1. Other Detection System of Theorem Proving 2004. 2. 10 Park, Ji-Yoon

2. February 10, 2004 APRL http://gene.hanyang.ac.kr 2 3 × 3 Matrix Chip (1) 1 × 3 Matrix 3 × 3 Matrix Poly-L-Lysine 45 mer 15 mer 45 mer 15 mer 45 mer 15 mer 45 mer

3. February 10, 2004 APRL http://gene.hanyang.ac.kr 3 Experimental Steps 1. Poly-L-Lysine Coating 3. Washing & Dry 4. Attachment of Target DNA 6. Washing & Dry 7. Confocal LIF Detection 5. S1 nuclease Digestion 2. Attachment of Probe DNA

4. February 10, 2004 APRL http://gene.hanyang.ac.kr 4 Amine-Coated Slide glass (Corning) FAM (ST~Q) Cy3 (~P) Cy5 (R) ~S ~T ~RPQ Target DNA Probe DNA

5. February 10, 2004 APRL http://gene.hanyang.ac.kr 5 Poly-L-Lysine Patterned Slide glass FAMCy5 Overlay

6. February 10, 2004 APRL http://gene.hanyang.ac.kr 6 Problems & Discussion  PDMS Chip  Channel Cross-talking  Large sample volume require (~ 10 ul/channel)  We’ll use fresh PDMS Chip for every experiments  Using Thin PDMS Chip  Low Intensity of Cy3  Cy 3 → Alexa fluoro dye (Molecular Probe)

7. February 10, 2004 APRL http://gene.hanyang.ac.kr 7 More Consideration Hybridization (6 strands) Ligation Surface Filtration Nil Detection S, T, Q, ￢ P, R ￢ S, ￢ T, Q, P, ￢ R 5’ ST ￢ Q ￢ P￢ P￢ P￢ PR QP ￢ R 5’ ￢S￢S￢S￢S ￢T￢T￢T￢T

8. February 10, 2004 APRL http://gene.hanyang.ac.kr 8 Nanoparticle-based Detection (2) Nature 382, 607-609 (1996) 15 mer 45 mer

9. February 10, 2004 APRL http://gene.hanyang.ac.kr 9 Experimental Step 1. Au modification with thiol-capped oligonucleotides - Note: Oligonucleotide: non-complementary 3-thiol-TACCGTTG 3’-thiol-TTTGCTGA Au Au 2. Assembly (700 nm: aggregation) - Addition of linking DNA duplex 5’-ATGGCAACTATACGCGCTAG 3’-ATATGCGCGATCTCAGCAAA 3 3. Immediately Color change - with naked eyes

10. February 10, 2004 APRL http://gene.hanyang.ac.kr 10 Fig 1. (A) The UV-vis spectrum of oligonucleotide- modified 13-nm particles before (red line) and after (blue line) DNA-induced assembly (B) Solutions of 13-nm-diameter Au particles before (cuvette A) and after (cuvette B) DNA-induced assembly (c) After extended periods of time a polymeric precipitate forms and settles to the bottom of the cuvette (cuvette C) Expected Results (1)

11. February 10, 2004 APRL http://gene.hanyang.ac.kr 11 Fig 2. TEM images of DNA-linked nanoparticle assemblies at early stages in the growth process Expected Results (2)