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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