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Valerie Goss14 May 2010

Oral Candidacy Exam

In situ AFM imagingDuring

electrochemical manipulation of

directed DNA origami self-assembly

in a liquid environment

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Outline• What is molecular electronics?

• What is DNA origami?

• How might DNA origami be used to assemble molecular electronic components?

• My aims and how I plan to achieve them. wide area studies patterned surfaces

nanostructures on patterns 3D origami structures

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Molecular electronicsMolecular electronics

is a new paradigm for electronic

circuitry..

Like all electronics, molecular electronics is based on components and their connectivity.

“Molecular electronics describes the field in which molecules are utilized as the active (switching, sensing, etc.) or passive (current rectifiers, surface passivants) elements in electronic devices.”

Annual Reviews

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Molecular electronics

Molecular electronics is a new paradigm for electronic circuitry.

How can new molecular structures be designed and assembled to yield useful circuits?

DNA origami is a promising technology for creating molecular electronic circuitry. …so, what is DNA origami?

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What is DNA Origami?

How are these shapes possible?

P. W. K. Rothemund, Nature, 2006, vol. 440, pp. 297-302.

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Insights to DNA origami

DNA Annealing

P. W. K. Rothemund, Nature, 2006, vol. 440, pp. 297-302.

In a test tube, combine oligo mixture and circular genone DNA in TAE/Mg2+

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Insights to DNA origami

DNA Annealing

P. W. K. Rothemund, Nature, 2006, vol. 440, pp. 297-302.

In a test tube, combine oligo mixture and circular genone DNA in TAE/Mg2+

DNA origami High yield and low defects Well-defined shape and large

size

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How might DNA origami be used to assemble molecular electronic

components?Genomic organization in molecular electronicsBuild ligands and place them in addressable locations on the origami structure.

- Nanomagnets (information storage) Professors Wolfgang Porod and Gary H. Bernstein

Magnetic cellular automata

-For example, chemical attachment of carbon nanotubes (charge transport) to the surface of the origami structures.

Gyoergy, et al. Field-coupled computing in magnetic multilayers. Journal of Computational Electronics (2008), 7(3), 454-457.

Hareem , et al. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nature Nanotechnology (2010), 5(1), 61-66.

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My overall goal and how I plan to achieve it?

Organize in a surface array, ligand enhanced DNA origami, where the ligands are the components of the circuit.

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Research Approach• What? Our group desires to pattern origami for nanoelectronic applications

• Why? Model biological systems use low energy interactions to achieve

high fidelity assembly (eg DNA base pairing, protein tertiary structure), maybe we can capitalize on this concept.

• How? I will use a silicon surface as the electrode material. Modified with APTES, DNA orgami will have a cushion of cations to facilitate binding. Unfortunately, the strong binding occurs and this results in may binding errors.

• Upshot? I would like to electrically tune the surface to allow gentle

binding by reducing surface energy.

Reversible (binding) attachment of DNA origami to high-doped silicon surfaces: In situ electrochemical monitoring

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Basic AIM-Wide AreaWhat?

Apply small voltages to a modified silicon surfaces with deposited DNA origami

Why?

To relax origami strong binding and to allow self-correcting binding events on surface

Expectations?

1. I will obtain a series of in situ AFM images to analyze changes in origami orientation2. I will obtain binding metrics as a function of applied voltage3. I will submit a manuscript for publication

How?

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Electrochemical AFM CellGold wire connected to WE and potentiostat

WE

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APTES Aminopropyltriethoxysilane

“cationic cushion”

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--

Gold wire connected to WE and potentiostat

Not drawn to scale, binding is not one-to -one

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Persistent attachment of DNA origami

• H.Yan1 DNA origami

• Silicon/APTES/origami

• Some rolled structures, origami binding

• AFM Image (air) courtesy of Koshala Sarveswaran2

1Y.Ke, S. Lindsay, Y.Chang, Y. Liu, H. Yan, Science, 2008, vol. 319, 180, p. S14.

2Sarveswaran, K., Go, B., Kim, K. N., Bernstein, G. H. & Lieberman, M.,SPIE Proceedings (2010)

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2.00 nm

0.00 nm

1.0µm

VGoss AFM image in fluid

AFM Fluid images on mica“control surface”

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2.00 nm

0.00 nm

1.0µm

5.00 nm

0.00 nm

1.0µm

VGoss AFM images in fluid

4 nM DNAP.Rothemund rectangle, no edge modifications

AFM Fluid images on mica

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2.00 nm

0.00 nm

1.0µm

5.00 nm

0.00 nm

1.0µm

5.09 nm

0.00 nm

400nm

Tight binding platform

VGoss AFM images in fluid

AFM Fluid images on mica

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Packing, layering observed in fluid images DNA origami on mica

VGoss AFM image

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Processing silicon samples

P-Si [100]

= 200 nm Al

= debris

= 20 nm Ti

chloroform

HF clean + re-grow oxide

clean surface

Prior to placement of Al contacts, the chips will cleaned with piranha solution, material followed by HF and RCA 1 & 2

10 Ωcm

Collaboration with Electrical Engineering Professor Gary R. Bernstein and graduate student , Faisal Shah

VGoss cleaning process

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Al Si

300.00 nm

0.00 nm

2.0µm

10.00 nm

0.00 nm

3.0µm

5.00 nm

0.00 nm

1.0µm

Si chip following chloroform with HF cleaning, and re-growing oxide layer. RMS = 0.296

Cleaning with chloroformRMS= 0.431

Si chips cleaned after Al contacts

VGoss AFM images in fluid

Al and Ti impurity not on surface

22Binding Energy

Survey Spectrum

Inte

nsity

(C

PS

)

x 103

Ti

Al

A preliminary result:DNA origami on APTES treated silicon

VGoss AFM image in fluid 23

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Proposed Experiments

• Optimizing applied voltages– DNA origami should be ejected from the surface at

negative potentials• Optimizing ionic concentration

– Low ionic concentration compared to high ionic concentration at various potentials

• Determining buffer concentration dependencies– DNA buffer concentration effects on origami binding

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Basic AIM-Patterned SurfaceWhat?

The binding density and binding energies of DNA origami on anchor pads will be determined at different applied voltages and different ionic strengths, buffer compositions

Why?

To demonstrate high fidelity origami binding with proper orientation on an EBL patterned surface

Expectations?

1. In situ AFM images of controlled binding on a anchor pads.2. EBL patterns with size variations for comparative binding.2. I will obtain binding energy as a function of applied voltage3. I will submit a manuscript describing this work

How?

Molecular Lift-off Fabrication of Electron Beam Lithography anchor pads

I will obtain AFM images under buffer, before and after applied voltages. I will count the number of origami that are aligned in the image, and prepare histograms at various experimental conditions to illustrate binding percentage.

If reversibility binding is observed (origami displaced from anchor pads and then reabsorbed on anchor pads), a binding affinity curve can be developed to explain concentration dependent origami binding to site-specific locations.

Sarveswaran, K., Go, B., Kim, K. N., Bernstein, G. H. & Lieberman, M.,SPIE Proceedings (2010)

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Binding Thermodynamics

Chemical equilibrium between DNA origami surface reversible binding sites, S; DNA origami bound to surface sites, SD; and DNA origami in solution [D].

Gao, B., et al. (submitted Langmuir 2010).

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Basic AIM-NanostructuresWhat?

The binding density and binding energies of gold nanoparticles, nanomagnetics, and cow pea virus on anchor pads will be determined as a function of applied voltages and different ionic strengths, buffer compositions.

Why?

To demonstrate high fidelity nanoparticle binding with proper orientation on an EBL patterned surface

Expectations?

1. I will obtain a series of in situ AFM images to analyze changes in origami orientation.2. I will obtain binding energy as a function of applied voltage3. I will submit a manuscript for publication

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Basic AIM- 3D Origami Nanostructures

What?The binding density and binding energies of 3D nanostructures

Why?

To demonstrate high fidelity binding with proper orientation on an EBL patterned surface

Expectations?1. I will obtain a series of in situ AFM images under potential control2. I will obtain binding energy3. I will submit a manuscript for publication

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New skills needed

• Potentiostat measurements and control combined with real-time AFM The potentiostat will be used in my studies to explore DNA binding. By making the surface negatively charged, I expect to observe DNA origami being desorbed from the APTES surface. The potentiostat will allow me to dial up or down the voltage to characterize origami response to the charging surface.

• Electron beam lithography (EBL) Patterning of well-defined lines on silicon and gold are important for providing specific binding locations.

• Fluorescence Microscopy An important precept of the project is the ability to

position origami in an exact location and orientation. This fluorescence technique will allow me to visualize and quantifying binding rapidly.

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Teaching Career Professional Development

• NDeRC activities– Working with HS student on portable AFM– Teaching Forum– Science Café– Spooktackular at ETHOS– Penn High School Visits with portable AFM– Turner Drew Elementary School– Biweekly pedagogy seminars– EYH (Expanding Your Horizons)– KANEB Outstanding Graduate Student Teacher Award for Excellence in Teaching– KANEB (Striving for Excellence in Teaching)

• Presentations – Ivy Tech Nanotechnology Workshop with portable AFM– Turkey Run– PINDU– 37th Annual Conference NOBCChE – NSF GK-12– FNANO– Chemistry & Biochemistry Seminar Presentation

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Summary

• DNA origami is an inexpensive, well-tested technology, which has the potential to be useful in microelectronics fabrication.

• Well-orientated structures on a silicon surface will be achieved via electrochemical methods.

• Other nanostructures will be tested on patterned surfaces to compare control and differences in binding energy.

• I am excited about results and working on this project.

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Acknowledgements• Marya Lieberman• Lieberman Group• Gary Bernstein• Faisal Shah• OCE Committee• Chemistry & Biochemistry Office• NDeRC Community• Fellow Chemistry Graduate Students• Family

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Thank you!

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In situ Experimental E-circuit to eject DNA from the surface

Potentiostat

Au Ag/AgCl

Pt

AFM computer

and electronics

Si (100)

= DNA origami

Potential sweeps from -1 to 1 V

Al contact

Schematic not drawn to scale

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AIMSA. Under buffer conditions, I will determine the potentials necessary

for APTES modified silicon surfaces to be relaxed to reduce tight binding when applying a small potential, and obtain real-time in situ AFM images of origami experiencing voltage induced desorption from the surface, allowing time for self-imposed binding corrections.

B. AFM images under buffer, before and after applied voltages to determining binding percentages, and reversible binding.

C. Measure the fluorescence intensity to provide an efficient method to screen origamis that are bound to the anchor pads.

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AIMS, cont.

D. The binding density and binding energies of DNA origami on different sized EBL anchor pads will be determined.

E. The binding density and binding energies of nanoparticles on anchor pads will be determined at different applied voltages and different ionic strengths, buffer compositions.

F. Design tube shaped DNA origami to determine if long range structure can be reproduced with this larger 3D nanostructure on silicon surfaces. This project may provide a new focus area for research.

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Rants paper

• The DNA layer is being actuated by electric fields. Alternating potentials (DC) are applied in an aqueous salt solution between our gold working electrode (area) and a Pt wire counter electrode. The applied bias polarizes the electrode interfaced, leading to the formation of a Gouy-Chapmen-Stern screening layer on the solution side. The resulting electric field is confined to the electrode proximity (extension merely a few nanometers) but very intense with a field strength of up to 100 kV/cm even for low bias potentials (<1 V). Because DNA is intrinsically negatively charged along its deprotonized phosphate backbone, the molecules align in the electric field and the DNA conformation can be switched between surface and solution, depending on the polarity of the applied bias.

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Resistivity

ρ = ΩA/L

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Cross-overs, and staples spanning three helices

Seams are strengthened by merges and briges from stapes that cross the seam.

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Processing silicon samples

P-Si [100]

= 200 nm Al

= debris

= 20 nm Ti

chloroform

HF clean + re-grow oxide

clean surface

Prior to placement of Al contacts, the chips will cleaned with piranha solution, material followed by HF and RCA 1 & 2

10 Ωcm

Collaboration with Electrical Engineering Professor Gary R. Bernstein and graduate student , Faisal Shah

VGoss cleaning process

Resistivity is an intrisic property of a material that is measured as its resistance to current per unit length for a uniform cross sections

Material Resistivity, Ω.cm reference

Al2O3 1.12 x 1014 CRC handbook of Chemistry and Physics

Ge 57 Cuntell& kenneth, Physics 4th Ed.

Ultra pure H2O 1.82 x 107 Millipore

Aluminum 2.82 x 10-6 CRC handbook of Chemistry and Physics

Gold 3.5 x 10-8 CRC handbook of Chemistry and Physics

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Structure of APTES monolayer

Figure belongs to Lieberman Group

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h

--Gold wire connected to WE and potentiostat

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Fig. 1. a) 17 nm wide stripes of APTES made via molecular liftoff on silicon c) DNA nanostructures bound to APTES stripe. Background binding is < 2 %

a) APTES stripe b) DNA on APTES

Image belongs to Lieberman Group

Anchor pads in PMMA smaller than 10 nm can be created with EBL tool in Electrical Engineering

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DNA in applied fields

• Stable guanine monolayer on graphite between -200 to 600 mV (AFM and STM)

• N.J.Tao and Z. Shi, 1994, Surface Science Letters

Electronic Effects- Spin-Orbit Coupling

Ti Metal Ti Oxide

X-ray Photoelectron Spectroscopy

Small Area DetectionX-ray Beam

X-ray penetration depth ~1mm.Electrons can be excited in this entire volume.

X-ray excitation area ~1x1 cm2. Electrons are emitted from this entire area

Electrons are extracted only from a narrow solid angle.

1 mm2

10 nm

XPS spectral lines are identified by the shell from which the electron was ejected (1s, 2s, 2p, etc.).

The ejected photoelectron has kinetic energy:

KE=hv-BE- Following this process, the

atom will release energy by the emission of an Auger Electron.

Conduction Band

Valence Band

L2,L3

L1

K

FermiLevel

Free Electron Level

Incident X-rayEjected Photoelectron

1s

2s

2p

The Photoelectric Process

L electron falls to fill core level vacancy (step 1).

KLL Auger electron emitted to conserve energy released in step 1.

The kinetic energy of the emitted Auger electron is:

KE=E(K)-E(L2)-E(L3).

Conduction Band

Valence Band

L2,L3

L1

K

FermiLevel

Free Electron Level

Emitted Auger Electron

1s

2s

2p

Auger Relation of Core Hole

XPS Energy Scale

The XPS instrument measures the kinetic energy of all collected electrons. The electron signal includes contributions from both photoelectron and Auger electron lines.

KE = hv - BE - spec

Where: BE= Electron Binding Energy

KE= Electron Kinetic Energy

spec= Spectrometer Work Function

Photoelectron line energies: Dependent on photon energy.

Auger electron line energies: Not Dependent on photon energy.

If XPS spectra were presented on a kinetic energy scale, one would need to know the X-ray source energy used to collect the data in order to compare the chemical states in the sample with data collected using another source.

XPS Energy Scale- Kinetic energy

XPS Energy Scale- Binding energyBE = hv - KE - spec

Where: BE= Electron Binding Energy

KE= Electron Kinetic Energy

spec= Spectrometer Work Function

Photoelectron line energies: Not Dependent on photon energy.

Auger electron line energies: Dependent on photon energy.

The binding energy scale was derived to make uniform comparisons of chemical states straight forward.

Angle-resolved XPS

q =15° q = 90°

More Surface Sensitive

Less Surface Sensitive

Information depth = dsinqd = Escape depth ~ 3 l q = Emission angle relative to surface l = Inelastic Mean Free Path

q

q

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Poly methyl methacrylate

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Figure shows the liquid cell holder with the connecting electrodes. Figure 2 shows the set-up. The channels have a slight yellow-green color, we can see the fluid. The electrode clips electrodes are not in contact with the white kim-wipes (barrier to catch fluid). The imperfect set-up after the experiment is shown in Figure 3. The gold foil coating on the mica has been removed due to friction, rubbing of the black O-ring on the surface of the foil. We did not have a tight seal. Future experiments will need to correct for this, because (1) fluid was lost from the cell, and (2) the current did not follow because of the gaps created on the surface. The foil shows a black arc which is the location of where the O-ring unevenly rubbed away the fragile gold coating on the surface. The missing gold is actually on the O-ring; however, it is difficult to see the gold residue in the image. Interestingly, tiny dark blue-green flakes were observed on the white KIM-wipes, an iron precipitate formed. After experiments the desk top was cleaned with soapy water.

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