg J, Dehmelt H. (1986). Shelved optical electron amplifier: observation of quantum lumps. Phys. Rev. Lett. 56, 2797-2799. (doi:10.1103/PhysRevLett.56.2797)
11. Rotman B. (1961). Measurement of activity of single molecules of beta-D-galactosidase. Proc. Natl Acad. Sci. USA 47, 1981-1991. (doi:10.1073/pnas.47. 12.1981)
12. Hirschfeld T. (1976). Optical microscopic observation of single small molecules. Appl. Opt. 15, 2965-2966. (doi:10.1364/AO.15.002965)
13. Nguyen DC, Keller RA, Jett JH, Martin JC. (1987). Detection of single molecules of phycoerythrin in hydrodynamically focused flows by laser-induced fluorescence. Anal. Chem. 59, 2158-2161. (doi:10. 1021/ac00144a032)
14. Moerner WE, Kador L. (1989). Optical detection and spectroscopy in a solid. Phys. Rev. Lett. 62, 2535-2538. (doi:10.1103/PhysRevLett.62.2535)
15. Ashkin A. (1970). Acceleration and trapping of particles by radiation pressure. Phys. Rev. Lett. 24, 156-159. (doi:10.1103/PhysRevLett. 24.156)
16. Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S. (1986). Observation of a single-beam gradient force optical trap for dielectric particles. Opt. Lett. 11, 288-290. (doi:10.1364/OL.11.000288)
17. Svoboda K, Block SM. (1994). Biological applications of optical forces. Annu. Rev. Biophys. Biomol. Struct. 23, 247-285. (doi:10.1146/annurev.bb.23.060194. 001335)
18. Moffitt JR, Chemla YR, Smith SB, Bustamante C. (2008). Recent advances in optical tweezers. Annu. Rev. Biochem. 77, 205-228. (doi:10.1146/annurev. biochem.77.043007.090225)
19. Gittes F, Schmidt CF. (1998). Interference model for back-focal-plane displacement detection in optical tweezers. Opt. Lett. 23, 7-9. (doi:10.1364/OL.23. 000007)
20. Svoboda K, Schmidt CF, Schnapp BJ, Block SM. (1993). Direct observation of kinesin stepping by optical trapping interferometry. Nature 365, 721-727. (doi:10.1038/365721a0)
21. Finer JT, Simmons RM, Spudich JA. (1994). Single myosin molecule mechanics: piconewton forces and nanometre steps. Nature 368, 113-119. (doi:10. 1038/368113a0)
22. Smith SB, Cui Y, Bustamante C. (1996). Overstretching B-DNA: the elastic response of individual doublestranded and single-stranded DNA molecules. Science 271, 795-799. (doi:10.1126/science.271. 5250.795)
23. Liphardt J, Onoa B, Smith BS, Tinoco Jr I, Bustamante C. (2001). Reversible unfolding of single RNA molecules by mechanical force. Science 292, 733-737. (doi:10.1126/science.1058498)
24. Kellermayer MS, Smith SB, Granzier HL, Bustamante C. (1997). Folding-unfolding transitions in single titin molecules characterized with laser-tweezers. Science 276, 1112-1116. (doi:10.1126/science. 276.5315.1112)
25. Tskhovrebova L, Trinick J, Sleep JA, Simmons RM. (1997). Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature 387, 308-312. (doi:10.1038/387308a0)
26. Leake MC, Wilson D, Bullard B, Simmons RM. (2003). The elasticity of single kettin molecules using a two-bead laser-tweezers assay. FEBS Lett. 535, 55-60. (doi:10.1016/S0014-5793(02)03857-7)
27. Leake MC, Wilson D, Gautel M, Simmons RM. (2004). The elasticity of single titin molecules using a two-bead optical tweezers assay. Biophys. J. 87, 1112-1135. (doi:10.1529/biophysj.103.033571)
28. Binnig G, Rohrer H, Gerber Ch, Weibel E. (1982). Tunneling through a controllable vacuum gap. Appl. Phys. Lett. 40, 178-180. (doi:10.1063/1.92999)
29. Binnig G, Quate CF, Gerber C. (1986). Atomic force microscope. Phys. Rev. Lett. 56, 930-933. (doi:10. 1103/PhysRevLett.56.930)
30. Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE. (1997). Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276, 1109-1112. (doi:10.1126/science.276. 5315.1109)
31. Ha T, Enderle Th, Ogletree DF, Chemla DS, Selvin PR, Weiss S. (1996). Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl Acad. Sci. USA 93, 6264-6268. (doi:10.1073/pnas.93.13.6264)
32. Noji H, Yasuda R, Yoshida M, Kinosita KJ. (1997). Direct observation of the rotation of F1-ATPase. Nature 386, 299-302. (doi:10.1038/386299a0)
33. Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR. (2003). Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science 300, 2061-2065. (doi:10.1126/science.1084398)
34. Schmidt T, Schütz GJ, Baumgartner W, Gruber HJ, Schindler H. (1996). Imaging of single molecule diffusion. Proc. Natl Acad. Sci. USA 93, 2926-2929. (doi:10.1073/pnas.93.7.2926)
35. Gelles J, Schnapp BJ, Sheetz MP. (1988). Tracking kinesin-driven movements with nanometre-scale precision. Nature 331, 450-453. (doi:10.1038/331450a0)
36. Michalet X et al. (2013). Development of new photoncounting detectors for single-molecule fluorescence microscopy. Phil. Trans. R. Soc. B 368, 20120035. (doi:10.1098/rstb.2012.0035)
37. Sako Y, Minoguchi S, Yanagida T. (2000). Singlemolecule imaging of EGFR signalling on the surface of living cells. Nat. Cell Biol. 2, 168-172. (doi:10. 1038/35004044)
38. Axelrod D, Burghardt TP, Thompson NL. (1984). Total internal reflection fluorescence. Ann. Rev. Biophys. Bioeng. 13, 247-268. (doi:10.1146/annurev.bb.13. 060184.001335)
39. Byassee TA, Chan WC, Nie S. (2000). Probing single molecules in single living cells. Anal. Chem. 72, 5606-5611. (doi:10.1021/ac000705j)
40. Chiu S-W, Leake MC. (2011). Functioning nanomachines seen in real-time in living bacteria using single-molecule and super-resolution fluorescence imaging. Int. J. Mol. Sci. 12, 2518-2542. (doi:10.3390/ijms12042518)
41. Leake MC. (2010). Shining the spotlight on functional molecular complexes: the new science of singlemolecule cell biology. Commun. Integr. Biol. 3, 415-418. (doi:10.4161/cib.3.5.12657)
42. Dobbie IM, Robson A, Delalez N, Leake MC. (2009). Visualizing single molecular complexes in vivo using advanced fluorescence microscopy. J. Vis. Exp. 31, 1508. (doi:10.3791/1508)
43. Yan Y, Petchprayoon C, Mao S, Marriott G. (2013). Reversible optical control of cyanine fluorescence in fixed and living cells: optical lock-in detection immunofluorescence imaging microscopy. Phil. Trans. R. Soc. B 368, 20120031. (doi:10.1098/rstb.2012.0031)
44. Leake MC, Chandler JH, Wadhams GH, Bai F, Berry RM, Armitage JP. (2006). Stoichiometry and turnover in single, functioning membrane protein complexes. Nature 443, 355-358. (doi:10.1038/nature05135)
45. Delalez NJ, Wadhams GH, Rosser G, Xue Q, Brown MT, Dobbie IM, Berry RM, Leake MC, Armitage JP. (2010). Signal-dependent turnover of the bacterial flagellar switch protein FliM. Proc. Natl Acad. Sci. USA 107, 11 347-11 351. (doi:10.1073/pnas.1000284107)
46. Ulbrich MH, Isacoff EY. (2007). Subunit counting in membrane-bound proteins. Nat. Methods 4, 319-321. (doi:10.1038/nmeth1024)
47. Leake MC, Greene NP, Godun RM, Granjon T, Buchanan G, Chen S, Berry RM, Palmer T, Berks BC. (2008). Variable stoichiometry of the TatA component of the twin-arginine protein transport system observed by in vivo single-molecule imaging. Proc. Natl Acad. Sci. USA 105, 15 376-15 381. (doi:10. 1073/pnas.0806338105)
48. Lenn T, Leake MC, Mullineaux CW. (2008). Are Escherichia coli OXPHOS complexes concentrated in specialised zones within the plasma membrane? Biochem. Soc. Trans. 36, 1032-1036. (doi:10.1042/BST0361032)
49. Lenn T, Leake MC, Mullineaux CW. (2008). In vivo clustering and dynamics of cytochrome bd complexes in the Escherichia coli plasma membrane. Mol. Microbiol. 70, 1397-1407. (doi:10.1111/j. 1365-2958.2008.06486.x)
50. Ritchie K, Lill Y, Sood C, Lee H, Zhang S. (2013). Single-molecule imaging in live bacteria cells. Phil. Trans. R. Soc. B 368, 20120355. (doi:10.1098/rstb. 2012.0355)
51. Klotzsch E, Schütz GJ. (2013). A critical survey of methods to detect plasma membrane rafts. Phil. Trans. R. Soc. B 368, 20120033. (doi:10.1098/rstb. 2012.0033)
52. Plank M, Wadhams GH, Leake MC. (2009). Millisecond timescale slimfield imaging and automated quantification of single fluorescent protein molecules for use in probing complex biological processes. Integr. Biol. 1, 602612. (doi:10.1039/b907837a)
53. Cai L, Friedman N, Xie XS. (2006). Stochastic protein expression in individual cells at the single molecule level. Nature 440, 358-362. (doi:10.1038/nature04599)
54. Elf J, Li GW, Xie XS. (2007). Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191-1194. (doi:10.1126/science.1141967)
55. Reyes-Lamothe R, Sherratt DJ, Leake MC. (2010). Stoichiometry and architecture of active DNA replication machinery in Escherichia coli. Science 328, 498-501. (doi:10.1126/science. 1185757)
56. Klenerman D, Shevchuk A, Novak P, Korchev YE, Davis SJ. (2013). Imaging the cell surface and its organization down to the level of single molecules. Phil. Trans. R. Soc. B 368, 20120027. (doi:10.1098/rstb. 2012.0027)
57. Wang Y, Irudayaraj J. (2013). Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology. Phil. Trans. R. Soc. B 368, 20120026. (doi:10.1098/rstb.2012.0026)
58. Duzdevich D, Greene EC. (2013). Towards physiological complexity with in vitro single-molecule biophysics. Phil. Trans. R. Soc. B 368, 20120271. (doi:10.1098/rstb.2012.0271)
59. Sielaff H, Börsch M. (2013). Twisting and subunit rotation in single F0F1-ATP synthase. Phil. Trans. R. Soc. B 368, 20120024. (doi:10.1098/rstb.2012.0024)
60. Bilyard T, Nakanishi-Matsui M, Steel BC, Pilizota T, Nord AL, Hosokawa H, Futai M, Berry RM. (2013). Highresolution single-molecule characterization of the enzymatic states in Escherichia coli F1-ATPase. Phil. Trans. R. Soc. B 368, 20120023. (doi:10.1098/rstb. 2012.0023)
61. Robson A, Burrage K, Leake MC. (2013). Inferring diffusion in single live cells at the single-molecule level. Phil. Trans. R. Soc. B 368, 20120029. (doi:10. 1098/rstb.2012.0029)
62. Ullman G, Wallden M, Marklund EG, Mahmutovic A, Razinkov I, Elf J. (2013). High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking. Phil. Trans. R. Soc. B 368, 20120025. (doi:10.1098/rstb.2012.0025)