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1

Making DNA Expressions Minimal

van Vliet R., Hoogeboom H.J.

Fundamenta Informaticae

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2013

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Vol. 123, nr 2

199--226

EN

DNA expressions constitute a formal notation for DNA molecules that may contain nicks and gaps. Different DNA expressions may denote the same DNA molecule. We describe an algorithm to rewrite a given DNA expression into a DNA expression of minimal length denoting the same molecule.

2

A Minimal Normal Form for DNA Expressions

van Vliet R., Hoogeboom H.J.

Fundamenta Informaticae

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2013

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Vol. 123, nr 2

227--243

EN

DNA expressions constitute a formal notation for DNA molecules that may contain nicks and gaps. Different DNA expressions may denote the same DNA molecule. We define a (minimal) normal form for the language of DNA expressions, and describe an algorithm to rewrite a given DNA expression into the normal form.

3

Molecular NOR logic gate

Wąsiewicz P., Wójtowicz-Krawiec A., Płucienniczak A.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2008

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z. 165

237-244

EN

Molecular computing created for implementing logic systems, solving NP-difficult problems on nanoscale depends on DNA self-assembly abilities and on modifying DNA with the help of enzymes during genetic operations. In the typical DNA computing a sequence of operations executed on DNA molecules in parallel is called an algorithm, which is also determined by a model of DNA chains. This methodology is similar to the soft hardware specialized architecture driven here by heating, cooling and enzymes, especially polymerases used for copying strings. This work presents a unique approach to implementation of OR, NOR logic gates on molecules. It requires the representation of signals by DNA molecules. The presented method allows for constructing logic gates with many inputs and for executing them at the same quantity of elementary operations, regardless of a number of input signals. The NOR gate was implemented with the help of modified polymerase Taq, which stops its activity, when it meets a molecular obstacle on its way. The appropriate experiment was conducted to confirm the possibilities of the suggested implementation. Laboratory results were discussed.

4

Long DNA strands synthesis optimizing

Nowak R., Romaniuk M.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2008

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z. 165

157-163

EN

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.

5

A molecular inference via colorimetric change

Mulawka J.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2008

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z. 165

139-146

EN

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.

6

Searching DNA decision trees using quantum dots detection

Mulawka J.J.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2006

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z. 156

281-290

EN

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.

7

DNA computing

Formanowicz P.

Computational Methods in Science and Technology

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2005

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Vol. 11, nr 1

11-20

EN

DNA computing is an alternative method of performing computations. It is based on the observation that in general it is possible to design a series of biochemical experiments involving DNA molecules which is equivalent to processing information encoded in these molecules. In classical computing devices electronic logic gates are elements which allow for storing and transforming information. Designing of an appropriate sequence or a net of “store” and “transform” operations (in a sense of building a device or writing a program) is equivalent to preparing some computations. In DNA computing the situation is analogous. The main difference is the type of computing devices, since in this new method of computing instead of electronic gates DNA molecules are used for storing and transforming information. From this follows that the set of basic operations is different in comparison to electronic devices but the results of using them may be similar. Moreover, the inherent massive parallelism of DNA computing may lead to methods solving some intractable computational problems. In this paper basic principles of DNA computing are described and examples of DNA based algorithms solving some combinatorial problems are presented.