The Inference via DNA Computing Piort Wasiewicz et al. Proceedings of the 1999 Congress on...

The Inference via DNA The Inference via DNA ComputingComputing

Piort Wasiewicz et al.

Proceedings of the 1999 Congress on Evolutionary Computation, vol. 2, pp. 988-993

Cho, Dong-Yeon

© 2001 SNU CSE Biointelligence Lab

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IntroductionIntroduction

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


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The Inference MechanismsThe 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


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The Inference Method Based The Inference Method Based on Circular DNA Moleculeson 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 concl

usion sector from one rule is complementary to the premise sector from the second rule.


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A set of indirect rules may be interpreted as a rule tree. If one or more rules are absent, then a tree is

incomplete.


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DNA Basic Fragments (DBFs) The structure of DBF is similar t

o the rule structure. First single strand part is complem

entary 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


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Molecular Rules and DBFs


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DNA Inference System The graph of DNA inference system


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Experimental VerificationExperimental Verification

Circular DNA Inference Path

A B C A A B D A


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Experimental Steps Preparation of fragments representing rules

B1: B1 only B2: B2 only B1+: B1, R1, R2 B2+: B2, R1, R3

B1-: B1, R1, R3 B2-: B2, R1, R2

Annealing: 5 minutes in 37C Ligation

T4 polinucleotide kinase 37 C or just room temperature

PCR Denaturation: 2 minutes in 95C After each cycle, the test tubes were kept for 30 seconds in 25 C.

Gel Electrophoresis: 6% acrylamid gel


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Results Ligation 24h in room temperature, PCR – 25 cycles

Strong 189bp bands DBFs sometimes anneal with themselves 20bp and 21bp strands


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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


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ConclusionConclusion

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 bact

eria cells after transformation into these cells. More sophisticated inference systems with rules having

several premises and conclusions should be developed and improved.

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