1. Lecture 9 Designed self-assembly with Biomolecules DNA

2. Parameters of A-, B-, and Z-DNA Double Helices (after Dickerson, et al., 1982) Property A-Form B-Form Z-Form Helical sense Right-handed Right-handed Left-handed Repeating helix unit 1 base pair 1 base pair 2 base pairs Rotation/base pair (degrees) 33.6 35.9 +/- 4.2 -60/2 Mean base pairs/turn 10.7 10.0 +/- 1.2 12 Inclination of base normals to helix axis (degrees) +19 -1.2 +/- 4.1 -9 Rise/base pair along helix axis (Å) 2.3 3.32 +/- 0.19 3.8 Pitch/turn of helix (Å) 24.6 33.2 45.6 Mean propeller twist (degrees) +18 +16 +/- 7 ~0 OccurrenceDehydratedMost commonRare - certain in solutionsequences http://www.clunet.edu/BioDev/omm/dna.htm (Needs chime plugin) Different DNA structures

3. Copying DNA - the polymerase chain reaction

6. Attaching things to DNA 1.Biotin Streptavidin interaction - generic molecular adapters 2.Thiols - Nanoparticles 3.Fluorohores - for sensitive detection 4.Proteins - protein/DNA recognition 5.Proteins - semi-synthetic conjugation 6.Metal - metallisation for conductors

7. DNA detection using nanoparticle assembly Chad MirkinThiol terminated ssDNA Sensitivity - femtomol(ar) Selectivity - 100,000 : 1 for point mutations (single base pair changes)

8. Chad Mirkin DNA detection using nanoparticle assembly

9. Chad Mirkin Using DNA bar codes to detect proteins Science 2003, 301, 1884-1886.

10. Chad Mirkin Using DNA bar codes to detect proteins Science 2003, 301, 1884-1886. 3 aM 30 aM Sensitivity aM = attomolar = 10 -18 M

11. NiemeyerDNA protein conjugates - ImmunoPCR Protein diagnostics using DNA

12. DNA as a scaffold for something else Biotin Streptavidin interaction - generic molecular adapters

13. NiemeyerDNA directed immobilisation (DDI) DNA as a scaffold for something else

14. Niemeyer Protein directed DNA organisation ChainsRingsNetworks Ionic strength dependent supercoiling Chembiochem. (2001) 2, p260-4

15. DNA directed Protein organisation NiemeyerEnzyme localisation ChemBioChem (2003) 2, p242-245

16. DNA metallisation Braun, and othersNature (1998) 391, p775-8

17. DNA metallisation - use of protein masks Braun, and others Science, (2003) 302, p1380-1382

18. DNA superstructure metallisation Finkelstein and others Yan et al Science (2003) 301 p1882 Ribbons

19. Finkelstein and others Yan et al Science (2003) 301 p1882 DNA superstructure metallisation Grids

20. DNA superstructures for positioning proteins. Finkelstein and others Yan et al Science (2003) 301 p1882 Streptavidin locations determined by Biotin labelled DNA grids

21. Peptide nanotubes - a silver cloud with a peptide lining Reches and Gazit Science (2003) 300, p625