1. Valerie Goss14 May 2010Oral Candidacy Exam 1

3. patterned surfaces

4. nanostructures on patterns

5. 3D origami structures2

6. Molecular electronics Molecular electronics is a new paradigm for electronic circuitry.. 3 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

7. 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? 4

8. What is DNA Origami? How are these shapes possible? 5 P. W. K. Rothemund, Nature, 2006, vol. 440, pp. 297-302.

9. Insights to DNA origami In a test tube, combine oligo mixture and circular genone DNA in TAE/Mg2+ DNA Annealing P. W. K. Rothemund, Nature, 2006, vol. 440, pp. 297-302. 6

11. High yield and low defects

12. Well-defined shape and large sizeIn a test tube, combine oligo mixture and circular genone DNA in TAE/Mg2+ DNA Annealing P. W. K. Rothemund, Nature, 2006, vol. 440, pp. 297-302. 7

14. 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. 9

15. 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 10

16. Basic AIM-Wide Area Why? What? To relax origami strong binding and to allow self-correcting binding events on surface Apply small voltages to a modified silicon surfaces with deposited DNA origami 11 Expectations? 1. I will obtain a series of in situ AFM images to analyze changes in origami orientation I will obtain binding metrics as a function of applied voltage I will submit a manuscript for publication How?

17. Electrochemical AFM Cell Gold wire connected to WE and potentiostat WE 12

18. APTES Aminopropyltriethoxysilane 13 “cationic cushion”

19. Gold wire connected to WE and potentiostat - - 14 Not drawn to scale, binding is not one-to -one

21. Silicon/APTES/origami

22. Some rolled structures, origami binding

23. AFM Image (air) courtesy of Koshala Sarveswaran21Y.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) 15

24. 16 AFM Fluid images on mica “control surface” VGoss AFM image in fluid

25. 17 AFM Fluid images on mica 4 nM DNA P.Rothemund rectangle, no edge modifications VGoss AFM images in fluid

26. Tight binding platform 18 AFM Fluid images on mica VGoss AFM images in fluid

27. Packing, layering observed in fluid images DNA origami on mica 19 VGoss AFM image

28. Processing silicon samples = 200 nm Al = 20 nm Ti P-Si [100] = debris clean surface chloroform HF clean + re-grow oxide Prior to placement of Al contacts, the chips will cleaned with piranha solution, material followed by HF and RCA 1 & 2 10Ωcm VGoss cleaning process Collaboration with Electrical Engineering Professor Gary R. Bernstein and graduate student , Faisal Shah 20

29. Al Si Si chips cleaned after Al contacts Si chip following chloroform with HF cleaning, and re-growing oxide layer. RMS = 0.296 Cleaning with chloroform RMS= 0.431 21 VGoss AFM images in fluid

30. x 103 Survey Spectrum Al and Ti impurity not on surface Ti Intensity (CPS) Al 22 Binding Energy

31. A preliminary result:DNA origami on APTES treated silicon VGoss AFM image in fluid 23

32. 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 24

33. Basic AIM-Patterned Surface What? Why? 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 To demonstrate high fidelity origami binding with proper orientation on an EBL patterned surface 25 Expectations? In situ AFM images of controlled binding on a anchor pads. EBL patterns with size variations for comparative binding. I will obtain binding energy as a function of applied voltage I will submit a manuscript describing this work How?

34. Molecular Lift-off Fabrication of Electron Beam Lithography anchor pads Sarveswaran, K., Go, B., Kim, K. N., Bernstein, G. H. & Lieberman, M.,SPIE Proceedings (2010) 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. 26

35. 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). 27

36. Basic AIM-Nanostructures What? Why? 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. To demonstrate high fidelity nanoparticle binding with proper orientation on an EBL patterned surface 28 Expectations? 1. I will obtain a series of in situ AFM images to analyze changes in origami orientation. I will obtain binding energy as a function of applied voltage I will submit a manuscript for publication

37. Basic AIM- 3D Origami Nanostructures Why? What? The binding density and binding energies of 3D nanostructures To demonstrate high fidelity binding with proper orientation on an EBL patterned surface 29 Expectations? 1. I will obtain a series of in situ AFM images under potential control I will obtain binding energy I will submit a manuscript for publication

38. 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. 30

39. 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 31

40. 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. 32

41. Acknowledgements Marya Lieberman Lieberman Group Gary Bernstein Faisal Shah OCE Committee Chemistry & Biochemistry Office NDeRC Community Fellow Chemistry Graduate Students Family 33

42. Thank you! 34

43. In situ Experimental E-circuit to eject DNA from the surface Potential sweeps from -1 to 1 V Potentiostat AFM computer and electronics Pt Au Ag/AgCl Al contact Si (100) = DNA origami 35 Schematic not drawn to scale

44. AIMS 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. 36

45. AIMS, cont. The binding density and binding energies of DNA origami on different sized EBL anchor pads will be determined. 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. 37

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47. 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. 39

48. Resistivity 40 ρ=ΩA/L

49. 41 Cross-overs, and staples spanning three helices Seams are strengthened by merges and briges from stapes that cross the seam.

50. Processing silicon samples = 200 nm Al = 20 nm Ti P-Si [100] = debris clean surface chloroform HF clean + re-grow oxide Resistivity is an intrisic property of a material that is measured as its resistance to current per unit length for a uniform cross sections Prior to placement of Al contacts, the chips will cleaned with piranha solution, material followed by HF and RCA 1 & 2 10Ωcm VGoss cleaning process Collaboration with Electrical Engineering Professor Gary R. Bernstein and graduate student , Faisal Shah 42

51. 43 Structure of APTES monolayer Figure belongs to Lieberman Group

52. h Gold wire connected to WE and potentiostat - - 44

53. 45 b) DNA on APTES a) APTES stripe 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 % Anchor pads in PMMA smaller than 10 nm can be created with EBL tool in Electrical Engineering Image belongs to Lieberman Group

54. 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 46

55. Electronic Effects- Spin-Orbit Coupling Ti Metal Ti Oxide

56. X-ray Photoelectron SpectroscopySmall Area Detection Electrons are extracted only from a narrow solid angle. X-ray Beam X-ray penetration depth ~1mm. Electrons can be excited in this entire volume. 10 nm 1 mm2 X-ray excitation area ~1x1 cm2. Electrons are emitted from this entire area

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

61. The kinetic energy of the emitted Auger electron is: KE=E(K)-E(L2)-E(L3). Conduction Band Fermi Level Valence Band L2,L3 2p L1 2s K 1s Auger Relation of Core Hole

62. 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.

63. XPS Energy Scale- Kinetic energy KE= hv - BE - spec Where: BE= Electron Binding Energy KE= Electron Kinetic Energy spec= Spectrometer Work Function Photoelectron line energies: Dependenton photon energy. Auger electron line energies: Not Dependenton 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.

64. XPS Energy Scale- Binding energy BE = 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: Dependenton photon energy. The binding energy scale was derived to make uniform comparisons of chemical states straight forward.

65. Angle-resolved XPS q =15° q = 90° q More Surface Sensitive Less Surface Sensitive q Information depth = dsinq d = Escape depth ~ 3 l q = Emission angle relative to surface l =Inelastic Mean Free Path

66. 55 Poly methyl methacrylate

67. 56 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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