What is Nano-Bio? Non-Covalent Interactions

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Joanna Sharp
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1 - - What is Nano-Bio? Physicist: Biotech: Biologists: -study of molecular interactions -application of nano-tools to study biological systems. -application of nano-tools to detect, treat, and prevent disease -we ve been studying Nano-Bio for several hundred years! ells build functional structures store / process information transduce energy replicate recognition 1-10 µm hemist / Mat Sci: -exploit molecular biology to make new materials pportunist: -an infinite source of funding! Electrostatic 100 mev Long range Non-ovalent Interactions Hydrogen Bond 40 mev = - --P- - - H + H-N- H N H Directional - strongest in a straight line van der Waals 4 mev Hydrophobic 100 mev Between any two atoms Very weak H H H H H H minimize contact with water H H H H H H 1

2 Biology: 4 families of small organic molecules Sugars Lipids - Nucleotides Peptides N - P - N N - +H 3 N R Larger structures from these building blocks Polysaccharides Biomembranes RNA / DNA Proteins R R R R --N---N---N---N---N---N---N R R R 2

3 Pre 1970 s: DNA was extremely difficult to analyze long and featureless. Significant advance: discovery of restriction nucleases which cut DNA. Target phosphodiester bonds at a specific 4-8 base sequence. P - Restriction Nucleases Hae III Blunt ends Eco RI Sticky ends 3

4 Denaturization / Hybridization At high temperature or extreme ph, hydrogen bonds will break and DNA will melt in single strands. Slow cooling (or normalizng ph) allows hydrogen bonds to reform: ~ 90 cool Hybridization can be highly specific for DNA lengths up to 1000 bases. Why So Specific? T Hydrogen bonds A G 4

5 DNA Nanomotor single strand, 17 bp DNA: TGGTTGGTGTGGTTGGT Exists as a tetraplex structure in isolation: Li and Tan, Nano Lett 2, 315 (2002) DNA Nanomotor Forms duplex double strand in presence of α TG GTT GGT GTG GTT GGT :nanomoter α: GTA GT G GA AA A A AA A Sticky End 5

6 DNA Nanomotor Add complementary strand b: TG GTT GGT GTG GTT GGT :nanomoter α: GTA GT G GA AA A A AA A β: AT AG GG TG GTT GGT GTG GTT GGT Initiated by sticky end pairing, propagated by branch migration DNA Nanomotor Nanomoter re-folds into its tetraplex state: 6

7 DUTE Nanomotor DUTE Nanomotor add α 7

8 DUTE Nanomotor add β DUTE Nanomotor add α 8

9 DUTE Nanomotor add β DUTE Nanomotor add α 9

10 DUTE Nanomotor add β DUTE Nanomotor add α 10

11 FRET Signal fluoresce quenched Add K+ (promotes TE) Add α S17mer nanomoter Nanomotors on Surfaces α β α β 11

12 Protein Structure Secondary Tertiary Non-covalent bonding between residues within the protein creates structural motifs. SEQUENE STRUTURE FUNTIN Protein Binding Protein function requires binding other molecules. ATP 12

13 Protein Binding Protein function requires binding other molecules. ATP Yet this binding must be highly SPEIFI to avoid binding other molecules. Protein Binding Protein function requires binding other molecules. Yet this binding must be highly SPEIFI to avoid binding other molecules. ATP Specificity is achieved through a set of weak non-covalent bonds and and matching contour between the protein and ligand. ligand binding site protein 13

14 Antibodies Strong, specific binding molecules. Remove antigens from an organism. Antibodies are technologically useful because they can be raised against any small molecule or nanostructure. 14

15 Biotin/Streptavidin Strong, permanent bond. Stable over wide range of T and ph. MSFET gate p Si 2 p n 15

16 BioMSFET protein p Si 2 p n BioMSFET protein p Si 2 p n 16

molecules must cover the 2D gate Nanowire

17 BioMSFET protein Field due to charged biomolecules create the inversion p Si 2 p n Limited sensitivity molecules must cover the 2D gate Nanowire Nanosensors streptavidin biotin p p Science 293, p

18 Nanowire Nanosensors Biotin/Streptavidin 25 pm streptavidin 1D systems are more sensitive to surface effects. Nanowire Nanosensors Biotin/Antibiotin - reversible 18

19 Synthetic Immobile DNA Junctions Genomic DNA strictly linear, but branch junctions exist transiently in nature and can be stabilized. N Seeman, Ann. Rev. Biophys. Biomol. Struct. 27, p225 (1998). 19

20 entral Dogma of Molecular Biology DNA RNA Protein (transcription) (translation) entral Dogma of Molecular Biology DNA RNA Protein (transcription) (translation) 1

21 Three DNA bases code for one protein residue. R R R R --N---N---N---N---N---N---N R R R Virus Small ( nm) Simple Parasitic Not technically living 2

Virus Life ycle Selection of peptides with semiconducting binding specificity for directed nanocrystal assembly Whaley, et al. Nature 405, p665 (2000). Biomolecules can.

22 Virus Life ycle Selection of peptides with semiconducting binding specificity for directed nanocrystal assembly Whaley, et al. Nature 405, p665 (2000). Biomolecules can. fabricate inorganic nanomaterials. assemble them into structures. be easily synthesized and manipulated an we extend this to inorganic materials with interesting electronic properties? GaAs(100) GaAs(111)A GaAs(111)B InP(100) Si(100) 3

23 Phage Display 1. ombinatorial phage libraries synthesized with millions of peptide sequences on coat 2. Phage exposed to the target of interest. 3. Non-bound phage are washed from the surface. 4. Bound phage are eluted from the surface. 4

24 Analyze or Repeat 5. Bacteriophage are amplified by infecting bacteria. Bacteriophage M nm x 9 nm, 5 proteins, 9 genes g3p 5

25 Phage Display with Electronic Materials Insert ~10 9 different 12 residue peptides into g3p. Expose to clean semiconductor surfaces. Wash and elute to isolate binding peptides. Amplified by 10 6 in bacteria. Repeat 3 to 5 times. Analyze genome of binding M13s Sequences which bind GaAs (100) 6

26 Sequences which bind GaAs (100) group random third fourth fifth type occurrence round round round Lewis 34% 41% 48% 55% Base **phage display selects for an increased proportion of residues that can donate an electron pair to the GaAs surface. **the 12-mer peptides sequences should be extended, and may be longer than necessary (working on 7-mers) Demonstrating Specificity 20 nm gold G13 (GaAs 100 binder) substrate 7

27 Demonstrating Specificity Peptide/Semiconductor interaction structural? chemical? electronic? GaAs Si Lipids Lipids DP - 8

28 Biomembrane Supported Membrane Substrate 9

29 Supported Membrane Dynamics Detection of Molecular Interactions at Membrane Surfaces through olloid Phase Transitions Michael M. Baksh et al,nature 427, normal lipids Ligands 10

30 ondensed phases (neutral or negative membrane) Dispersed phases (positive membrane) olloids are near a phase transition, determined by the colloid pair interaction. Add receptor protein Presence of the receptor protein alters the spacing, thus altering the van der Waals contribution to the pair interacion. 11

Phase transition provides signal amplification to observe molecular

31 Ligand: Trisialoganglioside (G T1B ) Receptor: Tetanus toxin (TT) Quantify with the pair distribution function: g( r) = e w( r) / K T B Phase transition provides signal amplification to observe molecular event. ontrol Gm1 only alters the pair potential with the holera Toxin B 12

Multiple choice questions (numbers in brackets indicate the number of correct answers)

1 Multiple choice questions (numbers in brackets indicate the number of correct answers) February 1, 2013 1. Ribose is found in Nucleic acids Proteins Lipids RNA DNA (2) 2. Most RNA in cells is transfer