The Inference via DNA Computing Piort Wasiewicz et al. Proceedings of the 1999 Congress on Evolutionary Computation, vol. 2, pp Cho, Dong-Yeon

© 2001 SNU CSE Biointelligence Lab 2 Introduction Overall research direction in symbolic computation devoted to molecular inference  The Inference process can be implemented either by backward or forward chaining with the help of DNA technology. We have developed new method of inference based on another concept of genetic engineering.  Circular inference paths

© 2001 SNU CSE Biointelligence Lab 3 The Inference Mechanisms Knowledge Representation  IF-THEN rules  Indirect rules Among rules we can distinguish those ones which conclusions are not final for the inference system.  Facts  If the premise of a rule is satisfied based on the facts and its conclusion part has been implemented, the rule is said to fire.  A method used by the inference mechanism in problem solving is called inference strategy.  Forward, backward, and mixed chaining

© 2001 SNU CSE Biointelligence Lab 4 The Inference Method Based on Circular DNA Molecules The Indirect Rules  All rules with one premise and one conclusion are converted to double DNA strands with sticky ends. The Indirect Rules Concatenation  Two rules can hybridize on that condition that the conclusion sector from one rule is complementary to the premise sector from the second rule.

© 2001 SNU CSE Biointelligence Lab 5 A set of indirect rules may be interpreted as a rule tree. If one or more rules are absent, then a tree is incomplete.

© 2001 SNU CSE Biointelligence Lab 6 DNA Basic Fragments (DBFs)  The structure of DBF is similar to the rule structure.  First single strand part is complementary to the ending conclusion represented by a given leaf of the decision tree.  Second single strand part is complementary to the first rule – the tree root.  The circular molecule created from rules and one DBF

© 2001 SNU CSE Biointelligence Lab 7 Molecular Rules and DBFs

© 2001 SNU CSE Biointelligence Lab 8 DNA Inference System  The graph of DNA inference system

© 2001 SNU CSE Biointelligence Lab 9 Experimental Verification Circular DNA Inference Path A  B  C  AA  B  D  A

© 2001 SNU CSE Biointelligence Lab 10 Experimental Steps  Preparation of fragments representing rules  B 1 : B 1 onlyB 2 : B 2 only  B 1 +: B 1, R 1, R 2 B 2 +: B 2, R 1, R 3  B 1 -: B 1, R 1, R 3 B 2 -: B 2, R 1, R 2  Annealing: 5 minutes in 37  C  Ligation  T4 polinucleotide kinase  37  C or just room temperature  PCR  Denaturation: 2 minutes in 95  C  After each cycle, the test tubes were kept for 30 seconds in 25  C.  Gel Electrophoresis: 6% acrylamid gel

© 2001 SNU CSE Biointelligence Lab 11 Results  Ligation 24h in room temperature, PCR – 25 cycles  Strong 189bp bands  DBFs sometimes anneal with themselves  20bp and 21bp strands

© 2001 SNU CSE Biointelligence Lab 12  Ligation 1h in room temperature, 21 or 24 cycles of PCR  Worse correct bands were obtained.  Ligation 2h in room temperature, 21 or 24 cycles of PCR

© 2001 SNU CSE Biointelligence Lab 13 Conclusion By using circular fragments derived from plasmids, the drawn inferences can be “read” after the experiments with higher precision and efficiency. Future Work  Plasmids with inference paths can be multiplied in bacteria cells after transformation into these cells.  More sophisticated inference systems with rules having several premises and conclusions should be developed and improved.