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Directed Evolution: A Historical Exploration into an Evolutionary Experimental System of Nanobiotechnology, 1965–2006

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Abstract

This study explores the history of nanotechnology from the perspective of protein engineering, which differs from the history of nanotechnology that has arisen from mechanical and materials engineering; it also demonstrates points of convergence between the two. Focusing on directed evolution—an experimental system of molecular biomimetics that mimics nature as an inspiration for material design—this study follows the emergence of an evolutionary experimental system from the 1960s to the present, by detailing the material culture, practices, and techniques involved. Directed evolution, as an aspect of nanobiotechnology, is also distinct from the dominant biotechnologies of the 20th century. The experimental systems of directed evolution produce new ways of thinking about molecular diversity that could affect concepts concerning both biology and life.

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Notes

  1. National Nanotechnology Initiative. What is Nanotechnology? http://www.nano.gov/html/facts/whatIsNano.html. Accessed August 30, 2008.

  2. The idea of ‘standard’ and ‘hidden’ histories of NT is indebted to historians of nanotechnology, such as David Baird, Ashley Shew, Cyrus Mody, and Patrick McCray. Mody and McCray have focused on hidden histories of NT related to material science and electrical engineering, such as molecular electronics and molecular beam epitaxy. See McCray (2007) and Choi and Mody (forthcoming). To see why hidden histories matter in the context of nanotechnology, see Mody (forthcoming). In this study, Mody is critical of the analogy between NT and BT because, as he claims, there is NT other than BT. I agree with his idea, but further criticize this analogy in a slightly different way, because the material culture of directed evolution as one of the nanobiotechnologies differs from those of dominant biotechnologies in the second half of the 20th century.

  3. Angela Belcher: Harnessing viral power: Letting nature do the work. http://alum.mit.edu/ne/opendoor/200507/belcher.html. Accessed 30 August 2008.

  4. One study of NT from the vantage of biology is Lenoir and Giannella (2006).

  5. More exactly, Roco defines the fourth generation of nanotechnology as ‘molecular nanosystems with heterogeneous molecules, based on biomimetics and new design’. Roco, M. The future of National Nanotechnology Initiative. http://www.Nano.Gov/html/res/roco_aiche_48slides.pdf. 31 August 2008.

  6. The radioactive materials were used to distinguish original Qβ-RNAs from any new RNAs that might be synthesized by Qβ replicase in test tubes. The synthesized RNAs would be radioactive.

  7. Spiegelman et al. claimed that if the number of infectious units in all the tubes corresponded to the amount of radioactive RNA found, this evidence could prove that the newly synthesized RNAs are identical copies of the original infectious RNAs (Qβ-RNA) (Spiegelman et al. 1965, p. 925).

  8. The first site was a structural gene called the ‘ebgA’, a mutation that was presumed to increase activity toward lactose. The second site was a regulatory gene called the ‘ebgR’, a mutation that would presumably increase the gene expression of ebgA (Hall 1978, p. 674).

  9. In this experiment, ethidium bromide inhibited the replication of a specific RNA variant called ‘V2’ from a class of RNA mutants.

  10. The proof-reading ability of DNA synthesis by Taq DNA polymerase is also reduced in the presence of Mn2+ (Leung et al. 1989, p. 12).

  11. This method first fragments the genes of progeny with the restriction of an enzyme called ‘DNaseI’ into a pool of random DNA fragments. The DNA fragments are assembled into a full-length gene through repeated cycles of annealing in the presence of Taq DNA polymerase. This method then selects the best recombinations. The selected pool of improved recombinants becomes the starting point for a subsequent round of DNA shuffling (Stemmer 1994b).

  12. Arnold (1998, p. 127) notes that ‘sex provides some significant benefits in natural evolution (to make up for its obvious costs?)’. Some of the benefits can be captured in the test tube. By recombining parental genes to produce libraries of different mutation combinations, we can quickly accumulate the beneficial mutations, while removing any deleterious ones. Using the ‘DNA shuffling’ method … we have been adding a little sex to our evolutionary design strategy’.

  13. Yeast display (i.e., cell surface display) can express proteins on the surface of a microorganism. Yeast display uses the fusion of proteins and agglutinin, a protein involved in cell adhesion. This protein can be tightly bound to a cell wall (Georgiou et al. 1997, p. 30). In 2001, yeast display was sold to Abbott Laboratories, which commercialized in 2002 a monoclonal antibody called Humira, which uses phage display.

  14. Flow cytometers consist of sorters and analyzers. They collect and analyze data on cells, but can also sort cells with desired properties. The development of sorters was indebted to the development of optics and lasers. Contemporary commercial high-speed cell sorters use one or two lasers and can generate between five and eight fluorescence signals from each cell (Ashcroft et al. 2000). The development of analyzers has resulted from the development of IT. Flow cytometers are equipped with computers that can automatically quantify the number of cells screened. .

  15. See Keating and Cambrosio (1994) for an early history of flow cytometry. Leonard Herzenberg at Stanford invented flow cytometry in 1969, using a mercury arc lamp; a second version followed in 1971 that used an argon ion laser to detect cells tagged with fluorescent markers. With funding from the National Institutes of Health, Herzenberg and the Stanford engineers commercialized their instruments through Becton Dickinson Inc. in 1975.

  16. Cell surface display, in conjunction with flow cytometry, begins with the incubation of peptide-displayed libraries with a florescence substance called FRET. FRET is able to emit blue light and red light, depending on the binding of this substrate with the peptides displayed on the cell surface—that is to say, if FRET binds a target peptide, it emits red light; otherwise, it emits blue light. Therefore, flow cytometers can sort and quantify screened cells (see Daugherty et al. 2000, p. 213).

  17. For an introduction of commercial flow cytometer, see Chapman (2000). Three companies, Becton Dickinson (San Jose, CA, USA) and Beckman Coulter (Fullerton, CA, USA) and Cytomation (Fort Collins, CO, USA) dominate the commercial flow cytometer market (Chapman 2000, p. 4; Battye et al. 2000) Moreover, according to Ashcroft et al. (2000, p. 14), technological origins of commercial flow cytometers can be traced to ‘groups in Europe, Australia and the USA. Europe had Radiobiological Institute (Netherlands) and the Max Planck Institutes (Germany), while biological groups in the US National laboratories, (Livermore, Los has seen a steady advance in the performance Alamos and Oak Ridge) plus groups at Stanford and Rochester were the US proponents. In Australia, researchers were at the Tumour Biology branch of the Ludwig Institute’.

  18. Available at http://www.maxygen.com/newsview.php?listid=91. Accessed on August 31, 2008.

  19. Radetsky, P. Speeding through evolution - Gerald Joyce's directed-evolution experiments. Discover (May 1994). http://findarticles.com/p/articles/mi_m1511/is_n5_v15/ai_15341763. Accessed 31 August 2008.

  20. Redox proteins and enzymes are metalloproteins. Redox proteins for bioelectronic devices are capable of electronic transfer and self-assembly at the nanoscale; they should be immobilized on an electrode surface and have multi-redox centers. According to Gilardi and Fantuzzi (2001), redox proteins ‘are ‘wired up’ in efficient electron-transfer chains, are ‘assembled’ in artificial multidomain structures (molecular Lego), [and] are ‘linked’ to surfaces in nanodevices for biosensing and nanobiotechnological applications’.

  21. Gilardi and Fantuzzi (2001) notes, ‘The aim of molecular Lego is to generate artificial redox chains by assembling genes of well characterized redox proteins and enzymes as prototypes for engineering systems that can be exploited by bioelectrochemistry. … The DNA shuffling of introns and exons generates multidomain proteins assembled from building blocks. The molecular Lego approach selects key domains, or building blocks, to assemble artificial redox chains with the desired properties, ultimately capable of communicating with electrode surfaces’ (my emphasis).

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Acknowledgements

This study is largely indebted to Linda Hogle’s thoughtful advice. I also would like to thank Alan Porter and Alex Stephens for their bibliometric analysis, as well as Erich Schienke, Doogab Yi, Byoungyoon Kim, and Cyrus Mody for their careful and critical comments. I conducted this research at the Center for Nanotechnology in Society-Arizona State University, at the University of Wisconsin-Madison. This study is based upon work supported by the National Science Foundation, under grant #0531194. Any opinions, findings, and conclusions or recommendations expressed in this study are those of the author, and they do not necessarily reflect the views of the National Science Foundation.

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    Eun-Sung Kim

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Kim, ES. Directed Evolution: A Historical Exploration into an Evolutionary Experimental System of Nanobiotechnology, 1965–2006. Minerva 46, 463–484 (2008). https://doi.org/10.1007/s11024-008-9108-9

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