Design and implementation of computational systems based on programmed mutagenesis

Khodor, Julia; Gifford, David K.

doi:10.1016/s0303-2647(99)00036-2

Cited by 21 publications

(9 citation statements)

References 17 publications

(26 reference statements)

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“…The above approach differs in the type of programming from previous experimental approaches to DNA computing in vitro (Adleman, 1994;Guarnieri et al, 1996;Sakamoto et al, 1999;Ouyang et al, 1997;Liu et al, 2000;Faulhammer et al, 2000) and in vivo (Khodor and Gifford, 1999). Instead of programming by a manual series of biochemical pipetting operations, the entire fluid flow is held constant and a single light pattern determines the program.…”

Section: Discussionmentioning

confidence: 99%

Optically programming DNA computing in microflow reactors

McCaskill¹

2001

Biosystems

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The programmability and the integration of biochemical processing protocols are addressed for DNA computing using photochemical and microsystem techniques. A magnetically switchable selective transfer module (STM) is presented which implements the basic sequence-specific DNA filtering operation under constant flow. Secondly, a single steady flow system of STMs is presented which solves an arbitrary instance of the maximal clique problem of given maximum size N. Values of N up to about 100 should be achievable with current lithographic techniques. The specific problem is encoded in an initial labeling pattern of each module with one of 2N DNA oligonucleotides, identical for all instances of maximal clique. Thirdly, a method for optically programming the DNA labeling process via photochemical lithography is proposed, allowing different problem instances to be specified. No hydrodynamic switching of flows is required during operation -the STMs are synchronously clocked by an external magnet. An experimental implementation of this architecture is under construction and will be reported elsewhere.

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Section: Discussionmentioning

confidence: 99%

Optically programming DNA computing in microflow reactors

McCaskill¹

2001

Biosystems

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“…In general the nature of errors may differ between chemical and enzymatic DNA synthesis, so biased-error chemical synthesis would most likely provide EC strands which most closely match the error profiles for probe DNA synthesized on a chip. Other mutagenisis Methods used for more general computations are given in [KG98]. DNA Self Assembly.…”

Section: (C) Other Methods For Generating Diverse Prefixes For Ec Strmentioning

confidence: 99%

DNA Computing

2001

Lecture Notes in Computer Science

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DNA Computing is a novel and fascinating development at the interface of computer science and molecular biology. It has emerged in recent years, not simply as an exciting technology for information processing, but also as a catalyst for knowledge transfer between information processing, nanotechnology, and biology. This area of research has the potential to change our understanding of the theory and practice of computing.The call for papers and poster presentations sought contributions of original research and technical expositions in all areas of bio-computation. A total of 33 abstracts were submitted of which 16 were accepted for presentation and included in the proceedings. The papers were selected by the program committee based on originality and quality of research and on relevance to the bio-computing field. Invited talks were given by Masami Hagiya (Tokyo University), Laura Landweber (Princeton University), John Reif (Duke University), Thomas Schmidt (Leiden University), and Lloyd M. Smith (University of Wisconsin). Invited papers based on the talks by Hagiya and Reif are included in this volume, along with the contributed papers. Additional tutorials were held on the first and last days of the conference.

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“…Several error detection and fault tolerance methods have been established to increase the accuracy of computation [14][15][16][17][18]. Among them, Deaton et al [19] studied the errors associated with imperfect hybridization (i.e., false positive and false negative ligations).…”

Section: Biocomputing For Np-complete Problemsmentioning

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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Design and implementation of computational systems based on programmed mutagenesis

Cited by 21 publications

References 17 publications

Optically programming DNA computing in microflow reactors

Optically programming DNA computing in microflow reactors

DNA Computing

Biomolecular computing: Is it ready to take off?

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