1. DNA-based Theorem Proving - Present Work
MEC Seminar
Dept. of Biochemistry
Park, Ji-Yoon

2. Scale-up of Theorem Proving (PHP)

3. PigeonHole Principle (PHP)
6 variable, 9 clause
3 Pigeon 32 22 12 31 21 11 , P Ø Ú
2 Pigeonhole

4. One of Proof Trees nil P11∨P12 ~P12∨~P22 P11∨~P22 P21∨P22 P11∨ P2110 10
P11∨~P12
P11∨P12
~P11∨~P31
~P11∨ P31 10
P11
~P11
nil

5. 1. Represent Clauses with DNA
Experimental Steps
1. Represent Clauses with DNA
2. Hybridization
3. Ligation
4. Gel Electrophoresis

6. PHP Implementation
A (90 bp)
B (90 bp)
C (90 bp) 1 2 3 4 M
Fig 1. The product of PHP implementation in 12% polyacrylamide gel electrophoresis
Lane 1: Ligated product A Lane 2: Ligated Product B
Lane 3: Ligated Product C
Lane 4: Final Ligated product
Lane M: 25 bp DNA ladder
90 bp

7. Discussion (T. T.) Confirmation of ligation product I
Denaturing polyacrylamide gel electrophoresis (from previous results)
Confirmation of major & minor band / S1 nuclease / Sequencing
Analysis of sequence
Adleman paper (94’, 02’)
Length of sticky end: more shorter (10 bp → 5 bp) comparison data
Experimental Procedure
Parallel reaction
Proper buffer (hybridization buffer: stringency)

8. Intermittent Contact Mode (ICM)
Introduction to Atomic Force Microscopy
Non Contact Mode (NCM)
[Constant Amplitude]
Intermittent Contact Mode (ICM)
[Tapping mode or Semicontact]

9. Atomic Force Microscopy Results (1)
AFM mode : Non contact
Scan area : 3 x 3 µm
Scan direction : Right to Left
1 µm
AFM mode : Intermittent contact
Sample Information
Name : pUC19 (E. coli cloning vector)
Structure : a small double-stranded DNA circle
Size : 2686 base pairs in length
Possible
DNA
Protein

10. Atomic Force Microscopy Results
Sample Information
Name : pUC19 (E. coli cloning vector)
Structure : a small double-stranded DNA circle
Size : 2686 base pairs in length
1 µm
AFM mode : Intermittent contact
Scan area : 3 x 3 µm
Scan direction : Right to Left
Scan area : 1 x 1 µm
300 nm

11. Atomic Force Microscopy Results (2)
2.468 nm

12. Paper & Further Work BioSystems online submitted (2003. 12.26)
Linear DNA implementation
US Patent Pending ( )
Further work
PHP problem
Theorem proving based diagnosis (with Digital genomics)