Fumiaki Tanaka

Developing Support System for Sequence Design in DNA Computing

Sequence design is the important factor which governs the reaction of DNA. In related researches, the method to minimize (or maxmize) the evaluation function based on knowledge of sequence design has been used. In this paper, we develop support system for sequence design in DNA computing, which minimizes the evaluation function calculated as the linear sum of the plural evaluation terms. Our system not only searches for good sequences but also presents contribution ratio of each evaluation term to the evaluation function and can reduce the number of combination of evaluation terms by reduction of the evaluation function. It helps us to find a good criteria for sequence design in DNA computing.

Towards a general-purpose sequence design system in DNA computing

Sequence design has turned out to be a crucial factor in successful DNA computing. We present a support system for sequence design in DNA computing. Our system can fit various requirements for sequence design. The /spl beta/-version of this software is available for download.

Sequence design for stable DNA tiles

DNA tile nanostructures have lately attracted a lot of attention as a new calculation technique and material on the nanometer scale. In forming DNA tiles, sequences need to bond in tile conformation. Conventional work can design sequences using overlapping subsequence. In this paper, we design tile sequences based on free energy. As a result of optimization, we show that we can design tile sequences as stable as conventional tiles. Moreover, we illustrate that the tile designed by the proposed method is perhaps more stable than conventional one. This method will be useful to design many tiles when forming large scale and complex DNA nanostructures.

Nearest-Neighbor Thermodynamics of DNA Sequences with Single Bulge Loop

Forty thermodynamic parameters were estimated for DNA duplexes with a single bulge loop. In DNA computing, sequences need to form wanted structures, not unwanted structures. To achieve this, we should design sequences with low free energy (ΔG 37°) in wanted structures and high free energy in unwanted structures. Conventional sequence design strategies have not prevented the formation of bulge loop structures completely. Estimation of the ΔG 37° of the bulge loop with the loop length from the chemical experimental data has not been enough to predict the ΔG 37° of the bulge loop structure. To investigate the effect of the type of bulged base and its flanking base pairs, we applied the nearest-neighbor model to DNA sequences with a single bulge loop. We also estimated the effect of loop position on the stability of a single bulge loop.

The effect of the bulge loop upon the hybridization process in DNA computing

To improve the efficiency of DNA computing, we need to prevent hybridization errors. In this paper, we focus on the bulge loop structures, which cannot be prevented by current sequence design methods. To estimate the formation of bulge loop structure, we measured the melting temperature (Tm) and the binding intensity of sequences with a single bulge loop in some simple experiments. Based on the experimental results, we mainly discuss the effect of the base type and the position of the loops. We also discuss the possibilities for modeling the formation of bulge loops based on these experimental results.

Sequence design support system for 4 × 4 DNA tiles

A DNA computation model by DNA tiles needs sequence design in order to correctly form tile structure and self-assembly. We design sequence, demonstrate biochemical experiments by a trial and error approach, and, repeatedly analyze tiles. Because no integrated sequence design system computes data that indicates properties of sequences, we must analyze designed sequences by hand and many types of software. In this paper, we develop a sequence design support system for 4 × 4 DNA tiles that analyzes and optimizes tile sequences to support sequence design. The most remarkable feature of this system is optimization based on free energy. The optimization strategy is developed so that the energy of perfect tile is the stablest.