DNA Nanotechnology

By:
Michael Simonetty
Tim Slininger
Natalie Smadi

http://en.wikipedia.org/wiki/DNA
 What is Nanotechnology?

• the study
th t d anddddevelopment
l t
of structures and devices on
the scale of 100 or less
nanometers(10-9m)
• Very large and diverse field
• Fast growing field

Adapted from
http://www.independent.co.uk/news/science/the-big-
question-what-is-nanotechnology-and-do-we-put-the-
world-at-risk-by-adopting-it-1015518.html
 What is DNA nanotechnology?

• DNA nanotechnology
t h l is
i the
th field
fi ld iin nanotechnology
t h l th
thatt uses th
the
unique structure of DNA to create different structures
• DNA has different characteristics, like carrying
y gggenetic information,
but its structural material is what is used in DNA nanotechnology
• A major goal of DNA technology is to assemble a biochip computer

http://www.ict4us.com/r.kuijt/images/en_dna.jp
g
 Basic Structure of DNA
Made up of two
polymer chains
(long repeating
units) called
nucleotides that
run side by side
in the opposite
di ti
direction

http://science.howstuffworks.com/cellular-microscopic-
biology/dna1.htm
 Backbone
• The backbone is made
of a phosphate group
and a ssugar
gar
(deoxyribose), joined
by ester bonds

• The 5’ side ends with

ith
an phosphate group
and the 3
3’ side ends
with a hydroxyl group

http://en.wikipedia.org/wiki/DNA
 Nitrogen bases
• 2 kinds of nitrogen bases
bonded to the sugar
– Purines (double ringed)
– Pyrimidines (single
ringed)

4 types of Nitrogen bases:

• Thymine (purine)
• Adenine (pyrimidine)
• Guanine(purine)
• Cytosine
C t i ((pyrimidine)
i idi )

• This sequence
q encodes information

http://science.howstuffworks.com/cellular-
microscopic-biology/dna1.htm
 Molecule bonding details
• Purine pairs with
pyrimidine (base pairing)
– Adenine with thymine
– Cytosine with guanine
• Complimentary bonding-
duplicates all information

• Nitrogen bases bonded

together with weak
h d
hydrogen b
bonding
di so can
be pulled apart like a
zipper

• Sugar and phosphate

covalently bonded
http://science.howstuffworks.com/cellular-
microscopic-biology/dna1.htm
 Molecule bonding (cont)
• Nitrogen bases
– Guanine and cytosine
form three hydrogen
bonds
– Adenine
Ad i and d th
thymine
i
form two hydrogen
bonds
• Therefore strands with
more G-C bonding g are
stronger-interacting

http://en.wikipedia.org/wiki/DNA
 DNA B
Bonding
di

•DNA molecules recognizeg

other DNA molecules by their
base pairing relationships
•Example: Adenine prefers to
pair with thymine
•The hydrogen bonding bring
the DNA molecules closer
t
together
th
•In order to bond to other
strands, the double helix has a
single stranded overhang
(sticky-end) that will hydrogen
bond with another
complimentary strand

http://www.foresight.org/Conferences/MNT05/P
apers/Seeman/
 Conformations of DNA
What they depend on:
• hydration level
• DNA sequence
• the amount and direction
of supercoiling
• chemical modifications of
th bases
the b
• the type and concentration
of metal ions
• presence of polyamines
(two or more organic
groups) in solution

Adapted from
http://ezbiomed.vghtpe.gov.tw/files/Pre
sentation%20Files%20of%20Good%20
t ti %20Fil %20 f%20G d%20
Seminars/0328%20seminar/0328%20s
eminar.files/slide0041_image021.jpg
 Conformations of DNA
– A-DNA
A DNA
• Wider right handed spiral, dehydrated samples
– B-DNA
• Most
M common iin cells,
ll not wellll d
defined,
fi d hihigh
hhhydration
d i llevels
l
– Z-DNA
• DNA were bases have been chemically modified, turn about the
axis
i on th
the lleft
ft h
hand
d side
id
• Common modification is methylation: happens at C-PO3-G
sites, the cytosine will become 5-methylcytsosine

A-DNA B-DNA Z-DNA

 DNA Constructing

• Specific base pairing of DNA allows DNA strands to

bond together in a controlled manner
• In
I order
d tot construct
t t materials
t i l att a larger
l scale,
l the
th
DNA’s ends need to be programmed asymmetrically
• Asymmetric ends form polyhedrons
polyhedrons, and the are easy
to control
• The sticky end of the double helix structure of DNA can
bind to another double helix’s sticky end to make one
single double bond helix
• Hydrogen bonding is involved in the combination of two
DNA molecules
 DNA crossover molecules
• Holliday Junction
• Uses branched DNA
to make DNA
complexes
l
• Four strands of DNA
combined
• Transforming a DNA
molecule from a
linear molecule to a
j
junction
ti bby b
base Holliday junction molecular structure
pairing
• Use rigidity to have
control on a
geometrical level and
topographical level
http://en.wikipedia.org/wiki/DNA_nanotechnology
 Types of Crossover structures
• Five different
Fi diff t arrangements
t
described by their codes
– The first letter is the double helix, D
– The second letter is the relative
orientation
– The third letter is the number of
helical half turns
– The fourth is needed to describe the
parallel double crossover molecules
with an odd number of helical half-
turns

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1
302964/
 Crossover Structures
– DAE
• Double helix, D
• A=anti-parallel
• E=even number of half turns
– DAO
• A=anti-parallel
• O=odd number of half turns
– DPE
• P=parallel
• E=even number of half turns
– DPOW
• P=parallel
• O
O=odd
odd number half turns
• W=major wide groove separation
– DPON
• N
N=narrow
narrow groove separation

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1
302964/
 Crossover Structures

• grooves ini th
the crossover
structures
– Provide access for
binding of proteins to
their regulatory
sequences
q
– Major (wide)
– Minor (narrow)

• makes the DNA a better

building block by making it
stuck in one position instead of
flexible
Adapted from
ttp // sc pps edu/ e s/s /s
http://www.scripps.edu/news/sr/sr
99/mbgen6.html
 DNA Cube

• The DNA axes can b

Th be
connected to form a cube
• Each edgeg of the cube has two
strands of DNA molecules
linked to each other
• It contains 6 different cyclic
strands
• The cube was one of the first
th
three di
dimensional
i l DNA
structures designed

http://www.foresight.org/Conferences/MNT05/P
apers/Seeman/
/S /
 Truncated Octahedron Shaped DNA

• This is the top view of a 3-D

truncated octahedron
• It contains 6 squares and 8
hexagons
g
• Each edge has 2 strands of
double helical DNA
• There is a total of 14 cyclic
strands of DNA
• This figure contains 36 edges

http://seemanlab4.chem.nyu.edu/nano-oct.html
 DNA Origami

• Technique
T h i tto makek 2d or even 3d
figures out of DNA
• Helpp make DNA a useful structural
material
• Designs are made by folding a
single long strand of DNA bound
into place by smaller strands of
DNA
• Aff d bl and
Affordable d simple
i l with
ith hi
high
h
yields
• Hope to use the technology to
Adapted from
make faster and smaller computers http://www.dna.caltech.edu/~pwkr/
 DNA Nanotubes

• Double
D bl crossover arrays can b
be
folded to form DNA nanotubes.
• Can be made to self-assemble
th
themselves
l
• Can be made at specific diameters
• More easily connect and modified
than carbon nanotubes
• Can be made into rings and spirals
• Potential Uses:
U
– Drug delivery
Adapted from
– Gene Therapy http://www.nature.com/nnano/reshigh/2008/0808
/full/nnano.2008.264.html
– Electronic circuits
 Advantages of Using DNA Nanotechnology

•Easy
E tto program andd predict
di t
intermolecular interactions with
DNA sticky ends
•Local structure of DNA is known,
making it easy to manipulate DNA
for constructingg
•DNA can hold components in
place for molecular electronic
devices
•DNA’s solid support synthesis
can be used for DNA based
computingi
Adapted from
•DNA can also be manipulated http://www.flickr.com/photos/hydrogen
usingg different enzymes
y /195976461/
 Advantages of Using DNA Nanotechnology Continued

• DNA iis th
the b bestt nanowire
i in
i
existence because…
1. It can self assemble
2. It can self replicate
3. It can adopt various
states and conformations
• Different DNA can be
insulating, semiconducting, or
metallic

Adapted by
http://www.nature.com/nnano/journal/v4/n4/covers/index.
html
 Uses of Nanotechnology
• DNA used as a structural material instead of a carrier of
genetic information
• Uses the molecular recognition properties of DNA
• Wide range of uses ranging from building blocks to
robotics
• More uses are being found every day

Adapted from
http://www.rsc.org/chemistryworld
/restricted/2009/April/IsDNAnanot
echnologycomingofage.asp
 DNA Scaffolding

• DNA can be used as a foundation

on which
hi h other
th partst can bbe
precisely assembled.
• Can be used to p precisely
y assemble
nanotubes, nanoparticles, and
nanowires at a resolution of 6 nm
• The DNA acts as a staple to hold
the nano-components at set places.
• Can make much smaller microchips
th the
than th currentt semiconductor
i d t
fabrication technology

Adapted from
http://www.tgdaily.com/con
t t/ i /43638/135/
tent/view/43638/135/
 Cell Surface Engineering
• DNA’s very specific bonding
properties can be used to attach
DNA arrays to different cell surfaces.
• Can label certain types of cells(e.g.
cancer cells)
• May be able to eventually carry
molecular cargo to specific cell types
• Might be used to deliver drugs to
specific cell types

Adapted
p from
http://www.nanowerk.com/spotlight/spotid=
12717.php
 DNA Tweezers
• The highly selective bonding of DNA can be used to grab and
release particles.
• Can be used to grasp and transfer an object to another place
• Can go back and forth with almost no lose in efficiency

Adapted from
http://www.nanowerk.com/spotlight/spotid=8048.php
 DNA Factories

• DNA nanotechnology
t h l can bbe used
d tto make
k a nano-sized
i d ffactory.
t
• DNA’s bonding properties can be used to assembly pieces one by
one like a factory.
y
• Each piece of DNA bonds a certain molecule.
• These molecules can then be added together to create an end
product.
product

http://io9.com/5187278/hamsters-and-teeny-
factory-workers-show-us-our-nanotech-future
 DNA Walkers

• DNA nanotechnology
t h l
can be used to create
walking bipedal
nanorobots.
• The walkers move on
a DNA track.
• Each step increases
the number of base
pairs helping the DNA
walker function
autonomously.

Adapted from
http://www.sciencedaily.com/releases/2
009/04/090402143507.htm
 DNA Computers

• DNA can b be used

d tto make
k
computers instead of silicon.
• Maya-II
y is an example.
p It can
play tic-tac-toe and takes 30
minutes to make a move.
• Can be used in fluids and the
body unlike silicon computers
• Can make decisions on a
cellular
ll l llevell

Adapted from
http://www.medgadget.com/archives/2006/10/computer
_with_d.html
 DNA Sensors

• Takes advantage of the specific

bonding patterns of DNA
• Can respond to the PH by opening
and closing
• Each end is attach with a fluorescent
dye
• Can tell by the color what the PH is
• Th change
The h is
i reversible.
ibl
• Can be observed in real time
• Can be used inside living g organisms
g
• Very highly accurate
Adapted from
ttp // atu e co / a o/jou a / /
http://www.nature.com/nnano/journal/v4/n
5/full/nnano.2009.101.html
 DNA Sensors

• DNA can b be made

d tto d
detect
t t any
metal.
• Much faster than traditional test
for lead and mercury
• DNA nanotechnology is a way
for real-time
real-time, inexpensive testing
testing.
• A fluorescent molecule and a
fluorescent quencher is on each
endd off th
the DNA
DNA.
• When a metal is near, it cleaves
the DNA letting the fluorescent
molecule become visible. Adapted from:
http://www.rsc.org/chemistryworld/Issues/2003/Septe
mber/sequence.asp
http://www.eetimes.com/story/OEG20001228S0016
p y
 Conclusion
• DNA nanotechnology has
the potential to greatly affect
the future.
• The very specific bonding
properties makes DNA a
widely useable structural
material.
• In the future more and more
uses of DNA nanotechnology
will be continued to be found.
Adapted from
http://www.nisenet.org/catalog/programs/
dna-exploring-nanostructures
 DNA Nanotechnology
• Uses DNA as a structure
U t t nott a
carrier of genetic information
• Takes advantage of the very
specific
ifi b
bonding
di properties
ti off
DNA
• Can be used in the body
• Self-assembles
• Highly programmable and can
be made into many 2D and 3D
configurations.
• These structures can be used in
many different fields
– Computer chips
– Drug delivery
By:
– Gene therapy Michael Simonetty
– DNA computers and sensors Ti Slininger
Tim Sli i
Natalie Smadi