dna mediated self-assembly of nanoarchitectures rakesh voggu cpmu seminar 17/11/2006
TRANSCRIPT
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.
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
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
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
1982: Immobile Branched Junctions with sticky ends
Formation of a two-dimensional lattice from an immobile junction with sticky ends
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
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)
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)
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)
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