Head. Tail. Carboxyl group. group. group. air water. Hydrocarbon chain. lecture 5-sa Seth Copen Goldstein 2.

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1 Lipids Some lipid structures Organic compounds Amphipathic Polar head group (hydrophilic) Non-polar tails (hydrophobic) Lots of uses Energy storage Membranes Hormones Vitamins HO O C H 2 C CH 2 H 2 C CH 2 H 2 C CH 3 Fatty acid Carboxyl group Hydrocarbon chain air water Hydrophobic interactions are important Head group Tail group monolayer Lipid is an amphipathic molecule, but rarely exists as a monomer. Micelle Inside-out (in nonpolar solvent) Lipid bilayer lecture 5-sa Seth Copen Goldstein lecture 5-sa Seth Copen Goldstein 2 Micelles/Bilayers Examples Lipid micelles Water Lipid bilayers No water Serine Phosphate Hydrophilic heads interact with water Lipids and water form tiny compartments Hydrophobic tails interact with each other Red blood cells Hydrophilic heads interact with water lecture 5-sa Seth Copen Goldstein 3 lecture 5-sa Seth Copen Goldstein 4

2 Using Lipids as Membranes Relative Permeabilities Phospholipid bilayer Planar bilayers: Artificial membranes Hydrophobic molecules O 2, CO 2, N 2 Water Water Lipid bilayer Small, uncharged polar molecules H 2 O, glycerol Large, uncharged polar molecules Glucose, sucrose Membrane is selectively permeable Ions H +,Na +,NCO 3, Ca 2+,CL -,Mg 2+,K + lecture 5-sa Seth Copen Goldstein 5 lecture 5-sa Seth Copen Goldstein 6 DNA/RNA/Proteins Why study? Here are just the basic basics DNA made up of double strands of adenine (A), guanine (G), cytosine (C) and thymine (T) Pair up: C-G, A-T RNA Single stranded U for T Proteins do the work DNA -> RNA -> Proteins DNA H-bonds lecture 5-sa Seth Copen Goldstein 7 lecture 5-sa Seth Copen Goldstein 8

3 Protein Levels of Structure Linear polymer of amino acids linked by peptide bonds Average 200 amino acids, can be >K Complex structure Primary structure sequence of AAs Secondary structure local arrangements Tertiary structure how the local structures pack in 3D Quaternary structure how chains fold lecture 5-sa Seth Copen Goldstein 9 lecture 5-sa Seth Copen Goldstein 0 Forces determining structure Van der Waals.4 4 KJ/mol Hydrogen bonds 2-30 KJ/mol Ionic bonds 20 KJ/mol Hydrophoic interactions <40KJ/mol Amino Acids 20 natural ones Formed from Central carbon Amino group Carboxyl group H Side-chain Only difference is side-chain Polar/non-polar Alanine Cysteine Aspartic AciD Glutamic Acid Phenylalanine Glycine Histidine Isoleucine Lysine Leucine Methionine AsparagiNe Proline Glutamine ARginine Serine Threonine Valine Tryptophan Tyrosine Ala A Cys C Asp D Glu E Phe F Gly G His H Ile I Lys K Leu L Met M Asn N Pro P Gln Q Arg R Ser S Thr T Val V Trp W Tyr Y lecture 5-sa Seth Copen Goldstein lecture 5-sa Seth Copen Goldstein 2

4 Secondary structures Alpha helix Beta Sheet Loop regions Often binding sites Often hydrophilic Come between alpha s and beta s Represented as ribbon diagrams Coiled alpha Arrow beta Thin-loops VHL protein Stebbins et al, Science, 284:455. Using all this info Protein-based memory DNA as wires DNA-based assembly Templates Smart-glue tiles lecture 5-sa Seth Copen Goldstein 3 lecture 5-sa Seth Copen Goldstein 4 DNA as wires DNA-templates for wires DNA is conducting, 986 and on π-bonding D-A, holes, Hopping DNA is insulator, 999 and on λ-bridge between oligos on gold Insulator Lower T -> more insulating DNA is semiconductor, 2000 and on Consider series of quantum dots Maybe difference in fermi-level with contacts Conclusion? lecture 5-sa Seth Copen Goldstein 5 lecture 5-sa Seth Copen Goldstein 6

5 Interfacial Nanowire Assembly DNA as glue Au surface Au surface Selectivity 4 n unique sequences for oligo of length n base pairing determines thermodynamic stability Versatility sequence 5 or 3 terminal -SH, -NH 2, biotin, etc. Reversibility temperature, base Challenges: Gravity High interfacial tension Incompatible with DNA, high salt lecture 5-sa Seth Copen Goldstein 7 lecture 5-sa Seth Copen Goldstein 8 Temperature-programmed Raft Assembly bird s eye view: 70 o C 58 o C 48 o C 38 o C cross-section view: Necessary components of raft assembly: Hybridization-compatible interface DNA-coated nanowires at the interface Hybridization-driven nanowire assembly Thermal control over assembly process Deterministic rafts will be assembled at the aq/aq interface via sequential assembly of nanowires harboring decreasing lengths of oligonucleotides A and A as the sample is cooled. 5 HS-C 2 H 24 -TTG AGA CCG TTA AGA CGA GGC AAT CAT GCA ATC CTG 3 Length 36-mer 2-mer 8-mer 5-mer 9-mer T m 75 o C 6 o C 5 o C 4 o C 28 o C lecture 5-sa Seth Copen Goldstein 9 lecture 5-sa Seth Copen Goldstein 20

6 Aqueous-aqueous interfaces polymeric solutes, few weight % particles collect at interface low, tunable interfacial tensions compatible with DNA, high salt stable up to 95 o C DNA-directed assembly at the interface? Minutes after removal from shaker noncomplementary complementary PEG/Au Colloid Dextran 70-nm Au nanowires MESA-derivatized PEG/dextran ATPS hybridization buffer hybridization-induced nanowire assembly at the aq/aq interface DNA-coated nanowires at aq/aq interface form reflective interface after gentle agitation lecture 5-sa Seth Copen Goldstein 2 lecture 5-sa Seth Copen Goldstein 22 Melt curves for interface and solution assemblies Nanowire rafts removed from interface Higher T m than solution-prepared counterparts Large aggregates lead to high scattering Observe greater change upon melting more DNA was hybridized interface concentrates nanowires for assembly Nanowire concentration at the interface favors assembly Absorbance at 260nm Absorbance at 540nm interface interface solution solution Temperature (Deg. C) Controlling T m by surface dilution.0 Absorbance Absorbance Temperature (deg C) Surface dilution of proper DNA sequence decreases T m We can control coverage from -5 x 0 3 strands/cm 2 (40-50/particle) This approach can be used to tailor T m s for temperature-programmed assembly T m = 5 o C surface diluted w/ polya T m = 55 o C lecture 5-sa Seth Copen Goldstein 23 lecture 5-sa Seth Copen Goldstein 24

7 nm da Temperature-controlled Dissociation distinct melting events Temperature (deg C) C C C Initial proof-of-concept for temperatureprogrammed assembly 2-nm Au nanoparticles A, B = 2 mers C, D = 8 mers lecture 5-sa Seth Copen Goldstein 25 Potential-Assisted Raft Positioning lithographically-defined landing pads derivatize with complementary DNA hold at positive potential allow rafts to hybridize to pads reverse potential for stringency raft side-view landing pad raft side-view landing pad lecture 5-sa Seth Copen Goldstein 26 DNA Tiles lecture 5-sa Seth Copen Goldstein 27