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

DNA mediated Self-assembly of

Nanoarchitectures

Rakesh VogguCPMU Seminar

17/11/2006

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.

Nature(1991) JACS(1994)

Nature(1997) Chem.Comm(2004) Nature(2004)

Structures Constructed From DNA

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:

Sugar + base + phosphate

nucleoside

P CO

N

N

base

sugar

5’

3’OH

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.

The bases of nucleotides and nucleic acids are derivatives of either pyrimidine or purine.

Nitrogenous Bases

PurinesPyrimidines

Nucleotides

DCMP DTMP DUMP

DAMP DGMP

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

B-DNA Z-DNAA-DNA

Alternate forms

Why Develop DNA Architectures ?

DNA as a Building Block for Nanotechnology

Programmable Assembly

Convenient Chemistry

Scientific Insight

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

Programmable Assembly

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 3D DNA Lattice

a. double-helical regions

b. sticky ends

c. bulge loops

d. hairpin loops

e. junctions

f. crossovers

Suitable DNA sequences allows the generation of complex motifs

Crossover molecules

Crossover Molecules

Double crossover molecules

Crossover molecules

DX DNA tile TX DNA tile 12-helix DNA tile

Rhombus motif TriangularFour armed junctions

other triangular motifs

Other motifs

DNA Motifs Assembly

DNA Holliday Junction Arrays

1-D Self Assembly2-D Self Assembly

JACS(1999)AFM AFM

Double Crossover DNA Arrays

Using two different double crossover molecules

Nature(1998)

AFM

Double Crossover DNA Arrays

Using four different double crossover molecules

Nature(1998)

AFM

Nature(1998)

Triple Crossover DNA Arrays

JACS(2000)

AFM

Triple Crossover DNA Arrays

JACS(2000)

AFM

+

DNA Triangles and Self-Assembled Hexagonal Tilings

AFM imagesJACS(2004)

Three-Dimensional Structures from DNA

Covalent Cube

Nature(1991)

– piecewise assembly

– 3-arm junctions

– Not rigid

Step-wise assembly on solid support

4-arm junctions

Not rigid

Truncated Octahedron

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 ssDNA + five 40 bp oligos

Folded (no knots, PX edges, loose junctions)

Rigid

Nature(2004)

Visualization of the DNA octahedron structure by cryo-electron microscopy.

three-dimensional map generated from single particle reconstruction of the DNA octahedron

Folded Octahedron

Nature(2004)

DNA Nanotubes

Angew. Chem(2006)AFM Images

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)

Applications of DNA Nanoarchitectures

DNA Self-Assemblies of Proteins

2D

Nano Lett(2005)

DNA Self-Assemblies of Proteins

1D

Nano Lett(2005)

Aptamer-Directed Self-Assembly of Proteins

Protein( Throbin protein )

Angew. Chem(2005)

Assembly of Nanoparticles

Nano Lett(2006)Nano Lett(2004)

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