We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (DeltaG (min)). Sequences that satisfy these constraints can be utilized in computations, various… (More)
This paper presents a hierarchical DNA memory based on nested PCR. Each 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.
In the field of DNA computing, more and more efforts are made for constructing molecular machines made of DNA that work in vitro or in vivo. States of some of those machines are represented by their conformations, such as hairpin and bulge loops, and state transitions are realized by conformational changes, in which such loops are opened. The ultimate goal… (More)
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… (More)
In this paper, we propose a new architecture for a multi-state DNA machine whose conformation of repeated hairpin structures changes sequentially in response to input oligomers. As an application of the machine, we also propose molecular memory in which the machine is used as a memory unit. Addressing in the memory is realized through state transitions of… (More)