dna nanoscience
TRANSCRIPT
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Overview
1. DNA nanoscience and its relationto molecular-scale electronics
2. DNA as material for nanoconstruction
3. DNA nanostructures
4. DNA nanomachines
5. Summary + Outlook
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DNA basics
Franklin & Wilkins:X-ray diffraction
on DNA fibers (1950s)
Watson & Crick:interpretationof X-ray data (1953)
WC model model of B-DNA
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Single-stranded DNA
DNA is directed
DNA is highlycharged !
nucleotide
nucleoside=Ribose+Base
nucleotide=nucleoside+phosphate
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DNA bases and base-pairing
purines
pyrimidines
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Double-stranded DNA
0.34 nm
10.5 bp~ 3.57 nm
2 nm
5 TGATCACTTAGAGCAAGC 33 ACTAGTGAATCTCGTTCG 5
majorgroove ~ 2.2 nm
minorgroove ~ 1.2 nm
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The A,B,Z of DNA
A form B form Z form
Helical Sense right
handed
right
handed
left
handed
Diameter 2.6 nm 2.0 nm 1.8 nm
bp/turn 11 10.5 12
base tilt 20 6 7
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DNA: the simple picture
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other base-pairing interactions
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G quadruplex formation
stability similar to WC base pairs
occurs in G rich sequences,e.g. in telomeres
occurs intra- and intermolecular
(single-, double- and four-stranded)
telomere consensus:GGGTTA (human)GGGTTG (Tetrahymena)
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A short note on mechanical properties of DNA
2
0
'2 =
s
dstddsH
(0) (s)
)/exp()]0((s)cos[ pLs=
TkL
B
p =persistence length
dsDNA is well described by theWLC model (semirigid polymer)
ds
ssDNA ~ 1nm
EI=bending modulus:
4
4
RI
=moment of inertia:
J. Howard, Mechanics of Motor Proteinsand the Cytoskeleton, Sinauer, 2001
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The biochemical toolbox for DNA
http://www.bioteach.ubc.ca/MolecularBiology/RestrictionEndonucleases/endonuclease%202.gif
restriction enzymes:
cut DNA at specific sequences
ligases:link two DNA pieces covalently
helicase: unwinds DNA
topoisomerases: changetopology (linking,winding number)
DNA/RNA polymerases:make copies
DNA binding proteins:help in recombination, function as
transcriptional modulators, etc. ligation of sticky ends
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Polymerase chain reaction (PCR)
heat andanneal primers
polymerizenew strands
cycle Iamplificationof DNA in a thermocyclerusing a thermostableDNA polymerase
cycle II cycle III
polymerizenew strands
separate strands,anneal primers
polymerizenew strands
separate strands,anneal primers
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Interesting features summarized:
structure is determined by sequence
automated DNA synthesis
structurally rigid double helix
DNA-modifying enzymes available
PCR, cloning & other biochemistry
relatively stable
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Overview
1. DNA nanoscience and its relationto molecular-scale electronics
2. DNA as material for nanoconstruction
3. DNA nanostructures
4. DNA nanomachines
5. Summary + Outlook
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3. DNA nanostructures
3.1 Supramolecular construction
3.2 Arranging nanoobjects
3.3 Modified DNA
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3.1 Supramolecularconstruction
Synthesis of a cube Chen et al Nature 350 631-633 (1991)
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Synthesis of a cube Chen et al.,Nature 350, 631 633 (1991)
building the cube and proving it
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building the cube and proving it
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a truncated octahedron
Zhang, Y. W. and N. C. Seeman (1994). "Construction Of A Dna-Truncated Octahedron." JACS 116(5): 1661-1669.
Li bl
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Linear assembly
simple but boring long range order not possible with dsDNA(persistence length 50nm or less (nicks))
2m x 2m
2D assembly: The Holliday junction
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2D assembly: The Holliday junction
http://www.st-andrews.ac.uk/~mfw2/Images/junction.jpg
a mobile (Holliday) junction
an immobile junction
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Holliday intermediate during
homologous recombination
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http://bioweb.wku.edu/
Holliday modelof recombination
only a short pieceof DNA exchanged
Holliday junction + branch migration
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Holliday junction + branch migration
four armbranch migration
recombination proteinsRuvA und RuvBbound to a Hollidayjunction
Rafferty et al., Science 274,415-421 (1996).
Networks of four arm junctions (I)
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Networks of four arm junctions (I)
Assembly disordered due tohigh flexibility of the junctions +long connectors
perfectly oriented
with two
orientations
Stefan Beyer
Networks of four arm junctions (II)
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Networks of four arm junctions (II)
preformtrianglesfrom junctions,anneal triangles
Turberfield et al.,to be published
Networks of four arm junctions (III)
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Networks of four arm junctions (III)
Sha, R. J., F. R. Liu, et al. (2002). "Force microscopic measurement of the interdomain angle in symmetric Hollidayjunctions." Biochemistry 41(19): 5950-5955
Double crossover (DX) structures
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Double crossover (DX) structures
make less flexible structures with multiple crossovers
Seeman, N. C., H. Wang, et al. (1998). "New motifs in DNA nanotechnology." Nanotechnology 9(3): 257-273.
DX + TX tiles
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DX + TX tiles
Seeman, N. C. (2001). "DNA nicks and nodes and nanotechnology." Nano Letters 1(1): 22-26.
2D crystals from DX assemblies
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ligation + denaturation produces long strands reporter for successful lattice formation
Winfree, E., F. R. Liu, et al. (1998). Design and self-assembly oftwo-dimensional DNA crystals. Nature 394(6693): 539-544.
Winfree et al. 98
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Algorithmic self-assembly: assembly = computation
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g y y p
Erik Winfree,figure from:Seeman, N. C. (2003)."DNA in a material world."Nature 421(6921): 427-431.
Making circuit patterns with
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algorithmic self-assembly
Cook, Rothemund, Winfree, Self-assembled circuit patterns, DNA based computers 9
a demultiplexer
Algorithmic self-assembly:Si i ki i l
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Sierpinski triangle
PWK Rothemund et al.,submitted
DNA crossbars
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Yan, H., S. H. Park, et al. (2003). "DNA-templated self-assembly of protein arraysand highly conductive nanowires." Science 301(5641): 1882-1884.
Tensegrity: Using
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g y gTriangles as building blocks a tensegrity
structure
Liu, D., M. S. Wang, et al. (2004). "Tensegrity: Construction of rigid DNAtriangles with flexible four-arm DNA junctions." JACS 126(8): 2324-2325
Towards 3D structures
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Shih, W. M., J. D. Quispe, et al. (2004). "A 1.7-kilobase single-stranded DNA thatfolds into a nanoscale octahedron." Nature 427(6975): 618-621.
3.2 Arranging nanoobjects
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g g j
organization of Au nanoparticlesand CdSe nanocrystals
Mirkin et al. Nature 382, 607 (1996),
Alivisatos et al., Nature 382, 609 (1996),Coffer et al., APL 69, 3851-3853 (1996)
ordering of proteins
Niemeyer et al., Nucleic Acids
Research 27, 4553-4561 (1999)
DNA-carbon nanotube conjugates
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Williams, K. A., P. T. M. Veenhuizen, et al. (2002). "Nanotechnology - Carbon nanotubes withDNA recognition." Nature 420(6917): 761-761.
Arranging carbon nanotubes using DNA binding proteins and antibodies
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Keren, K., R. S. Berman, et al. (2003). "DNA-templated carbon nanotube field-effect transistor." Science 302(5649): 1380-1382.
DNA-directed synthesis
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DNA-directed synthesis
Gartner, Z. J. and D. R. Liu (2001). "The generality of DNA-templated synthesis as a basis for
evolving non-natural small molecules." JACS 123(28): 6961-6963.
Using DX assemblies
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gfor the arrangement
of nanoparticles
Xiao, S. J., F. R. Liu, et al. (2002). "Selfassembly of metallicnanoparticle arrays by DNA scaffolding." Journal of NanoparticleResearch 4(4): 313-317.
3.3 Modified DNADNA l f h d i i
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DNA can act as a template for the depositionof metals, semiconductors, conductive polymers
Keren, K., M. Krueger, et al. (2002). "Sequence-specific molecular lithographyon single DNA molecules." Science 297(5578): 72-75.Richter, J. (2003). "Metallization of DNA." Physica E16(2): 157-173.
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Copper sulfide on DNA
copper ions bind strongly to DNA
reaction with hydrogen sulfide
yields the semiconductor CuS
Dittmer & Simmel, APL 85, 633 (2004)
Polyaniline on DNA
anilinium ions bind to DNA
oxidative polymerization along theDNA template yields conductivepolymer wires
Nickels et al., submitted
Metallization of DNA nanotubes
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