DNA mediated Selfassembly of Nanoarchitectures Rakesh Voggu CPMU

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

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

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

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

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

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

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 nitrogenous bases.

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

Nucleotides DAMP DGMP DCMP DTMP DUMP

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

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

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

Alternate forms A-DNA B-DNA Z-DNA

Alternate forms

Why Develop DNA Architectures ?

DNA as a Building Block for Nanotechnology § Programmable Assembly § Convenient Chemistry § Scientific Insight

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

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

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

DNA Motifs

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

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

1982: Protein in 3 D DNA Lattice

Suitable DNA sequences allows the generation of complex motifs a. double-helical regions b. sticky ends c. bulge loops d. hairpin loops e. junctions f. crossovers

Crossover molecules

Crossover Molecules Double crossover molecules

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

Other motifs Rhombus motif Triangular other triangular motifs Four armed junctions

DNA Motifs Assembly

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

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

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

Nature(1998)

Triple Crossover DNA Arrays AFM JACS(2000)

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

Three-Dimensional Structures from DNA

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

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

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

Folded Octahedron § Expressible 1, 669 bp ss. DNA + five 40 bp oligos § Folded (no knots, PX edges, loose junctions) § Rigid Nature(2004)

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)

DNA Nanotubes AFM Images Angew. Chem(2006)

Complex Patterns Using DNA Scaffolded DNA origami: folding of a 7. 3 kb single stranded viral genome into various 2 D shapes with complex patterns, and their hierarchical assembly into larger structures Nature(2006)

Applications of DNA Nanoarchitectures

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

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

Aptamer-Directed Self-Assembly of Proteins Protein( Throbin protein ) Angew. Chem(2005)

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

B-Z Rotator § This is based on the transition between B and Z forms of DNA by changing the ionic strength of the medium. § The motion is monitored by FRET In B form fluoresence is quenched Nature(1999)

Hybridization Tweezer § Specific Fuel § Equilibrium Control Nature(2000)

Autonomous Walker Angew. Chem(2005)

Autonomous Walker PAGE monitoring the movement of DNAzyme Angew. Chem(2005)

Conclusions § DNA can self-assemble into nanoarchitectures § DNA structure can be used to self assemble ligands and nanoparticles § DNA can be used to prepare nanomachines

Recombination via holliday junction

Semi-imobile junctions