Nanobiologie, nieuwe mogelijkheden op de grens van nano en bio Cees Dekker

Transcription

1 Nanobiologie, nieuwe mogelijkheden op de grens van nano en bio Cees Dekker Kavli Institute of NanoScience, Delft University of Technology, The Netherlands,

2 Nano Bio

3 Fantastic Voyage (1966)

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5 Gattaca (1997)

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7 The real world (geen science fiction)

8 an astonishing question: What if we can start nanoengineering this world of biology?

9 Outline Introduction to nanotechnology Introduction to synthetic biology Some work from my lab Motor proteins working out in a lab on a chip Nanopores Outlook to society 9

10 Nano: De wereld van het kleine keer keer km 10 cm 10-9 m 1 nanometer

11 nanos is een dwerg: 1 nanometer = 1 miljoenste millimeter = 6 koolstof atomen op een rij 1 nanometer een menselijke haar: nanometer!

12 What is nanotechnology? Imaging, manipulating, and measuring on single atoms and molecules Don Eigler

13 Een korte geschiedenis van nano Leucippus of Miletus, voor Christus Democritus, voor Christus poneerden atomen: ondeelbare deeltjes, die door een verschillende rangschikking stoffen met verschillende eigenschappen vormen

14 Microscopie Antoni van Leeuwenhoek ( )

15 Richard Feynman Lezing in 1959 : There is plenty of room at the bottom " in the great future - we can arrange the atoms the way we want; the very atoms, all the way down! "

16 Scanning tunneling microscope (STM) en andere tastmicroscopen

17 Don Eigler

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19 What is synthetic biology? Synthetic biology is the engineering of biology: the synthesis of complex, biologically-based (or bio-inspired) systems, which display functions that do not exist in nature. In essence, synthetic biology will enable the design of biological systems in a rational and systematic way. (EU-synthetic biology expert group)

20 First Kavli Futures Symposium: The merging of bio and nano The Ilulissat statement Some quotes: Fifty years from now, synthetic biology will be as pervasive and transformative as is electronics today. And as with that technology, the applications and impacts are impossible to predict in the field s nascent stages. Nevertheless, the decisions we make now will have enormous impact on the shape of this future. Synthetic biology offer solutions to daunting problems of climate change, energy, health, and water resources: microorganisms that convert plant matter to fuels or that synthesize new drugs or target and destroy rogue cells in the body. The potential benefits are truly extraordinary. See

21 Goal of synthetic biology is to make biology easy to engineer Treating life as a machine If you consider nature to be a machine, you see it is not perfect and it can be revised and improved. Drew Endy A garage technology I predict that the domestication of biotechnology will dominate our lives during the next fifty years at least as much as the domestication of computers has dominated our lives during the previous fifty years. Freeman Dyson

22 Convergence of technologies At the boundary between living and nonliving Nano Non-living Info Bio Living Cogno

23 Synthetic biology: engineering of biology Engineering design: abstraction hierarchy modularity standardization isolation, separation of concerns flexibility Real world complexity (= minerals, trees) Prefabrication Design Stones, glass. (= building blocks) Construction Constructed complex ( = house + waste products) Tom Knight, MIT

24 Synthetic biology: engineering of biology Engineering design: abstraction hierarchy modularity standardization isolation, separation of concerns flexibility Real world complexity (= food ) Design = genome dntps Amino acids Na +, K +, Mg 2+. (= building blocks) Constructed complex ( = living system + waste products)

25 Catalog of standard biological parts

26 Two approaches in synthetic biology top-down biology in vivo bottom-up biology? in vitro

27 in vivo

28 Synthetic biology in vivo - Synthetic chromosomes - Codon reassignment - Incorporation of non-natural amino acids - From triplet to quadruplet code (64 -> 256) - Artificial gene networks - Reprogramming of signaling pathways - Large-scale engineering of metabolic pathways Keasling et al (2006) Nature, 440, 940

29 Synthetic biology in vitro Hybrid materials: bio-synthetic - Interfacing cells and proteins with macroscopic world - Self-assembling components - Synthesizing and sequening DNA

30 Example: Sequencing and synthesizing DNA Reading and writing DNA

31 Another use: DNA as a physical building material

32 DNA origami Paul W.K. Rothemund

33 Current research in my own research group Chromatin, remodeling, DNA break repair, homologous recombination Dynamics of evolution of bacteria in microfabricated landscapes Solid state nanopores

34 Motor-protein-mediated transport in nanofabricated channels

35 Kinesins are motor proteins that walk along microtubules

36 The vision: Can we use such biomotors for transport, sorting, analysis, Advantages - Active transport - Specific and selective - Work against flow Need to control: - Confinement - Direction - Docking - Steering

37 Inverted assay: microtubules move on a carpet of kinesins Text

38 Lots of technology.. Van den Heuvel & Dekker, Science, 2007

39 Rectification of kinesin-driven microtubule motility Rectification efficiency 92 % in open structures 100% in closed fluidic channels van den Heuvel, M. G. L.;Butcher, C. T.; Smeets, R. M. M.; Diez, S.; Dekker, C. Nano Lett. 2005, 5,

40 Electrical steering of microtubules in nanostructures V 0 V 1 F +V

41 This new biomotor-powered nanofluidic technology: 1. is a useful demonstrator for applications 2. provides new handles for single-molecule biophysics: persistence length from microtubule trajectories curvature of field-induced microtubule trajectories electrophoresis of individual MTs

42 EXAMPLE 2: Solid state nanopores for genomic screening

43 Idea of the experiment: For a review see: C. Dekker, Nature Nanotech. 2, 209 (2007)

44 Nanopores in biology: ion channels nuclear pore complexes viral infection protein secretion bacterial gene transfer etc etc

45 Dreams of nanopore-based DNA sequencing

46 α-hemolysin membrane pores Aksimentiev et al.,

47 solid-state nanopores

48 dsdna translocation through a 10 nm nanopore A. Storm et al, Phys. Rev. E71, (2005)

49 Translocation of proteins and protein-coated DNA Screening of local structures along DNA, e.g., proteins, transcription factors, nucleosomes, etc

50 Local patches of RecA protein along DNA S. Kowalczyk, et al, 2009

51 DNA RecA-DNA mixed NA mixed 2 ns 2 ms

52 Use solid-state nanopores as a chassis to build biomimetic artificial nuclear pore complexes in collaboration with Roderick Lim and Ueli Aebi (Basel) & Dirk Gorlich (MPI Gottingen)

53 Idea of our approach: 1. Build an artificial nuclear pore complex real pore: mimic: 2. Measure on that artificial nuclear pore complex Use current as probe Probe transport of translocating proteins

54 Individual Importin-Beta translocations through a pore ImpB through a bare pore ImpB through a modified pore <t dwell > = 0.12±0.02 ms <t dwell > = 2.2 ± 0.5 ms

55 Maatschappelijke impact van (bio)nanotech

56 Wat kun je nu met die nanobuisjes..? Velerlei toepassingen van nanoelektronica Meer rekenkracht van (quantum) computers Cryptografie Goedkopere bottom-up productietechnieken Ambient intelligence

57 Wat kun je met die biomoleculen..? Velerlei toepassingen van bionanotechnologie Genomic analysis en labs-on-a-chip (DNA chips, eiwitchips,..) Koppeling zenuwcellen en elektronica (pacemakers, behandeling dwarslaesie,..) Nieuwe types medicijnen (drug delivery systemen) Biobrandstoffen, groene chemie

58 Niet alleen toepassingen maar ook ethische overwegingen To what extent will the new manipulability of life lead to new understandings of life? Deconstructing cells may reveal minimal conditions of life Constructing cells might become a future possibility and lead to new conceptions of life What is at stake here in terms of cultural understandings? We may expect (religious) contestation as soon (?!) as these developments touch upon human life: synthesizing a human genome, creating conditions for genetic enhancement Edinburgh scientists create cell division shortcut Researchers from Edinburgh University have discovered a way to redesign the process by which cells divide. This development could lead to treatments of genetic disorders at some point in the future (04 July 2009) Dirk Stemerding and Rini van Est Cultural understandings of engineering life

59 Grote mogelijkheden voor (bio)nanotechnologie Ook mogelijke gevaren?

60 Maatschappelijke issues, droombeelden en schrikbeelden Deels betreft dit nano, deels nieuwe technologie in het algemeen Wel reële vraag: Wat is het effect van nieuwe nanodeeltjes op mens en milieu? from Jeff Johnson at Hybrid Medical Animation Uit het Rathenau rapport het kleine te waarderen Om

61 Samenvatting Nano en Bio zijn fascinerend; de combinatie geeft intrigerende mogelijkheden Bionanotechnologie is heel divers en zal breed maatschappelijke impact hebben De discussie over die impact is al vroeg gestart

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