DNA-based Theorem Proving - Present Work

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Presentation transcript:

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

Scale-up of Theorem Proving (PHP)

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

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

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

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

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)

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

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

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

Atomic Force Microscopy Results (2) 2.468 nm

Paper & Further Work BioSystems online submitted (2003. 12.26) Linear DNA implementation US Patent Pending (2003. 5. 30) Further work PHP problem Theorem proving based diagnosis (with Digital genomics)