Bio-lab Technique used in DNA computing

1. Bio-lab Technique used in DNA computing Jung-Ah Kim Seoul National Uninversity 2002. 6. 5. Cell & Microbial Engineering Lab.

2. Contents • Bio-lab techniques • PCR • Separation & Detection… • DNA computing on a chip • A new detection method Array –based Electrical Detection of DNA with Nanopartical probes Cell & Microbial Engineering Lab.

3. Bio-lab technique(1) • Separation • Gel electrophoresis • Polyacylamide gel electrophoresis • Capillary electrophoresis • Bead separation Cell & Microbial Engineering Lab.

4. Gel electrophoresis • Molecular size fraction technique • Detect the specific DNA Bead Separation • Solution detection or filtering step! Cell & Microbial Engineering Lab.

5. Gel Electrophoresis Cell & Microbial Engineering Lab.

6. Bead Separation (1) Magnetic Beads Magnet Complementary Cell & Microbial Engineering Lab.

7. Biotin (Vitamin H) Bead Separation (2) Cell & Microbial Engineering Lab.

8. Bio-lab technique(2) • Detection • RFLP • SSCP • DGGE • TGGE • SNP-PCR Cell & Microbial Engineering Lab.

9. RFLP(Restriction Fragment Length Polymorphysm) -제한효소의 인지위의 존재여부의 차이에 의한 절단된 단편의 크기가 다름을 관찰하는 방법 • SSCP(Single Strand Conformation Polymorphysm) -염기서열의 차이에 따라 입체구조의 차이를 갖게 되어 전기영동 상에서 이동 속도의 차이를 보임. Cell & Microbial Engineering Lab.

10. DGGE(Denaturing Gradient Gel Electrophoresis) - detect differences in the melting behavior of small DNA fragments • TGGE(Temperatuer Gradient Gel Electorphoresis) • - gradient of increasing temperature down the gel Cell & Microbial Engineering Lab.

11. SNP-PCR • Single base-pair difference at a specific site in the DNA • PCR하는 동안 증폭된 특정유전자를 형광 hybridization probe를 이용해 검출 Cell & Microbial Engineering Lab.

12. DNA computin on surfaces (Liu et al.,Nature 403 ,143-144 ,2000) Cell & Microbial Engineering Lab.

13. Overvies of the surface-based approach to DNA computation Cell & Microbial Engineering Lab.

14. Encoding Scheme Problem: Cell & Microbial Engineering Lab.

15. Four cycles of SAT computation Destroyed using the single strand specific E.coli exonuclease I Cell & Microbial Engineering Lab.

16. Fluorescence profile & intensity histogram Cell & Microbial Engineering Lab.

17. A new technique for detection • Array –based Electrical Detection of DNA with Nanopartical probes(So-Jung Park et al.,Science 295,1503-1506, 2002) Cell & Microbial Engineering Lab.

18. Scheme showing behind electrical detection of DNA Cell & Microbial Engineering Lab.

19. Capture DNA strand • Target DNA strand • Probe DNA strand Cell & Microbial Engineering Lab.

20. FE-SEM image of the nanoparticle probe on an glass surface • (a) Before silver depositon • Afer a treatment with the enhancer soultion • (b) 3min • (c) 6min • (d) 9min Cell & Microbial Engineering Lab.

21. Resistance of the electrode arrays measured as a function of increasing silver enhancing time Cell & Microbial Engineering Lab.

22. 장점: high sensitive(1:100,000) PCR 불필요 mismatch된 DNA를 줄일 수 있다. 단점: variable수가 적을 때에 유용 Cell & Microbial Engineering Lab.

23. Referance • Liu et al.,Nature 403 ,143-144 ,2000 • So-Jung Park et al.,Science 295,1503-1506, 2002 • Elghanian et al, Science 277,1078-1081,1997 • Li et al., Nucleic Acid Research 30,1558-1562,2002 • Taton at al.,Science 289,1757-1759,2000 Cell & Microbial Engineering Lab.