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Course outline

Course outline. Introduction. What is self-organisation?. System with discrete components Spontaneously ordered properties Global Order from Local, random interactions. Living systems. Self-organized catalytic set of molecules Origin of life RNA world Driving force is G

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Course outline

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  1. Course outline

  2. Introduction

  3. What is self-organisation? • System with discrete components • Spontaneously ordered properties • Global Order from Local, random interactions

  4. Living systems • Self-organized catalytic set of molecules • Origin of life • RNA world • Driving force is G • Goal is self-replication

  5. Artificial self-organisation systems • Self-Reproducing (cellular) Automata • Artificial Neural Networks • Boolean Networks • Artificial Life Systems • Evolutionary Systems • DNA Systems

  6. Self-organisation DNA systems • Seeman-Winfree • Construction of Specific Geometrical and Topological Targets from DNA • Construction Process => Computation • Cellular Automata and Tilings • Basic Building Block is Stiff DNA Double-Crossover Molecule (DX)

  7. Self-assembly • A process involving the spontaneous self-ordering of substructures into superstructures. • Is a Bottom-up Process rather than a Top-Down process used in most manufacturing or lithography processes

  8. Cellular self-assembly • Cells perform a multiplicity of self-assemblies: • Cell walls (via lipids), • Microtubules • Cellular Superstructures and Transport Structures • Utilize the specificity of ligand affinities to direct the self-assembly

  9. Construction with smart brick

  10. Tiles binding mechanisms Molecular affinity • hydrogen bonding of complementary DNA or RNA bases Magnetic attraction (U. of Wisconsin materials science group) • pads with magnetic orientations constructed by curing polymer/ferrite composites in the presence of strong magnet fields, or • pads with patterned strips of magnetic orientations [Reif]. Capillary force [Whitesides], [Rothmemund, 1999] • using hydrophobic/hydrophilic (capillary) effects at surface boundaries that generate lateral forces. Shape complementarity [Whitesides] • using the conformational shape affinity of the tile sides to hold them together.

  11. Scale of tiling assembly • Meso-scale tiling assemblies • have tiles of size a few millimeters up to a few centimeters. • Molecular-scale tiling assemblies • have tiles of size up to a few hundred Angstroms.

  12. Magnetic meso-scale self-assembly • Self assembly on Water/Air Interface. • Pads with magnetic orientations constructed by curing polymer/ferrite composites in the presence of strong magnet fields. Wisconsin material sciences group

  13. Magnetic meso-scale self-assembly Wisconsin material sciences group

  14. Magnetic meso-scale self-assembly Wisconsin material sciences group

  15. Programming 2-d DNA lattices • for the construction of molecular scale structures • for rendering patterns at the molecular level

  16. Programming 2-d DNA lattices A 2D DNA lattice is constructed by a self-assembly processBegins with the assembly of DNA tile nanostructures DNA tiles of size 14 x 7 nanometers Composed of short DNA strands with Holliday junctions  These DNA tiles self-assemble to form a 2D lattice: The assembly is programmableTiles have sticky ends that provide programming for the patterns to be formed. Alternatively, tiles self-assemble around segments of a DNA strand encoding a 2D pattern.

  17. Programming 2-d DNA lattices Patterning • Each of these tiles has a surface perturbation depending on the pixel intensity. • pixel distances 7 to 14 nanometers Key Applications • Assembly of molecular electronic components and circuits • molecular robotic components • image rendering • cryptography • mutation detection

  18. Programming 2-d DNA lattices

  19. DX molecules • DX is double crossover • Antiparallel strands • 4-arm junctions • Full turn in B-form of DNA (10.5 bp) • Even or Odd number of half turns • DAE, DAO

  20. DX molecules • DNA crossover molecules self-assembled from artificially synthesized single stranded DNA.

  21. DX molecules

  22. DNA tiles • Double-crossover (DX) Tiles [Winfree, Seeman]: • consist of two double-helices fused by crossover strands. • DAE contains an Even number of helical half-turns between crossover points. • DAO contains an Odd number. • Anti-parallel crossovers: • cause a reversal in direction of strand propagation through the tile following exchange of strand to a new helix. • DAO and DAE are double-crossover DX tiles with two anti-parallel crossovers.

  23. DNA tiles • Pads: • Tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles. • The sticky ends facilitate the further assembly into tiling lattices. • Total of 4 Pads of single stranded DNA at ends.

  24. TX tiles • Triple-crossover (TX) Tiles consist of three double-helices fused by crossover strands. • TAE contains an even number of helical half-turns between crossover points. • TAO contains an odd number. • Total of 6 Pads of single stranded DNA at ends. [LaBean et al, J. Am. Chem. Soc., 2000]

  25. TX tiles [LaBean et al, J. Am. Chem. Soc., 2000]

  26. TX tiles Unique Sticky Ends on DNA tiles. Input layers can be assembled via unique sticky-ends at each tile joint thereby requiring one tile type for each position in the input layer. Tiling self-assembly proceeds by the selective annealing of the pads of distinct tiles, which allows tiles to compose together to form a controlled tiling lattice.

  27. TX tiles

  28. Another way

  29. Still another way

  30. Or another way

  31. Self assembly and computation • A tiling is an arrangement of tiles (shapes) that covers a plane • Tiles fit based on matching rules (complementary shapes)

  32. Self assembly and computation XOR tile

  33. Self assembly and computation Wang Tile

  34. Self assembly and computation • Given a Turing machine, tiles and matching rules can be designed so that the tilings formed correspond to a simulation of the Turing Machine. • Computation by tiling is hence Universal i.e. all SA structures can be viewed as computation.

  35. C-tile, P-tile and XOR tile Error rate 0.2%, 2.2%, 14.7% for C, P and XOR tiles; % error= mismatches/(mismatches+bonds)

  36. DNA The powerful molecular recognition system of base pairing can be used in • Nanotechnology to direct the assembly of highly structured materials with specific nanoscale features • DNA computation to process complex information. Appealing features include • Minuscule size, with a diameter of about 2 nanometres • Short structural repeat (helical pitch) of about 3.4–3.6 nm, • ’Stiffness', with a persistence length (a measure of stiffness) of around 50 nm.

  37. DNA as building material Sticky ended cohesion-ligation

  38. DNA as building material Assembly of branched junctions into a 2-d lattice

  39. DNA as building material Holiday junction

  40. DNA as building material Flexibility of DNA branched junctions

  41. DNA as building material a b • DNA drawn as a series of right angle turns • Each edge of square contain 2 turns of helix in a but only 1.5 turns in b

  42. Constructing DNA objects

  43. Constructing DNA objects Borromean Rings Truncated Octaheadron

  44. Construction of tiles • Design & Synthesize Oligonucleotides • Formation of H-bonded Complex • Purification using Gel Elecrophoresis to eliminate the linear strands • Phosphorylation and Ligation

  45. Construction of tiles

  46. Crossover molecules Single molecule gaps

  47. Limitations • Fault tolerance: • Result is probabilistic, e.g. 2-5% error in XOR computation • Only open one set of sticky ends at a time to prevent incorrect binding (correct competes with partially correct) • Performance highly sensitive to process (melting) conditions • Differences from periodic tiling • Correct tiles compete with partially correct tiles, thus amplifying error • Efficiency (for small problems): • Many serial chemistry steps for preparation, ligation, and analysis, e.g. a few days for XOR computation • Scalability • Reporter strand technique limited to 20-30 ligated crossovers • Then can we layout 3D materials, e.g. circuit patterns?

  48. DNA topological structures Ned Seeman

  49. DNA topological structures Ned Seeman

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