DNA mediated Self-assembly of Nanoarchitectures

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DNA mediated Self-assembly of Nanoarchitectures
Rakesh Voggu CPMU Seminar 17/11/2006
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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.
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Structures Constructed From DNA
Nature(1991)
JACS(1994)
Nature(1997)
Chem.Comm(2004)
Nature(2004)
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Outline

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

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DNA structure
Francis Crick and James Watson pointing out
features of their model for the structure of DNA.
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Nucleic Acids
Nucleic acid contains linear polymer of
nucoletides
Nucleotides
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Sugar
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Nitrogenous Bases
The bases of nucleotides and nucleic acids are
derivatives of either pyrimidine or purine.
Pyrimidines
Purines
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Nucleotides
DAMP
DGMP
DCMP
DTMP
DUMP
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Nucleic Acids
Nucleic acids are linear polymers of nucleotides
linked 3' to 5' by phosphodiester bridges
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DNA Double Helix
DNA has two polynucleotide strands wound together
to form a long, slender, helical molecule, the
DNA double helix.
B-DNA
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Stability of double helix structure

• Internal and external hydrogen bonds
• Negative charge of phosphate groups
• Base pair stacking

Major and Minor Grooves
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Alternate forms
B-DNA
Z-DNA
A-DNA
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Alternate forms
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Why Develop DNA Architectures ?
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DNA as a Building Block for Nanotechnology

• Programmable Assembly
• Convenient Chemistry
• Scientific Insight

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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

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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

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Scientific Insight

• Templated self-assembly
• Proteins
• Nanoparticles
• Macromolecular machinery
• Molecular Motors
• Assembly-based computation

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DNA Motifs
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1982 Immobile Branched Junctions

• No symmetry
• All WC pairs
• Unique tetramer
• Redundant trimers

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1982 Immobile Branched Junctions with sticky ends
Formation of a two-dimensional lattice from an
immobile junction with sticky ends
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1982 Protein in 3D DNA Lattice
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Suitable DNA sequences allows the generation of
complex motifs

1. double-helical regions
2. sticky ends
3. bulge loops
4. hairpin loops
5. junctions
6. crossovers

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Crossover molecules
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Crossover Molecules
Double crossover molecules
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Crossover molecules
TX DNA tile
12-helix DNA tile
DX DNA tile
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Other motifs
Four armed junctions
Rhombus motif
Triangular
other triangular motifs
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DNA Motifs Assembly
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DNA Holliday Junction Arrays
1-D Self Assembly
2-D Self Assembly
AFM
AFM
JACS(1999)
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Double Crossover DNA Arrays
AFM
Using two different double crossover molecules
Nature(1998)
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Double Crossover DNA Arrays
AFM
Using four different double crossover molecules
Nature(1998)
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Nature(1998)
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Triple Crossover DNA Arrays
AFM
JACS(2000)
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Triple Crossover DNA Arrays
AFM
JACS(2000)
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DNA Triangles and Self-Assembled Hexagonal Tilings

AFM images
JACS(2004)
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Three-Dimensional Structures from DNA
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Covalent Cube
piecewise assembly 3-arm junctions Not
rigid
Nature(1991)
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Truncated Octahedron

• Step-wise assembly on
• solid support
• 4-arm junctions
• Not rigid

JACS(1994)
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Simple Tetrahedron

• Self-assembled
• Nicked 3-arm junctions
• Rigid (w/ 2 base hinges)
• Chiral

Chem Comm(2004)
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Folded Octahedron

• Expressible 1,669 bp ssDNA five 40 bp oligos
• Folded (no knots, PX edges, loose junctions)
• Rigid

Nature(2004)
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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)
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DNA Nanotubes
Angew. Chem(2006)
AFM Images
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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)
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Applications of DNA Nanoarchitectures
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DNA Self-Assemblies of Proteins
2D
Nano Lett(2005)
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DNA Self-Assemblies of Proteins
1D
Nano Lett(2005)
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Aptamer-Directed Self-Assembly of Proteins
Protein( Throbin protein )
Angew. Chem(2005)
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Assembly of Nanoparticles
Nano Lett(2004)
Nano Lett(2006)
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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)
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Hybridization Tweezer

• Specific Fuel
• Equilibrium Control

Nature(2000)
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Autonomous Walker
Angew. Chem(2005)
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Autonomous Walker
PAGE monitoring the movement of DNAzyme
Angew. Chem(2005)
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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

FUTURE ?
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Thank You
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Recombination via holliday junction
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Semi-imobile junctions