Download Biological and Bioinspired Self‑Assembly

Bridging
the
Gap:
Biological
and
Bioinspired
Self‑Assembly
Mary Nora Dickson
05/14/2013
Today’s
Schedule
I. Introduction to Self-Assembly
10AM-11AM
II. RapidTech Tour/ Demo
11:00 AM-12PM
•  Proteins
–  Structure and Synthesis
–  Building with Protein
•  DNA
–  Structure and Synthesis
–  DNA Construction
–  Device Integration
III. DIY DNA!
1PM-4PM
•  DNA Synthesis
•  DNA Purification
–  HPLC
•  DNA Characterization
–  MALDI
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
2
Bridging
the
Molecular
Scale
and
the
Device
Scale
Modern devices need single molecular functionality
Microscale
“Top‐Down”
Biomolecules!!
Angstrom
scale
“BoEom‐Up”
Image:
Roy,
X.
et
al.
Angew.
Chem.
Int.
Ed.
51,
12473–12476
(2012).
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
3
How
Does
Biology
Build
this
Bridge?
Self
Assembly
Proteins
and
DNA
are
large
structures
made
up
of
small
molecules
which,
directed
by
other
proteins,
“Self
Assemble”
Just
as
a
bridge’s
roadbed
is
built
piecewise
alongside
a
suspension
scaffold,
DNA
Polymerase
facilitates
self
assembly
of
a
complementary
DNA
strand
along
a
template
strand
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
4
The
Key:
Self
Assembly
is
Hierarchical
(e.g. Muscle Fibers)
0.5nm
Amino
Acid
1‐10nm
Small
coil
or
sheet
structure
1‐100nm
2nm
Width
of
Myosin
(2
heavy
chains,
4
light
chains)
1‐2
μm
10nm‐μm
scale
10nm
hEp://bima[cs.blogspot.com/2009/02/structure‐hierarchy‐of‐
hEp://www.sensible‐health‐related‐fitness.com/fast‐twitch‐
proteins‐video.html
muscle‐fibers.html
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
5
Self
Assembly
is
Hierarchical
(e.g. DNA packing)
Add
Core
Histones
23.7
Å
Width
of
a
DNA
Strand
Add
Histone
H1
10nm
Diameter
of
”beads
on
a
string”
fibre
Add
Scaffold
Proteins
30nm
Diameter
of
chromaGn
fibre
Add
Further
Scaffold
Proteins
250nm
Fibre
diameter
1‐2
um
Length
of
average
metaphase
chromasome
hEp://upload.wikimedia.org/wikipedia/commons/4/4b/Chroma[n_Structures.png
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
6
What
makes
Self
Assembly
Special?
What makes it different than other bottom up methods?
•  Governed by non-covalent or weak
interactions (e.g. poly peptide vs.
protein)
– 
– 
– 
– 
Van der Waals
Electrostatic
Hydrophobic interactions
H-bonding
•  Dynamic process
–  Molecules must not “stick” upon contact
–  Molecules can self-assemble and then
Pieces
nestle
into
place
based
on
disassemble
molecular
interac[ons.
There
is
–  Biological self-assembly occurs in
usually
a
“right
way”
for
them
to
fit
“mild” conditions (moderate pH,
into
place.
temperatures, salt concentrations)
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
7
Introduction
to
Self
Assembly
Roadmap
•  Proteins
–  Structure and Synthesis
–  Building with Proteins
•  DNA
–  Structure and Synthesis
–  DNA Construction
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
8
Protein:
The
Body’s
Workhorse
hEp://publica[ons.nigms.nih.gov/structlife/chapter1.html
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
9
Hierarchical
Protein
Structure
hEp://bima[cs.blogspot.com/2009/02/structure‐hierarchy‐of‐proteins‐video.html
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
10
Primary
Structure
of
a
Protein
Peptide bonds formed by condensation
of amino group and carboxyl group
(releases H2O)
Glycine
Alanine
Dipep[de
•  Sequence of Amino Acids
–  Carbon-nitrogen backbone
Polypep[de
•  21 Amino Acids found in
eukaryotes
–  Differentiated by the side
chain (R) on the backbone
05/14/13
hEp://en.wikipedia.org/wiki/File:Glycine‐condensa[on‐2‐3D‐balls.png
hEp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/
PrimaryStructure.html
MN
Dickson,
Bio
Nano
Summer
School
11
Protein
Secondary
Structure
Sulfur Bridges affect protein folding
Cysteine
Hydrogen bonding throughout chain leads
to more complex secondary structures
Hydrogen
Bonding
b‐pleated
sheet
05/14/13
a‐helix
MN
Dickson,
Bio
Nano
Summer
School
12
Tertiary
Structure
of
a
Protein
Dihydrofolate
reductase:
Hydrophobic
core,
Hydrophilic
exterior
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
13
Building
With
Proteins:
Peptide Nanotubes
amino acid: diphenylalanine
Possible applications: 1) These would form an ideal template for metal nanowire
growth. 2) Dense nanotube arrays with large surface areas and the capability to
interact with other biological molecules could lead to highsensitivity sensors for
both environmental and medical diagnostic applications.
05/14/13
Reches.
et.
al.
Nature
Nanotechnology.
1,
195‐201.
(2006)
MN
Dickson,
Bio
Nano
Summer
School
14
Building
with
Proteins:
Protein Cages as Multifunctional Nanoplatforms
•  Proteins produced by
viruses can be modified
genetically or chemically
in order to impart
functionality
•  These protein cages have
three distinct interfaces
that can be synthetically
exploited:
–  the interior
–  the exterior
–  the interface between
subunits.
Uchida
et.
al.
Adv.
Mater.
2007,
19,
1025–1042
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
15
Protein
Summary
•  Proteins are large molecules with defined
structure made out of small building blocks
–  This structure is defined by self assembly
–  This structure is difficult to predict
•  By controlling the structure of proteins:
–  We can build functional microstructures
–  We can control the placement of molecules and
integration of these molecules into devices or
larger systems (e.g. nanowires, drug delivery)
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
16
DNA
•  DNA
–  Structure and Synthesis
–  DNA Construction
–  Device Integration
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
17
DNA:
Deoxyribonucleic
Acid
•  DNA is the genetic
material
•  Sequence directs
synthesis of protein
•  Replicates itself
preserving the base
sequence
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
18
DNA:
Deoxyribonucleic
Acid
Long
polymer
made
of
nucleo[des
05/14/13
Nucleo[de
base‐pairs
joined
by
hydrogen
bonding
MN
Dickson,
Bio
Nano
Summer
School
19
The
Double
Helix
20
Å
BP‐BP
3.4
Å
DNA can also
adopt different
conformations
A‐DNA
Z‐DNA
•  Two chains coil
around center axis to
form right-handed
double helix
•  36° rotation per base
•  ~10 bases per turn
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
20
A
Few
More
Characteristics…
•  Individual strands have polarity
One strand of helix has 5’ –OH group; other has 3’ -OH
•  Complementary strands run anti-parallel to one another
5’
3’
05/14/13
3’
5’
MN
Dickson,
Bio
Nano
Summer
School
21
Solid
Support
Synthesis
(General
scheme,
we
will
go
into
more
detail
later
)
!"#$%&'()*+"($#*
+,--"./*
!"
4,/";&/)#**
411);'(9*
!"0"#$1-).1)*
234*5"-,(&6"01**
"7*8&.9$0:*!"#$%&*&0#*'"()"#*"'+
5,.$%<&6"0*=*
>?&.&</).$@&6"0*
234*
3,<()"6#)1*
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
22
DNA
Construction
•  Versatility
–  Code with 4n permutations
–  Block by block assembly
–  Predictable intermolecular interactions
–  Easily modified with extreme precision and versatility
by synthetic chemistry or natural enzymes
•  Functional group incorporation
•  Recognition site incorporation
•  Commercialized / Automated synthesis
•  But it is 1D!
–  How do we make it a useful scaffold?
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
23
From
1D
to
2D
•  Adaptation for 2D use
–  Meiosis (Holliday
Junction)
–  DX DNA tile where 2
longer strands are pinned
together with smaller,
staple strands
•  These have been used for
various nanotechnology
applications (e.g. to
organize nanoparticles)
05/14/13
DNA
Junc[ons
DX
DNA
[le
A)  DNA
templated
“ridges”
of
64nm
spacing
B)  Array
of
6nm
gold
nanopar[cles
hybridized
to
the
DNA
ridges.
(AFM)
Top
image:
Seeman,
N.
C.
Nature
Nanotech.
4,
427‐431
(2003).
BoEom
image:
Yan,
H.
Science
301,
1882
(2003).
MN
Dickson,
Bio
Nano
Summer
School
24
Designer
2D
Motifs:
DNA
Origami
Images:
Rothemund,
P.
W.
K.
Nature
440,
297‐302
(2006).
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
25
Designer
3D
Motifs
Seeman
et
al
NATURE
|
Vol
461
|
3
September
2009
Liu,
Y.,
et
al.,
J.
Am.
Chem.
Soc.
(2005)
127,
17140
05/14/13
Mao
et
al
NATURE
|
Vol
452
|
13
March
2008
MN
Dickson,
Bio
Nano
Summer
School
26
En
Route
to
Device
Integration
Questions We’ve Answered
  What are the relevant
length scales for
devices?
  What is self assembly?
  How do we build with
proteins & DNA?
Questions to Answer
  How do we integrate these with
lithography techniques?
?
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
27
Controlled
Surface
Placement
Spatially controlled surface
presentation enables:
–  Construction of a hierarchical
device (e.g. integrated circuit)
–  Observation of discrete
processes (e.g. binding event)
–  Coupling of signal to a surface
transducer (e.g. electronic
circuit)
A lithographic template helps
Triangle
DNA
on
unpaEerned
surface
vs.
Triangle
DNA
origami
on
e‐beam
triangle
paEerned
surface
Kershner,
R.
J.
et
al.
Nature
Nanotech.
4,
557‐561
(2009).
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
28
NIL
Defined
Hydrophilic
Template
For Direct DNA Origami Placement
hydrophilic
hydrophobic
PMMA
HMDS
SiO2
Thermal
Nanoimprint
O2
plasma
Strip
PMMA
05/14/13
Penzo,
E.,
Wang,
R.,
Palma,
M.,
Wind,
S.
J.
J.
Vac.
Sci.
Technol.
B.
29(6)
2011.
06fF205.
MN
Dickson,
Bio
Nano
Summer
School
29
E‑Beam‑Defined
Hydrophilic
Template
For Direct DNA Origami Placement
E-beam etching allows triangular sections of
the resist (light blue) to be dissolved,
exposing the hydrophobic TMS layer
(orange). These triangular sections of
hydrophobicity are then destroyed, exposing
the hydrophilic layer. All the TMS
underneath the resist (dark blue) is protected
and remains hydrophobic.
hydrophobic
hydrophilic
Kershner,
R.
J.
et
al.
Nature
Nanotech.
4,
557‐561
(2009).
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
30
Controlled
Surface
Placement
vs.
Triangle
DNA
on
unpaEerned
surface
Triangle
DNA
origami
on
e‐beam
triangle
paEerned
surface
AFM
images
Kershner,
R.
J.
et
al.
Nature
Nanotech.
4,
557‐561
(2009).
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
31
NIL
Defined
Nanodot
Template
For DNA Origami Placement via Self-Assembly
SEM
image
of
sub
10nm
gold
dots
in
pairs,
60
nm
spacing
05/14/13
DNA
[les
modified
with
poly‐A
tails
which
bind
to
poly‐T
tails
upon
the
gold
nanodots
R.
Wang*,
M.
Palma*
et
al
Nano
Research
,
2013,
DOI:
10.1007/s12274‐013‐0318‐6
MN
Dickson,
Bio
Nano
Summer
School
32
Nanodot
Poly‑T
Modification
O
•  Thiol linker (-SH) incorporated
onto DNA backbone
–  Robust gold-thiol chemistry
binds a monolayer of DNA to
nanoparticles
–  This is called a DNA selfassembled monolayer
NH
HO
O
O
OP
HO O
N
O
O
NH
O
O
OP
HO O
N
O
O
NH
O
O
OP
HO O
N
O
O
NH
O
O
OP
HO O
N
O
O
NH
O
O
OP
HO O
N
O
O
NH
O
O
OP
HO O
N
O
O
NH
O
O
OP
HO O
N
O
O
HO P
O
O
O
O
NH
N
O
S
2/20/13
MN
Dickson,
CBEMS
Preliminary
Exam
33
NIL
Defined
Nanodot
Template
Unorganized
DNA
scaffolds
on
mica
surface
Nanopar[cle
Organized
DNA
scaffolds
R.
Wang*,
M.
Palma*
et
al
Nano
Research
,
2013,
DOI:
10.1007/s12274‐013‐0318‐6
05/14/13
MN
Dickson,
Bio
Nano
Summer
School
34