Lipids Some Lipid Structures Micelles/Bilayers Examples

Lipids Some lipid structures • Organic compounds • Hydrophobic interactions are important •Amphipathic Head •Lipid is an amphipathic molecule, – Polar head group (hydrophilic) group but rarely exists as a monomer. Tail – Non-polar tails (hydrophobic) group

HO O • Lots of uses Carboxyl C group –Energy storage H2C air CH 2 water –Membranes H C 2 Hydrocarbon CH –Hormones 2 chain Inside-out H2C monolayer Micelle CH – Vitamins 3 (in nonpolar Fatty acid solvent) Lipid bilayer lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 1 lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 2

Micelles/Bilayers Examples

Lipid micelles Water Lipid bilayers

No water Lipids and water form Serine tiny compartments Phosphate Hydrophilic heads interact with water

Hydrophobic tails interact with each other Red blood cells

lecture 5-sa 15-398 Hydrophilic© 2004-5 Sethheads Copen Goldstein interact with water 3 lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 4 Using Lipids as Membranes Relative Permeabilities Phospholipid bilayer

Planar bilayers: Artificial membranes Hydrophobic molecules O2, CO2, N2

Water Water

Lipid Small, uncharged polar molecules H2O, glycerol bilayer

Large, uncharged polar molecules Glucose, sucrose

Membrane is selectively permeable H+,Na+,NCO –, Ions 3 Ca2+,CL-,Mg2+,K+

DNA/RNA/Proteins DNA

•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 H-bonds • DNA -> RNA -> Proteins

lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 7 lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 8 Protein Levels of Structure • 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 fold

Forces determining structure Amino Acids Alanine Ala A Cysteine Cys C • Van der Waals .4 – 4 KJ/mol • 20 natural ones Aspartic AciD Asp D Glutamic Acid Glu E • Hydrogen bonds 12-30 KJ/mol •Formed from Phenylalanine Phe F Glycine Gly G –Central carbon Histidine His H • Ionic bonds 20 KJ/mol Isoleucine Ile I –Amino group Lysine Lys K • Hydrophoic interactions <40KJ/mol Leucine Leu L Methionine Met M –Carboxyl group AsparagiNe Asn N Proline Pro P –H Glutamine Gln Q ARginine Arg R –Side-chain Serine Ser S Threonine Thr T • Only difference is Valine Val V Tryptophan Trp W side-chain Tyrosine Tyr Y • Polar/non-polar

lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 11 lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 12 Secondary structures Using all this info • Alpha helix • Protein-based memory • Beta Sheet •DNA as wires • Loop regions • DNA-based assembly – Often binding sites – Templates –Often hydrophilic –Smart-glue – Come between alpha’s and beta’s – tiles • Represented as ribbon diagrams –Coiled –alpha – Arrow – beta VHL protein –Thin -loops Stebbins et al, Science, 284:455.

DNA as wires DNA-templates for 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?

Selectivity –4n unique sequences for oligo of length n – base pairing determines thermodynamic stability Au surface Versatility – sequence Au surface – 5’ or 3’ terminal -SH, -NH2, biotin, etc. Reversibility – temperature, base

1 1 2 3 1 1 •Challenges: 1 1 1 1 2 2 – Gravity 1 2 1 3 – High interfacial tension 1 1 1 1 – Incompatible with DNA, high salt 3 2

Temperature-programmed Raft Necessary components of raft Assembly bird’s eye view: assembly:

70oC58oC48oC38oC • Hybridization-compatible interface • DNA-coated nanowires at the interface • Hybridization-driven nanowire assembly cross-section view: • Thermal control over assembly process 18 2136 36 21 18

5’ HS-C12H24-TTG AGA CCG TTA AGA 3’ Deterministic rafts will be assembled at CGA GGC AAT CAT GCA ATC CTG the aq/aq interface via sequential Length Tm 36-mer 75oC assembly of nanowires harboring 21-mer 61oC decreasing lengths of oligonucleotides A 18-mer 51oC 15-mer 41oC and A´ as the sample is cooled. 9-mer 28oC

lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 19 lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 20 Aqueous-aqueous interfaces DNA-directed assembly at the interface? • polymeric solutes, few weight % noncomplementary • particles collect at interface • low, tunable interfacial tensions

• compatible with DNA, high salt Minutes after • stable up to 95oC removal from shaker complementary

PEG/Au Colloid hybridization-induced nanowire • 70-nm Au nanowires assembly at the aq/aq interface • MESA-derivatized • PEG/dextran ATPS Dextran • hybridization buffer • DNA-coated nanowires at aq/aq interface – form reflective interface after gentle agitation

Melt curves for interface and Controlling T by surface dilution solution assemblies m 1.6 interface Nanowire rafts removed from interface 2.0 • Surface dilution of proper DNA

1.4 1.0 – Higher Tm than solution-prepared counterparts 1.5 sequence decreases Tm – Large aggregates lead to high scattering 1.2 • We can control coverage from 1-5 x –Observe greater change upon melting 1.0

1.0 0.5 13 2 • more DNA was hybridized solution 10 strands/cm (40-150/particle) Absorbance 0.8 • interface concentrates nanowires for assembly Absorbance at 260nm 0.5 • This approach can be used to tailor

Tm’s for temperature-programmed 1.2 interface 0.4 assembly

1.0 0.2 surface diluted w/ polyA 0.3 0.8 0.2 0.6 Nanowire concentration at 0.1 0.1 0.4 Absorbance

the interface favors assembly Absorbance at 540nm solution 0.0 0.2

50 55 60 65 70 0.0 -0.1 40 50 60 70 o o Tm = 51 C Tm = 55 C Temperature (Deg. C) Temperature (deg C)

lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 23 lecture 5-sa 15-398 © 2004-5 Seth Copen Goldstein 24 Potential-Assisted Raft Temperature-controlled Dissociation Positioning 2 distinct 2 melting events 4080 °C °C 60 °C 1.0 raft side-view

1 0.5 Absorbance @540 nm Absorbance @540 Initial proof-of-concept for temperature- “landing pad” programmed assembly 0.10 • lithographically-defined “landing pads” • derivatize with complementary DNA 0.05 dA • hold at positive potential • allow rafts to hybridize to pads 12-nm Au nanoparticles raft side-view 0.00 40 50 60 70 80 90 A, B = 12 mers • reverse potential for stringency Temperature (deg C) C, D = 18 mers

DNA Tiles