Self-Organizing Bio-structures

1. Self-Organizing Bio-structures NB2-2009 L.Duroux

2. Lecture 5: DNA Self-Assembly Applications

3. The trends in nano-fabrication • The miniaturization, top-down ‘‘sizeshrinking’’ • microelectronics technology • pushing down the limits of size and • compactness of components and devices • The nanofabrication and nanomanipulation bottom-up • molecular nanotechnology • of novel nanolevel materials and methods • (e.g., near-field scanning microscopies) to • electrical devices built on carbon nanotubes • optical devices like optical sieves (69). • The supramolecular self-organization approach • complexity through self-processing, • self-fabrication by controlled assembly & hierarchical growth • connected operational systems

4. Remember Nucleic Acids (DNA) and their Self-Assembly properties • An example of a reciprocal exchange: Two DNA helices are connected by sharing two DNA strands (Seeman, 2001) D A B C Oligonucleotides

5. Advantages of nucleic acids as nanomaterials • Size: Ø of 1nm for ssDNA and Ø 2nm for dsDNA • Chemical stability and robustness • Production costs for synthesis are low • Self-assembly properties

6. DNA as scaffold for nano-architectures

7. 1. Using ssDNA as template to self-assemble nanostructures

8. A simple case of ssDNA-functionalized micro-beads • Specific and reversible aggregation of micro-beads grafted with oligonucleotides • The key to reversibility is preventing the particles from falling into their van der Waals well at close distances Polymer brush -> steric repulsion Valignat et al, 2005. PNAS 102(12): 4225-29 T= 50¤C T= 23¤C

9. Interaction Energies of micro-beads • Trick is: create a Uminimum well outside UvdW well • Balancing finely Urep and Udna • Limiting the number of base-pair bonds between two cDNAs

10. Lennard-Jones Potential • Potential function of: • Depth of potential well (E) • Distance at which potential is zero (s) • Term in power 12 describes repulsive forces

11. Directed Assembly of micro-beads with optical tweezers • Beads are immobilized on array of discrete optical traps • Optical tweezers to move the traps closer to trigger DNA hybridization

12. Effect of ssDNA length and rigidity • Micro-beads manipulated with optical tweezers • Two types of DNA hybrids: “flexi” and “rigid” Biancaniello et al, 2005. Phys Rev Lett. 94:058302

13. Binding Energies as function of rigidity of ssDNA • For identical Tm (43.7¤C), “rigid” spacer gives stronger U well

14. Effect of ssDNA density on aggregate structuration • DNA density of 14000 molecules / sphere lead to unstructured aggregates • DNA density of 3700 molecules / sphere lead to self-assembled crystallites 14000/sphere 3700/sphere 3700/sphere T >> Tm

15. 2. DNA tiles: the ”building bricks”

16. N. Seeman: the father of DNA nanotechnology • Any type of ss or dsDNA secondary structure can be exploited to create geometric shapes by self-assembly • Typically, junctions and sticky-ends are exploited for this purpose

17. Branch molecules and branch migration Dyad Axis of seq. symmetry Homologous duplexes Reciprocal exchange

18. Stable branch junction No Axis of seq. symmetry No complement sequence in corners

19. Stem formation on inexact complementary strands

20. Creation of stable motifs with DNA by reciprocal exchange

21. Combinatorial self-assembly of DNA nanostructures

22. AFM pictures of DNA tiles combinations

23. Topology measurements by AFM

24. Motif formed by quadruple cross-over (QX) & Lattice B A

25. The concept of DNA tiles B Example with triangle motifs Central core strands A C Side strands Horseshoe strands

26. Lattices from SA of triangle motifs Brun et al, 2006

27. Creation of 3D tiles with QX motifs B A C

28. 3D structures from DNA self-assembly(Seeman, 2003) A truncated octahedron A cube

29. Another tiling process using tecto-squares Chworos et al., Science306, 2068 (2004).

30. Applications of DNA lattices • Molecular Electronics: • Layout of molecular electronic circuit components on DNA tiling arrays. • DNA Chips: • ultra compact annealing arrays. • X-ray Crystallography: • Capture proteins in regular 3D DNA arrays. • Molecular Robotics: • Manipulation of molecules using molecular motor devices arranged on DNA tiling arrays.

31. DNA as template for electrical nano-wires A step toward “nano-electronics”

32. DNA for Molecular Lithography: principle Gazit, 2007. FEBS J. 274:317-322

33. DNA lithography: towards nanoelectronics Niemeyer, 2002. Science, 297:62-63.

34. Conducting DNA-nanowires 4x4 DNA tile Yan et al, 2003. Science 301:1882-84

35. DNA-Templated Self-Assembly ofMetallic Nanocomponent Arrays on aSurface

36. DNA-Templated Self-Assembly ofMetallic Nanocomponent Arrays on aSurface

37. DNA-Templated Self-Assembly ofMetallic Nanocomponent Arrays on aSurface

38. Templated array of proteins on 4x4 nanogrids • In nano-electronics designs: possibility to self-assemble proteins on DNA grid • Nano-electronics components Biotinylated DNA 4x4 tiles Streptavidin

39. Metallization and conductivity measurements of DNA 4x4 tile ribbons 500 nm 500 nm

40. Programmable Self-Assembly of DNA

41. Computation by Self-assembly of DNA Tilings • Tiling Self-assembly can: • Provide arbitrarily complex assemblies using only a small number of component tiles. • Execute computation, using tiles that specify individual steps of the computation. • Computation by DNA tiling lattices: • Fist proposed by Winfree (1998) • First experimentally demonstrated by Mao, et al (2000) and N.C. Seeman (2000).

42. Molecular-scale pattern for RAM-memory

43. 3 components for DNA computing • DNA computing (Adleman, 1994) • Theory of tilings (Grunbaum and Sheppard, 1986) • DNA nanotechnology (Seeman, 2003).

44. Implementation of abstract Wang-tiles with DNA tiles Winfree, 2003

45. The Tile Assembly Model • Only tiles with binding strength > 2 bonds will bind

46. Advantages of Biomolecular Computation • Ultra Scale: each ”processor” is a molecule. • Massively Parallel: number of elements could be 1018 to 1020 • High Speed: perhaps 1015 operations per second. • Low Energy: • example calculation ~10-19 Joules/op. • electronic computers ~10-9 Joules/op. • Existing Biotechnology: well tested recombinant DNA techniques.

47. Potential Disadvantages of BiomolecularComputation: • Many Laboratory Steps Required: • is very much reduced by Self-Assembly ! • Error Control is Difficult: • may use a number of methods for error-resilient Self-Assembly

48. Error-Resilient Self-assembly • Bounds on error rates of self-assembly reactions: • No complete studies yet. • Non-computational assemblies appear to be less error-prone. • Methods that may Minimize Errors in self-assembly: • Annealing Temperature Variation. • Improved Sequence Specificity of DNA Annealing. • Step-wise Assembly versus Free Assembly. • Use of DNA Lattices as a Reactive Substrate for Error Repair.

49. DNA and RNA Aptamers Selection of RNA and DNA aptamers that bind specifically to target proteins

50. SELEX: