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The method described in this paper helps to syntheses DNA (deoxyribonucleic acid) molecules with length about 1000 bp, using typical techniques enable to create strands of length up to 70 bp. The given DNA strand is divided into smaller fragments, and next these fragments are connected by proposed protocol in genetic laboratory. The evolutionary algorithm is used to find the optimal solution. The freely accessible application called longdna, based on presented ideas was implemented and tested on simulated and real data.
In this work the inference performed on DNA molecules is considered. The process known as self-assembling of DNA strands is fundamental to achieve longer chains of molecules encoding knowledge base. By proper organization of this process any logic operations can be accomplished. In particular, systems based on decision trees may be easy assembled. A severe problem of nano-systems is to provide communication between nano-world and real-world. To solve this problem it is proposed to make use of colorimetric change phenomenon. Here an inference procedure is proposed that allows to check the knowledge base in form of decision tree. Although DNA strands react in the nano-world, due to optical read-out the inference result is attained quickly and easy. Thus, complicated and expensive operations of genetic engineering laboratory are eliminated.
Concept of self-assembly of DNA molecules may be utilized to implement different algorithms of computing. In particular, this methodology is useful in artificial intelligence because it operates on symbols. As has been shown by the author [7] DNA computing is suitable for searching the decision tree which is encoded by DNA molecules. Thus, the algorithms of artificial intelligence can be performed by this technique. In the contribution we demonstrate that by proper encoding and manipulating with DNA molecules it is possible to implement reasoning procedure by searching the decision tree. The method uses standard genetic engineering operations like hybridization, ligation, and purification. Quantum dot technique is applied to speed up detection of the final output eliminating the slow operation of electrophoresis. The approach presented is very simple and fast because the technique used allows an enormous number of molecules to be labeled, reduces instrument tie-up and improves analysis throughout the process.
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