the 3 rd research on theorem proving mec meeting hanyang university proteome research lab hanyang...

The 3The 3rdrd Research on Research on Theorem ProvingTheorem Proving

MEC Meeting MEC Meeting

Hanyang University Hanyang University Proteome Research LabProteome Research Lab

2003. 1. 16 2003. 1. 16

Park, Ji-Yoon Park, Ji-Yoon

The 1The 1stst Year Year ResearchResearch

- Linear Implementation- Linear Implementation

2003. 1. 16 2003. 1. 16 Advanced Proteome Research Lab(APRL) http://gene.hanyang.ac.kr/ Advanced Proteome Research Lab(APRL) http://gene.hanyang.ac.kr/ 33

Theorem Proving using Resolution Theorem Proving using Resolution Refutation Refutation

NilNil

, add R as, add R as


PrimerPrimer SequenceSequence LengthLength ModificationModification GC ContentGC Content( % )( % )

ST¬QST¬Q5’ - AAG CAG TAG CGA CCA 5’ - AAG CAG TAG CGA CCA

ATT GAC GCA AAT TGA ATT GAC GCA AAT TGA CGT ACG TAC GCT GAA - 3’ CGT ACG TAC GCT GAA - 3’

45 mer45 mer NoneNone 46.746.7

¬RPQ¬RPQ5’- CAT ACA ATG AAC GCA 5’- CAT ACA ATG AAC GCA

GTC AAC GCA AGG CAG GTC AAC GCA AGG CAG TTC AGC GTA CGT ACG - 3’TTC AGC GTA CGT ACG - 3’

45 mer45 mer NoneNone 51.151.1

¬P¬P 5’- CTG CCT TGC GTT GAC - 3’5’- CTG CCT TGC GTT GAC - 3’ 15 mer15 mer 5’-phosphate5’-phosphate 60.060.0

RR 5’- TGC GTT CAT TGT ATG – 3’5’- TGC GTT CAT TGT ATG – 3’ 15 mer15 mer 5’-phosphate5’-phosphate 40.040.0

¬S¬S 5’ - TGG TCG CTA CTT –3’ 5’ - TGG TCG CTA CTT –3’ 15 mer15 mer 5’-phosphate5’-phosphate 53.353.3

¬T¬T 5’ - TCA ATT TGC GTC AAT-3’ 5’ - TCA ATT TGC GTC AAT-3’ 15 mer15 mer 5’-phosphate5’-phosphate 33.333.3

The Sequence for Linear The Sequence for Linear Implementation Implementation


587540504458434

267234213192184

124/123104

89/80

64/57/51/21/18/11/8

75 bp75 bp

M 1 2

The Amplification of Linear The Amplification of Linear MoleculeMolecule

Fig 1. Fig 1. The amplification of linearThe amplification of linear molecule in 3% agarose gel molecule in 3% agarose gel electrophoresis electrophoresis Lane 1: PCR product with S and ¬R Lane 1: PCR product with S and ¬R Lane 2: PCR products with ¬ S and R Lane 2: PCR products with ¬ S and R Lane M is a 25 bp molecular DNA ladder Lane M is a 25 bp molecular DNA ladder

The 2The 2ndnd Year Year ResearchResearch

- Hairpin Implementation- Hairpin Implementation


Sequence for Hairpin Sequence for Hairpin Implementation Implementation

5mer5mer

5mer5mer

6 mer6 mer

¬P¬P

PP ¬Q¬Q

Q Q

RR

P

Q

S

TP

Q

S

T


PrimerPrimer Sequence(5’ → 3’)Sequence(5’ → 3’) LengthLength ModificationModification GC ContentGC Content( % )( % )

PP TATTAAGACTTCTTGTAGTCT TATTAAGACTTCTTGTAGTCT 21 mer21 mer 5’-Phosphate5’-Phosphate 28.528.5

QQ TCATGTTCCT TCATGTTCCT 10 mer10 mer 5’-Phosphate5’-Phosphate 40.040.0

¬P¬P TAATAAGGAATAATAAGGAA 10 mer10 mer 5’-Phosphate5’-Phosphate 20.020.0

¬Q¬Q CATGA CATGA 5 mer5 mer 5’-phosphate5’-phosphate 40.040.0

¬R¬R TCATGTTCCTTCATGTTCCT 10 mer10 mer 5’-phosphate5’-phosphate 33.333.3

The Sequence for Hairpin The Sequence for Hairpin Implementation Implementation


The Amplification of Hairpin The Amplification of Hairpin MoleculeMolecule

Fig 2. The amplification of hairpin molecule in 3%Fig 2. The amplification of hairpin molecule in 3% agarose gel electrophoresis agarose gel electrophoresis

50 bp50 bp25 bp25 bp

The 3The 3rdrd Year Plan Year Plan


Design of Problem Design of Problem

6 variables, 9 clauses6 variables, 9 clauses322232122212

312131112111

323122211211

,,,,

,,

PPPPPPPPPPPP

PPPPPP


One of Proof TreesOne of Proof TreesPP1111∨P∨P1212 ~P12∨~P22

P11∨~P22 P21∨P22

P11∨ P21 ~P21∨~P31

P11∨~P31 P31∨P32

P11∨ P32 ~P12∨~P32

P11∨~P12 P11∨P12

P11

~P11∨~P21 P21∨P22

~P11∨ P22~P22∨~P32

~P11∨ ~P32P31∨P32

~P11∨ P31~P11∨~P31

~P11

nnilil

20~30

20~30


Experimental ProcedureExperimental Procedure

The Problem The Problem (6var, 9clau)(6var, 9clau)

Design of Oligo SeDesign of Oligo Sequence quence

Exonuclease III Exonuclease III (remove partial (remove partial solution) solution)

Step IStep I

Step IIStep II

Step IIIStep III

Step IVStep IV

Step VStep V

HybridizationHybridization(95°C→16°C (95°C→16°C cooling down) cooling down)

Synthesis & Synthesis & ModificationModification(5’-Phosphate)(5’-Phosphate)

LigationLigation(T4 DNA Ligas(T4 DNA Ligas

e: 16°Ce: 16°C

Step VIStep VI

Step VIIStep VII

Gel Electrophoresis Gel Electrophoresis

Step VIIIStep VIII

The Final The Final SolutionSolution

* * No Self-No Self-HomologyHomology* No Cross-* No Cross-HomologyHomology


Forward DirectionForward Direction DNA9 Conference DNA9 Conference

Abstract Submission(2/15)Abstract Submission(2/15) Experimental Work Experimental Work

Journal Version Journal Version Biochemical Journal Biochemical Journal Biological Computing Biological Computing

6.3736.373

7.6667.666

3.161 3.161

4.493 4.493

5.545 5.545

29.491 29.491

36.242 36.242

24.595 24.595

10.89610.896


Expected ResultExpected Result

Fragments of linear DNA migrate thFragments of linear DNA migrate through agarose gels with a mobility rough agarose gels with a mobility that is inversely proportional to the that is inversely proportional to the loglog1010 of their molecular weight of their molecular weight

Circular forms of DNA migrate in aCircular forms of DNA migrate in agarose distinctly differently from lingarose distinctly differently from linear DNAs of the same mass.ear DNAs of the same mass.


DiscussionDiscussion

the 3 rd research on theorem proving mec meeting hanyang university proteome research lab hanyang...

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