dna nanoscience

8/3/2019 DNA Nanoscience

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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


separate strands,anneal primers


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


4. DNA nanomachines

5. Summary + Outlook


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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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dna nanoscience

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