Molecular Computation by DNA Hairpin Formation

Sakamoto, Kensaku; Gouzu, Hidetaka; Komiya, Ken; Kiga, Daisuke; Yokoyama, Shigeyuki; Yokomori, Takashi; Hagiya, Masami

doi:10.1126/science.288.5469.1223

Cited by 355 publications

(136 citation statements)

References 20 publications

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“…In a similar way, constraints may be used to define the parameter space where computation under each method would be possible. For instance, the Whiplash PCR method for DNA computing recently proposed by Hagiya et al [86] may be constrained to single-stranded molecules of a certain optimal length, in a maximum concentration, and where the different variables are encoded with a minimum base-pairing disagreement for each pair of variables. This systems biology approach provides a basis for understanding of the structure and function of biological organisms through an incremental process that takes into consideration the expected lack of complete kinetic information.…”

Section: Discussionmentioning

confidence: 99%

Biomolecular computing: Is it ready to take off?

2007

Biotechnology Journal

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Biomolecular computing is an emerging field at the interface of computer science, biological science and engineering. It uses DNA and other biological materials as the building blocks for construction of living computational machines to solve difficult combinatorial problems. In this article, notable advances in the biomolecular computing are reviewed and challenges associated with this multidisciplinary research are addressed. Finally, several perspectives are given based on the review of biomolecular computing.K Ke ey yw wo or rd ds s: Biocomputing · DNA strand · Massive parallelism · Self-assembling · Steganography C Co or rr re es sp po on nd de en nc ce e: Professor Pengcheng Fu, Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, USA E E--m ma ai il l: pengchen@hawaii.edu F Fa ax x: +1-808-956-3542 A Ab bb br re ev vi ia at ti io on ns s: D DH HP P, directed Hamiltonian path; N NP P, non-deterministic polynomial time; P PN NA A, peptide nucleic acid

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Section: Discussionmentioning

confidence: 99%

Biomolecular computing: Is it ready to take off?

2007

Biotechnology Journal

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“…Otherwise, 0-1 programming problem and the satisfiability problem are both closely related, and 0-1 programming problem is a generalization of the satisfiability problem. Up to now, there have been many results for solving the satisfiability problem (Yoshida, 1999;Skamoto, 2000;Cukras et al, 1999;Braich et al, 2002). However, the model of 0-1 programming problem based on DNA computing has never been studied.…”

Section: The 0-1 Programming Problemmentioning

confidence: 99%

The general form of 0–1 programming problem based on DNA computing

Yin

Zhang

2003

Biosystems

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DNA computing is a novel method of solving a class of intractable computational problems, in which the computing speeds up exponentially with the problem size. Up to now, many accomplishments have been made to improve its performance and increase its reliability. In this paper, we solved the general form of 0-1 programming problem with fluorescence labeling techniques based on surface chemistry by attempting to apply DNA computing to a programming problem. Our method has some significant advantages such as simple encoding, low cost, and short operating time.

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“…From the practical point of view, the randomized algorithm is similar to the nondeterministic algorithm I present here. Sakamoto et al attempted to improve the efficiency of 3-SAT-solving, DNA computing systems by considering DNA encodings of clauses, rather than variables (Sakamoto et al 2000). However, implementing DNA computation presents significant challenges (Braich et al 2002), such as high error rates (Winfree and Bekbolatov 2003).…”

Section: Self-assembly and Tilesmentioning

confidence: 99%

“…Further, selfassembly systems allow for implementations that require a small, constant number of laboratory steps to execute, whereas DNA computing requires a larger number of steps. While some approaches have attempted to minimize this number of steps (Sakamoto et al 2000), it still typically depends on the size of the input (Winfree et al 1998). …”

Section: Self-assembly and Tilesmentioning

confidence: 99%

Efficient 3-SAT algorithms in the tile assembly model

Brun

2012

Nat Comput

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Self-assembly is a powerful process found in nature that guides simple objects assembling, on their own, into complex structures. Self-assembly is of interest to computer scientists because self-assembling systems can compute functions, assemble shapes, and guide distributed robotics systems. The tile assembly model is a formal mathematical model of self-assembly that allows the study of time and space complexities of self-assembling systems that lie at the heart of several molecular computer implementations and distributed computational software systems. These implementations and systems require efficient tile systems with small tilesets and fast execution times. The state of the art, however, requires vastly complex tile systems with large tilesets to implement fast algorithms. In this paper, I present S FS ; a tile system that decides 3-SAT by creating O H ð1:8393 n Þ nondeterministic assemblies in parallel, improving on the previous best known solution that requires Hð2 n Þ such assemblies. This solution directly improves the feasibility of building molecular 3-SAT solvers and efficiency of distributed software. I formally prove the correctness of the system, the number of required parallel assemblies, that the size of the system's tileset is 147 ¼ Hð1Þ; and that the assembly time is nondeterministic linear in the size of the input.

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Molecular Computation by DNA Hairpin Formation

Cited by 355 publications

References 20 publications

Biomolecular computing: Is it ready to take off?

Biomolecular computing: Is it ready to take off?

The general form of 0–1 programming problem based on DNA computing

Efficient 3-SAT algorithms in the tile assembly model

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