DNA mediated Self-assembly of Nanoarchitectures

1. DNA mediated Self-assembly of Nanoarchitectures Rakesh Voggu CPMU Seminar 17/11/2006

2. DNA Nanoarchitectures: Definition DNA Nanoarchitectures are… …extended assemblies made entirely of poly-nucleic acids whose structure is predictable and programmable in terms of well-understood interactions between nucleotides, such as base-pairing and base-stacking.

3. Structures Constructed From DNA Nature(1991) JACS(1994) Nature(1997) Chem.Comm(2004) Nature(2004)

4. Outline • Introduction : DNA structure • Design and Assembly of DNA Motifs • Three dimensional structures from DNA • Applications of DNA Nanoarchitectures

5. DNA structure Francis Crick and James Watson pointing out features of their model for the structure of DNA.

6. N base Sugar + base + phosphate N 5’ P C O nucleoside sugar OH 3’ Nucleic Acids Nucleic acid contains linear polymer of nucoletides Nucleotides:

7. Sugar • DNA and RNA both have five carbon sugars called pentoses. DNA contains 2-deoxy-D-ribose RNA contains D-ribose • In nucleotides, carbon atoms in sugar are numbered as 1', 2', 3', and so on to distinguish them from the ring atoms of the nitrogenousbases.

8. Nitrogenous Bases The bases of nucleotides and nucleic acids are derivatives of either pyrimidine or purine. Pyrimidines Purines

9. Nucleotides DAMP DGMP DCMP DTMP DUMP

10. Nucleic Acids Nucleic acids are linear polymers of nucleotides linked 3' to 5' by phosphodiester bridges

11. DNA Double Helix DNA has two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. B-DNA

12. Stability of double helix structure • Internal and external hydrogen bonds • Negative charge of phosphate groups • Base pair stacking Major and Minor Grooves

13. Alternate forms A-DNA B-DNA Z-DNA

14. Alternate forms

15. Why Develop DNA Architectures ?

16. DNA as a Building Block for Nanotechnology • Programmable Assembly • Convenient Chemistry • Scientific Insight

17. Programmable Assembly • Programmable molecular recognition –Watson-Crick base-pairing. • Programmable single stranded overhangs or sticky ends as “smart glue” to associate double-helical domains • “Smart” Materials –responsive to the chemical environment

18. Convenient Chemistry • DNA is easy to synthesize using automated phosphoramidite chemistry • Physically and chemically stable • Well established methods for DNA purification and structural characterization • Array of enzymes commercially available for DNA manipulation, for example, for site-selective DNA cleavage, ligation, labeling etc

19. Scientific Insight • Templated self-assembly – Proteins – Nanoparticles • Macromolecular machinery – Molecular Motors • Assembly-based computation

20. DNA Motifs

22. 1982: Immobile Branched Junctions • No symmetry • All W•C pairs • Unique tetramer • Redundant trimers

23. 1982: Immobile Branched Junctions with sticky ends Formation of a two-dimensional lattice from an immobile junction with sticky ends

24. 1982: Protein in 3D DNA Lattice

25. Suitable DNA sequences allows the generation of complex motifs • double-helical regions • sticky ends • bulge loops • hairpin loops • junctions • crossovers

26. Crossover molecules

27. Crossover Molecules Double crossover molecules

28. Crossover molecules TX DNA tile 12-helix DNA tile DX DNA tile

29. Other motifs Four armed junctions Rhombus motif Triangular other triangular motifs

30. DNA Motifs Assembly

31. DNA Holliday Junction Arrays 1-D Self Assembly 2-D Self Assembly AFM AFM JACS(1999)

32. Double Crossover DNA Arrays AFM Using two different double crossover molecules Nature(1998)

33. Double Crossover DNA Arrays AFM Using four different double crossover molecules Nature(1998)

34. Nature(1998)

35. Triple Crossover DNA Arrays AFM JACS(2000)

36. Triple Crossover DNA Arrays AFM JACS(2000)

37. DNA Triangles and Self-Assembled Hexagonal Tilings + AFM images JACS(2004)

38. Three-Dimensional Structures from DNA

39. Covalent Cube – piecewise assembly – 3-arm junctions – Not rigid Nature(1991)

40. Truncated Octahedron • Step-wise assembly on solid support • 4-arm junctions • Not rigid JACS(1994)

41. Simple Tetrahedron • Self-assembled • Nicked 3-arm junctions • Rigid (w/ 2 base hinges) • Chiral Chem Comm(2004)

42. Folded Octahedron • Expressible 1,669 bp ssDNA + five 40 bp oligos • Folded (no knots, PX edges, loose junctions) • Rigid Nature(2004)

43. Folded Octahedron three-dimensional map generated from single particle reconstruction of the DNA octahedron Visualization of the DNA octahedron structure by cryo-electron microscopy. Nature(2004)

44. DNA Nanotubes AFM Images Angew. Chem(2006)

45. Complex Patterns Using DNA Scaffolded DNA origami: folding of a 7.3 kb single stranded viral genome into various 2D shapes with complex patterns, and their hierarchical assembly into larger structures Nature(2006)

46. Applications of DNA Nanoarchitectures

47. DNA Self-Assemblies of Proteins 2D Nano Lett(2005)

48. DNA Self-Assemblies of Proteins 1D Nano Lett(2005)

49. Aptamer-Directed Self-Assembly of Proteins Protein( Throbinprotein ) Angew. Chem(2005)

50. Assembly of Nanoparticles Nano Lett(2004) Nano Lett(2006)