Satoshi Kashiwamura

Hierarchical DNA Memory Based on Nested PCR

This paper presents a hierarchical DNA memory based on nested PCR. Each DNA strand in memory consists of address blocks and a data block. In order to access specific data, we specify the order of the address primers, and nested PCR are performed by using these primers. Our laboratory experiments are also presented to demonstrate the feasibility of the proposed memory.

Development, evaluation and benchmarking of simulation software for biomolecule-based computing

Simulators for biomolecular computing, (both in vitro and in silico), have come to play an important role in experimentation, analysis, and evaluation of the efficiency and scalability of DNA and biomolecule based computing. Simulation in silico of DNA computing is useful to support DNA-computing algorithm design and to reduce the cost and effort of lab experiments. Although many simulations have now been developed, there exists no standard for simulation software in this area. Reliability, performance benchmarks, user interfaces, and accessibility are arguably the most important criteria for development and wide spread use of simulation software for BMC. The requirements and evaluation of such software packages for DNA computing software are discussed, particularly questions about software development, appropriate user environments, standardization of benchmark data sets, and centrally available common repositories for software and/or data.

Development of DNA relational database and data manipulation experiments

An enormous amount of data such as genomic data can be stored into DNA molecules as base sequences. DNA database is important for organizing and maintaining these data, because extracted data from DNA database can be directly manipulated by chemical reactions. In this paper, we develop a DNA relational database with a simple data model and realize a computational model (relational algebra) of data manipulation as a sequence of chemical experiments. By using the developed database, it is shown that we can execute query operations based on the contents of data (the values of attributes). Furthermore, we propose a conversion scheme of query input to a series of experiment operations.

Combining randomness and a high-capacity DNA memory

In molecular computing, it has long been a central focus to realize robust computational processes by suppressing the randomness of molecular reactions. To this end, several methods have been developed to control hybridization reactions of DNA molecules by optimizing DNA sequences and reaction parameters. However, another direction in the field is to take advantage of molecular randomness rather than avoid it. In this paper, we show that randomness can be useful in combination with a huge-capacity molecular memory, and demonstrate its application to an existing technology -- DNA ink.

Towards Optimization of PCR Protocol in DNA Computing

Recently, in the research field of DNA Computing, the improvement of reliability of computation has been expected. Since DNA Computing consists of some chemical reactions, it seems to be clearly important to optimize each reaction protocol in order to improve the reliability of computing. Moreover, the purpose of the reaction in DNA Computing crosses variably. We consider that the optimization of reaction protocol according to each purpose will be necessary. We try to derive positive impact factors on the reaction result from actual experiments by using DOE. From the results of experiments, we show the importance and necessity of optimizing reaction protocol according to each desired reaction.

Towards a high reliability of the PCR amplification process in DNA computing

Polymerase Chain Reaction (PCR) is the most important process in DNA computing. When the concentration of a DNA sequence is too little to investigate, PCR could amplify the sequence with a polymerase. PCR is frequently applied to obtain a result in DNA computing, because the result is generally shown by a little amount of DNA sequence. Therefore, the reliability of PCR must be assured for DNA computing. The authors define the reproducibility of PCR as the reliability. Similarly, the reaction time is defined as a reaction cost, and other parameters are defined as control factors in quality engineering. By adjusting the factors, we improve a PCR performance shown by the reproducibility and reaction cost.

DNA memory with 16.8M addresses

A DNA Memory with over 10 million (16.8M) addresses was achieved. The data embedded into a unique address was correctly extracted through addressing processes based on the nested PCR. The limitation of the scaling-up of the proposed DNA memory is discussed by using a theoretical model based on combinatorial optimization with some experimental restrictions. The results reveal that the size of the address space of the DNA memory presented here may be close to the theoretical limit. The high-capacity DNA memory can be also used in cryptography (steganography) or DNA ink.

TOWARDS A HIGH RELIABILITY OF THE PCR AMPLIFICATION PROCESS IN DNA COMPUTING

Polymerase Chain Reaction (PCR) is the most important experimental technique in DNA computing. When a concentration of DNA sequence is too small to investigate, PCR amplifies the DNA sequence by the addition of a polymerase. PCR is frequently used in DNA computing, because the calculation result is usually represented by a small concentration of DNA sequence. Therefore, PCR has a crucial influence on the calculation result. The reliability of PCR needs to be improved for DNA computing. In this paper, the reliability of PCR is defined by the reproducibility of the amplified concentration of DNA sequence. The PCR protocol is adjusted to improve the reliability. Quality Engineering efficiently supports this adjustment.