2004. 5. 25

Ji-Yoon Park

Nanoparticle-Based Theorem Proving

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 22

Target Problem

P∧Q→R, S∧T→Q, S, T, P R = True ?

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 33

DNA-Based Nanoparticle Assembly Strategy

Mirkin, 2000Mirkin, 2000

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 44

1. Purchase of gold nanoparticle

2. Preparation of 3’-(alkanethiol) modified oligonucleotides

3. Preparation of Linker DNA

4. Characterization of DNA-linked gold assembly

Experimental Section

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 55

Primer Sequence(5’→3’) Length Modification

ST¬Q AAG CAG TAG CGA CCA ATT GAC GCAAAT TGA CGT ACG TAC GCT GAA 45 mer None

¬RPQ CAT ACA ATG AAC GCA GTC AAC GCA AGG CAG TTC AGC GTA CGT ACG 45 mer None

¬P CTG CCT TGC GTT GAC 15 mer 5’-phosphate

R TGC GTT CAT TGT ATG 15 mer 3’-thiol

¬S TGG TCG CTA CTT 15 mer 3’-thiol

¬T TCA ATT TGC GTC AAT 15 mer 5’-phosphate

The Sequence of Oligonucleotides

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 66

Assembly

15 mer15 mer 15 mer15 mer 45 mer45 mer

S1 Digestion Hypothesis

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 77

Colloidal Gold

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 88

Full Assembly vs S1 Digestion

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 99

Partial Assembly vs S1 Digestion

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1010

TEM Image (Colloidal Gold)

(a)(a) (b)(b) (c)(c)

TEM image of the annealed DNA-linked assembly (a) Colloidal gold (b) Full-assembly of DNA-linked nanoparticles (c) S1 Nuclease digestion of full-assembled DNA-linked nanoparticles

Surface-Based Theorem Proving

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1212

Surface-based DNA Computation

Liu et al., 2000Liu et al., 2000

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1313

1. Purchase of gold nanoparticle

2. Preparation of 3’-(alkanethiol) modified oligonucleotides

3. Preparation of Linker DNA

4. Characterization of DNA-linked gold assembly

Experimental Section

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1414

I

II

III

IV

V

A B C

(a) (b) I

II

III

IV

V

I

II

III

IV

V

A B C

A B C

(c)

¬RPQ¬RPQ¬RPQ

¬T¬T¬T

¬S¬S¬S

P.CP.C P.C

N.CN.C N.C

R¬PST ¬Q

¬RPQ¬RPQ¬RPQ

¬T¬T¬T

¬S¬S¬S

P.CP.C P.C

N.CN.C N.C

Theorem Proving by Fluorescence Imaging

May 25, 2004 May 25, 2004 APRL http://gene.hanyang.ac.krAPRL http://gene.hanyang.ac.kr 1515

• Paper publish • Genotyping experiment• Structure & Theorem Proving

Further Work