Complex Materials & BioNanoTechnology

Prof. Jürgen Fritz

International University Bremen

Summer school on "Complex Materials: Cooperative Projects of the Natural Sciences, Engineering and Biosciences"

IUB, June 2006

Scope & Motivation

Complex Materialsnew materials with components on the micro- / nanometer scale with integrated functionand assembled by bottom up approach

BioNanotechnologyuse of natural components (biomolecules) for novel non-biological applicationsone dimension on nanometer scale influencing functionality

Outline general ideas on bio for physics, nano & interdisciplinarityenvironment for nano (surfaces and fluidics)systems (DNA, peptides, proteins)

(overview of the field related to our research but not on our research)

2 µm Kaw

ata,

Nat

ure

2001

bottom up top down

system size10 µm

cartilage cell micro-sculptured bull

J. Fritz, IUB 2006

blood cellsE. coli bacteriaflagella rotorantibody

quantum corral carbon nanotubemagnetic bitsintegrated circuits

DNA

separate, detect, quantify, analysestructure, function, organization

light/electron microscopy, X-rays,spectroscopy, ultracentrifuge,

MS, NMR, electrophoresis,patch clamp, …

single molecule methods,arrays, microfluidics,biosensors, system biology,simulations, …

toolsuniversal laws

self-assembly,molecular recognition, autonomy, molecular machines & electronics,efficiency, complexity …

concepts,designs

new approach to computation & ITenergy storage & conversion, actuation

Biology

Physics

biophysics &

nanotechnology

transistor

J. Fritz, IUB 2006

Physical versus biological systems

physical device

highly defined, reliable, reproduciblerobust & durablesimple materials, periodicsuperior electronic propertiestop down fabricationserial assembly of single componentshigh energy costs

biological system

individual, dependent on environmentflexible & short lifetimecomplex materials, aperiodicrecognition and self-assembly capabilitybottom up assembly parallel assembly of multiple componentslow energy costsintrinsic information processingself-replicating

J. Fritz, IUB 2006

"A Physicist looks at biology"

Other missconceptions by using biosystems

- evolution does not choose the best option, just the best available option- biosystems are selected for their function, but not every feature of a biological system

has a functional importance- there is no ideal or model biological system as in physics or engineering- error correction needed for bottom up approach & self-assembling

Max Delbrück (Nobelprize 1969, in: The Connecticut Academy of Arts and Sciences, 1949)

" There are no absolute phenomena in biology. Everything is time bound and space bound."

" The materials and phenomena (a physicists) works with are the same here and nowas they were at all times and as they are on the most distant stars. "

Biomolecules are normally not optimized for applications in engineering

J. Fritz, IUB 2006

Complex MaterialsBioNanotechnology

Physicsmechanics, electrodynamics,quantum mechanics, solid state physics,mesoscopic physics

Chemistrysynthesis, catalysiscolloids, nanotubes

Biologymolecular recognition,evolution, self-assembly,molecular machines

Modelling& Simulation

Engineeringelectronics, computing,microfabrication

Surface Sciencescanning probe methods, self assembled monolayers

devicesapplications

materialsapplications

complexityautonomy

toolslaws

Medicinediagnostics,health care

problemsapplications

J. Fritz, IUB 2006

Nanotechnology - small is different

mechanics & chemistry- surface properties gain importance (reactivity, surface to volume ratio)- increasing resonance frequencies- position affected by thermal noise, random motion and uncertainty principle

electromagnetic properties- interaction with light (diffraction, scattering, imaging and lithography)- electronic structure (density of state and term schemata)- magnetic structure (domain size, spin flip)

transport- transport properties: charges - diffusion, ballistic, hopping, tunneling

fluidics - turbulent vs. laminar- thermal relaxation time decreases

interaction forces- electromagnetic & van der Waals forces dominate (vs. gravity)

general description- ensemble properties vs. distribution of individual properties (statistics)

J. Fritz, IUB 2006

Driving BioNanotechnology

Scientific challenge & new insightsinterdisciplinarity, converging length scales in physics, chemistry and biology ...

Miniaturization in medicine, advances in pharmaceutical industryscreening, delivery, lab-on-a-chip, implantable devices,...

Future of electronics (information technology)Moores Law, shrinking devices, higher integration, ...

Chemical industry & engineeringcompound selection, intelligent materials,

improved performance, ...

source: Intel

J. Fritz, IUB 2006

Good to know for BioNanotechnology

Systemsbiomolecules, macromolecules, interactions, cells, ...>> objects of interest for modification, novel applications

Environmentsurfaces (surface chemistry, physics, ... )fluidics (microfluidics)>> positioning, delivery, manipulation of nanosystems

TechniquesSPM (STM, AFM, ...)fluorescence (FRET, FCS, ...)conductance measurements (ion channels, molecular wires, ...)modelling and simulation (molecular mechanics, molecular dynamics, ...) >> information on single molecules and nanoscale properties

Not covered here (chemical or optical systems):nanoparticles (metal, semiconducting, ...) nanotubespolymers, dendrimerssupramolecular chemistry....

Zhang, Science 2004

Kat

z &

Will

ner,

Che

mP

hysC

hem

200

4

J. Fritz, IUB 2006

Surfaces for NanoBiotechnology

General ideas

- bind nanosystem to surfaces todefine its position for precise analysis and manipulationsidentify system by selective binding

- use surfaces as support & templates for 2D structures

- position molecules in nanocontainers for well-defined reactions or transport

surfacesmicrofluidicsDNApeptidesproteins

" Surfaces and interfaces define the boundary of an object and its interactionswith other systems and they define the chemical environment of nanosystems "

J. Fritz, IUB 2006

Surface properties

Uni

vers

ity o

f B

asel

Typical surfacessilicon oxide (glass), gold, metal oxides, ...carbon, polymers, lipid membranes, ...

General surface propertiesroughness, flexibility, charge, hydrophobic/-philic, ...adhesive, repellent, ...

Surface functionalitiespermeability, reactivity, changing properties by functionalization, active switching, ...

J. Fritz, IUB 2006

Active control of surfaces

Example- reversible light-induced photoisomerization changes surface free energy- gradient in surface tension induces driving force for liquids on flat surfaces

írradiation with UV light> cis-azo groups

> increase in surface free energy> spread of drop

Ichimura, Science 2000

Other switching mechanism: electrowetting

" control surface properties to control fluids and objects "

Catalytic properties of surfaces

~ 400 nm

~ 2 µm

Pt catalyzes decomposition of hydrogen peroxide> oxygen gradient along rod

> interfacial tension along rod decreases with increase of oxygen> movement in direction of Pt

speed about ~ 10 body length per second (as bacterial flagellae)

rod trajectories

Paxton, JACS 2004

50 µm

Catchmark, Small 2005

" tailor reactivity of surface to control motion of nanoobjects "

Surfaces and nanocontainers

Phospholipids

liposomes as nanoreactorsinsert membrane channelsstabilize liposomes with polymers

lipid bilayer as functional membranes for nanocontainers

" design closed surfaces to protect or transport sample "

J. Fritz, IUB 2006

text

book

Nanotube - vesicle networks

forced shape transformation by micromechanicaltools: carbon fiber or pipette suction

1 - 50 µm vesicles, tubes 25 - 300 nm diameter

Karlsson, Annu Rev Phys Chem 2004Tokarz, PNAS 2005

" container networks by partitioning surfaces "

electrophoresis within nanotubes

Liquid environment for BioNanotechnology

surfacesmicrofluidicsDNApeptidesproteins

Aqueous solutionnatural environment for biological systems (buffer: pH, ions)buffer composition determines molecular conformation and interaction

of molecules and objects:- ionic distribution around charged objects / surfaces- ordering of water molecules (hydration forces, hydrophobicity)- end-to-end distance of polymers, swelling of gels, ...

Governing interactionsBrownian motion and diffusionviscous and inertial forces (turbulent or laminar flow)surface tension (capillary forces)

Small, well defined volumesshorter reaction times, less samplehigh concentrations with small number of moleculesdefined delivery of molecules or nanoobjects

" the two best defined experimental environments are UHV & low temperaturesor a pure & well defined solution (at fixed potential) "

25 nm

1 H+

pH 7.4 → pH 4J. Fritz, IUB 2006

Laminar flow

Reynolds number:

(velocity, length scale, density, viscosity)

Properties of laminar flow (small Re < 1000)viscous forces (friction) dominateno turbulenceno mixing except by diffusionreversible liquid motionliquid packets can be moved in a controlled way

Beebe, Annu Rev Biomed Eng 2002

ηρdv

FFRe

frict

inert ⋅⋅==

Gu, PNAS 2004

" motion in liquids is governed by inertial and frictional forces "

ship in water: inertial forces dominate, ship keeps movingeven when propulsion is stopped

bacteria in water: viscous (frictional forces) dominatewithout propulsion bacteria stops immediately

Quake group, Science 2000 & 2002

Large scale integration of microfluidics

air pressured valves out of PDMS

controlled motion of liquid packets

1 2

3 4

thousands of valves, hundreds of reaction chambers

Non-biological applications of DNA

surfacesmicrofluidicsDNApeptidesproteins

Why DNA ?- robust molecule, well defined structure- can be easily synthesized & modified- model system for molecular recognition and self-assembly- reversible hybridization - denaturation

hybridization

designed(probe)

sample(target)

ssDNA dsDNA

J. Fritz, IUB 2006

Conduction through DNA ?

since 1961: stack of base pairs along helix axis, with overlapping π system postulated: semiconducting with 1.5 - 3 eV gap

BUTconduction strongly depends on length, sequence, environment, structure, contact to electrodes...

unistep tunneling sequential hopping molecular band conduction

Porath, Nature 2000

DNA as a wire ?

600 nm long molecule ohmic

Fink, Nature 1999 Porath, Nature 2000

10 nm longsemiconducting

contradicting results from electronic measurements

Storm, Appl. Phys. Lett. 2001

40 - 500 nm longinsulating

DNA as template for electronics

aggregation of silver around DNA wirediameter ~ 100 nm

Braun et al., Nature 1998

Niemeyer, ChemBioChem 2001

assembly of biotinylated DNAand streptavidin

thiolated DNA and gold beads

Seeman, Nature 2003

Artificial DNA superstructures" use self-assembly of DNA to get microscopic 2D structures "

Holliday Junctions can form during meiosis

Design DNA sequences to interweave different strands

Micrometer sized DNA sheets

Winfree et al., Nature 1998

self-assembly of a mixture ofdifferent designed sequences(colors) in solutionscale bars 300 nm, 1 - 2 nm height

stripes:extruding hairpins

Design of arbitrary 2D DNA structures

Rothemund, Nature 2006scale bars 100 nm

one long strand of viral ssDNA (~ 7000 nt) as scaffoldthen design different short complementary strands

3D structures ?

Seem

an

Remote control of DNA

RF On = denaturated Off = hybridized

RF (1 GHz) magnetic radiation (~ mT, 0.4 to 4 W)

Hamad-Schifferli, Nature 2002

1.4 nm gold nanocrystal38mer oligonucleotide

UV absorption (hyperchromicity)

heat∆T + 13 C

ssDNA

dsDNA

Molecular Machines

MIT Media Laboratory

no beads

" bind / unbind DNA at will by external trigger "

control

Peptides for organic - inorganic interactions

surfacesmicrofluidicsDNApeptidesproteins

Why peptides ?more building blocks (20 amino acids) with more interactions (than DNA)- charged, polar, hydrophobic, aromatic

more structures possible

BUT: more sensitive than DNA, harder to analyze and synthesize

peptides:some ten amino acids

J. Fritz, IUB 2006

Self-assembly

- molecules form spontaneously ordered aggregates without external intervention- non-covalent interacting mobile components, reversible

Whitesides, Science & PNAS 2002

Natural peptide assemblies

Vendruscolo, Phil Trans R Soc Lond A 2003

Amyloid fibrilsresponsible for diseases like Alzheimer or type II diabetis10 nm diameter, beta-sheet rich structure

misfolding, e.g. lysozyme Goldsbury, JMB 1999

100 nm

growth of amylin (37 aa peptide hormone)

protein assembly: actin filaments, microtubules, bacterial S-layer, ...

Self-assembly of artificial peptides

Zhao, Trends Biotech 2004

peptide lego with alternating pos. and neg. residues and hydrophobic backsidepeptide surfactants with hydrophobic tails and hydrophilic headspeptides for self-assembling on surfaces, pattern surfaces

Peptides shape crystal growth

- crystals grown by marine organism differ dramatically from grown in solution- calcite (calcium carbonate) growth

pure calcite calcite + Mg2+ calcite + D-aspartic acid calcite + AP8 protein(from abalone nacre)

DeYoreo, Science 2004

Natural assembly of inorganic materialsMagnetosomesmagnetic nanoparticles inmagnetotactic bacteria

BäuerleinAngew Chem Int Ed 2003

Diatomssingle celled algae with sculptured wallsof amorphous silica

Drum, Trends Biotech 2003

Abalone shellsrigid (hard but brittle) by calcium carbonatetough (energy absorbant but flexible) by proteins

Addadi, Nature 1997, Rubner, Nature 2003

50 µm, 1 µm

100 nm

GaAs

SiO2

Surface recognizing peptides

evolutionary selection of 12mer peptides with surface recognition propertiespage display with M13 bacteriophage with peptide fused to coat protein

Belcher group, MIT

selective for:material, crystalline faces, identical lattice of different materialGaAs(100), GaAs(111), InP(100), Si (100)

many uncharged polargroups

Whaley, Nature 2000

" peptides can be evolved to recognize any (?) solid state surface "

ZnS-A7 phage film

Proteins - complex nanomachines

surfacesmicrofluidicsDNApeptidesproteins

lipid bilyer

water

water

aquaporin(water channel)~ 10 9 molecules /secexcludes H+ and ions

Why proteins?highly complex systems: enzymes, channels, motors, receptors, ...inspiring, the ultimate complex molecular system

BUT: not optimized for foreign environmements, difficult preparation and analysis(100 - 10.000 aa)

de Groot, Science 2001

J. Fritz, IUB 2006

Vale, Science 2000

Molecular motors

myosin on actin kinesin on microtubules

muscle contractionstepping motion5 nm step size8000 nm / sec

intracellular transportprocessive motion8 nm step size840 nm / sec

powered by ATP

Molecular shuttles by motor proteins

Hess, Rev Mol Biotech 2001

kinesin at surface, 1 mM ATPrhodamin labeled microtubules 1 - 10 µmcarefully triggered environment (pH, T, salt,...)

" molecular motors in artificial environment "

Molecular rotors

time

revo

lutio

ns

Yasuda, Cell 1998

Flow of protons across membrane (F0) is used to synthesizeATP (F1) and ATP hydrolysis can pump protons in reverse direction

F0 and F1 coupled by shaft which rotatesF1 ATPase activity > counter clockwise, stepwise rotation of 120 °around 1 rotation / sec

Forced ATP synthesis

Itoh, Nature 2004

" artificial synthesis of ATP by mechanical rotation "

magnetic bead attached to shaft of F1 ATPase, rotated shaft by magnets clockwisedetecting ATP synthesis by enzymatic reaction (fluorescence)5 min intervalls: N - no rotation, H - in hydrolysis direction, S - in synthesis directionca. 105 ATP per 5 min

Conclusions

- glimps of BioNanoTechnology & non-biological applications of biomolecules- overview of workshop topics- learning from nature on molecular scale: components for complex materials- interdisciplinarity:

important to understand concepts, language and thinking of your colleagues

Jürgen Fritz: Complex Materials & BioNanoTechnology

NanoBioTechnology at IUB

Prof. J. Fritz: AFM, biosensors, microfluidicsProf. M. Winterhalter: lipids, liposomes, membrane channelsProf. U. Schwaneberg: biochemical engineeringProf. M. Zacharias: biomolecular modelingProf. V. Wagner: organic field-effect transistors, molecular electronicsProf. S. Tautz: low temperature STM, small molecules on metalsProf. U. Kortz: synthetic chemistry, metal-oxygen clusters Prof. W. Nau: photochemistry, biomolecular dynamicsProf. R. Richards: nanoparticles, catalysis...

Tautz

Kortz

Schwaneberg

J. Fritz, IUB 2006

Some General References

IntroductionK. Satoshi et al.: Finer features for functional microdevices, Nature412 (2001) 697.M. Delbrück: A physicist looks at biology, Trans. Connecticut Acad. Arts Sciences 38 (1949) 173.

SurfacesK. Ichimura et al.: Light-driven motion of liquids on a photo-responsive surface, Science 288 (2000) 1624.W.F. Paxton et al.: Catalytic nanomotors: Autonomous movement of striped nanorods, JACS 126 (2004) 13424.M. Karlsson et al, Biomimetic nanoscale reactors and networks, Annu. Rev. Phys. Chem. 55 (2004) 613.

FlowD.J. Beebe et al.: Physics and applications of microfluidics in biology, Annu. Rev. Biomed. Eng. 4 (2002) 261.T. Thorsen et al.: Microfluidic large-scale integration, Science 298 (2002) 582.

DNAC. Dekker et al.: Electronic properties of DNA, Phys. World 14 (2001) 29.C.M. Niemeyer: Nanoparticles, proteins, and nucleic acids: Biotechnology meets materials science, Angew. Chem. Int. Ed. 40 (2001) 4128.N.C. Seeman: DNA in a material world, Nature 421 (2003) 427.P.W.K. Rothemund: Folding DNA to create nanoscale shapes and patterns, Nature 440 (2006) 297.K. Hamad-Schifferli et al.: Remote electronic control of DNA hybridization through inductive coupling to an attached metal nanocrystal antenna, Nature 413 (2002) 152.

PeptidesG.M. Whitesides et al.: Beyond molecules: Self-assembly of mesoscopic and macroscopic components, PNAS 99 (2002) 4769.X. Zhao et al.: Fabrication of molecular materials using peptide construction motifs, Trends Biotech. 22 (2004) 470.J.J. DeYoreo et al.: Shaping crystals with biomolecules, Science 306 (2004) 1301.R.W. Drum et al.: StarTrek replicators and diatom nanotechnology, Trends Biotech. 21 (2003) 325.N.C. Seeman et al.: Emulating biology: Building nanostructures from the bottom up, PNAS 99 (2002) 6451.

ProteinsR.D. Vale et al.: The way things move: Looking under the hood of molecular motor proteins, Science 288 (2000) 88.R. Yasuda et al.: F1-ATPase is a highly efficient molecular motor that rotates with discrete 120° steps, Cell 93 (1998) 1117.H. Itoh et al.: Mechanically driven ATP synthesis by F1-ATPase, Nature 427 (2004) 465.

J. Fritz, IUB 2006