lecture 5-sa 15-398© 2004-5 Seth Copen Goldstein1Lipids• Organic compounds•Amphipathic– Polar head group (hydrophilic)– Non-polar tails (hydrophobic)• Lots of uses–Energy storage–Membranes–Hormones– VitaminsCOHOH2CH2CH2CCH3CH2CH2Fatty acidCarboxylgroupHydrocarbonchainCOHOH2CH2CH2CCH3CH2CH2Fatty acidCarboxylgroupHydrocarbonchainCOHOH2CH2CH2CCH3CH2CH2Fatty acidCarboxylgroupHydrocarbonchainlecture 5-sa 15-398© 2004-5 Seth Copen Goldstein2Some lipid structures• Hydrophobic interactions are importantHeadgroupTailgroup•Lipid is an amphipathic molecule, but rarely exists as a monomer.monolayerairwaterMicelleLipid bilayerInside-out(in nonpolarsolvent)lecture 5-sa 15-398© 2004-5 Seth Copen Goldstein3Micelles/BilayersWaterNo waterSerinePhosphateHydrophilic heads interact with waterHydrophobic tails interact with each otherHydrophilic heads interact with waterLipid micellesLipid bilayerslecture 5-sa 15-398© 2004-5 Seth Copen Goldstein4ExamplesLipids and water form tiny compartmentsRed blood cellslecture 5-sa 15-398© 2004-5 Seth Copen Goldstein5Using Lipids as MembranesWater WaterLipidbilayerPlanar bilayers:Artificial membranesWater WaterLipidbilayerPlanar bilayers:Artificial membranesMembrane is selectively permeablelecture 5-sa 15-398© 2004-5 Seth Copen Goldstein6Relative PermeabilitiesHydrophobic moleculesSmall, uncharged polar moleculesLarge, uncharged polar moleculesIonsO2, CO2, N2H2O, glycerolGlucose, sucroseH+,Na+,NCO3–,Ca2+,CL-,Mg2+,K+Phospholipid bilayerlecture 5-sa 15-398© 2004-5 Seth Copen Goldstein7DNA/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 -> Proteinslecture 5-sa 15-398© 2004-5 Seth Copen Goldstein8DNAH-bondslecture 5-sa 15-398© 2004-5 Seth Copen Goldstein9Protein• Linear polymer of amino acids linked by peptide bonds• Average 200 amino acids, can be >1K• Complex structure– Primary structure – sequence of AAs– Secondary structure – local arrangements– Tertiary structure – how the local structures pack in 3D– Quaternary structure – how chains foldlecture 5-sa 15-398© 2004-5 Seth Copen Goldstein10Levels of Structurelecture 5-sa 15-398© 2004-5 Seth Copen Goldstein11Forces determining structure• Van der Waals .4 – 4 KJ/mol• Hydrogen bonds 12-30 KJ/mol• Ionic bonds 20 KJ/mol• Hydrophoic interactions <40KJ/mollecture 5-sa 15-398© 2004-5 Seth Copen Goldstein12Amino Acids• 20 natural ones•Formed from–Central carbon–Amino group–Carboxyl group–H–Side-chain• Only difference is side-chain• Polar/non-polarAlanine Ala A Cysteine Cys C Aspartic AciD Asp D Glutamic Acid Glu E Phenylalanine Phe F Glycine Gly G Histidine His H Isoleucine Ile I Lysine Lys K Leucine Leu L Methionine Met M AsparagiNe Asn N Proline Pro P Glutamine Gln Q ARginine Arg R Serine Ser S Threonine Thr T Valine Val VTryptophan Trp W Tyrosine Tyr Ylecture 5-sa 15-398© 2004-5 Seth Copen Goldstein13Secondary 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 -loopsVHL proteinStebbins et al, Science, 284:455.lecture 5-sa 15-398© 2004-5 Seth Copen Goldstein14Using all this info• Protein-based memory•DNA as wires• DNA-based assembly– Templates–Smart-glue– tileslecture 5-sa 15-398© 2004-5 Seth Copen Goldstein15DNA as wires• DNA is conducting, 1986 and on– π-bonding–D-A, holes, Hopping• DNA is insulator, 1999 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 15-398© 2004-5 Seth Copen Goldstein16DNA-templates for wireslecture 5-sa 15-398© 2004-5 Seth Copen Goldstein17Interfacial Nanowire Assembly•Challenges:–Gravity–High interfacial tension–Incompatible with DNA, high saltlecture 5-sa 15-398© 2004-5 Seth Copen Goldstein18DNA as “glue”Versatility– sequence– 5’ or 3’ terminal -SH, -NH2, biotin, etc.Selectivity–4nunique sequences for oligo of length n– base pairing determines thermodynamic stability Reversibility– temperature, baseAu surfaceAu surface1111111222223331111111lecture 5-sa 15-398© 2004-5 Seth Copen Goldstein195’HS-C12H24-TTG AGA CCG TTA AGA CGA GGC AAT CAT GCA ATC CTG 3’Length Tm 36-mer 75oC21-mer 61oC18-mer 51oC15-mer 41oC9-mer 28oCTemperature-programmed Raft Assembly70oC58oC48oC38oCbird’s eye view:363621 21 1818cross-section view: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.lecture 5-sa 15-398© 2004-5 Seth Copen Goldstein20Necessary components of raft assembly:• Hybridization-compatible interface • DNA-coated nanowires at the interface• Hybridization-driven nanowire assembly• Thermal control over assembly processlecture 5-sa 15-398© 2004-5 Seth Copen Goldstein21Aqueous-aqueous interfaces• 70-nm Au nanowires• MESA-derivatized• PEG/dextran ATPS• hybridization bufferPEG/Au ColloidDextran• polymeric solutes, few weight %• particles collect at interface• low, tunable interfacial tensions• compatible with DNA, high salt• stable up to 95oClecture 5-sa 15-398© 2004-5 Seth Copen Goldstein22DNA-directed assembly at the interface?• DNA-coated nanowires at aq/aqinterface – form reflective interface after gentle agitationMinutes after removal from shakernoncomplementarycomplementaryhybridization-induced nanowireassembly at the aq/aq interfacelecture 5-sa 15-398© 2004-5 Seth Copen Goldstein23Melt curves for interface and solution assembliesNanowire rafts removed from interface– Higher Tm than solution-prepared counterparts– Large aggregates lead to high scattering–Observe greater change upon melting•more DNA was hybridized•interface concentrates nanowires for assembly1.61.41.21.00.8Absorbance at 260nm1.21.00.80.60.40.2Absorbance at 540nm7065605550Temperature (Deg. C)interfaceinterfacesolutionsolutionNanowire concentration at the interface favors assembly lecture 5-sa 15-398© 2004-5 Seth Copen Goldstein24Controlling Tmby surface dilution• Surface dilution of