Automated constraint-based nucleotide sequence selection for DNA computation

Hartemink, Alexander J.; Gifford, David K.; Khodor, Julia

doi:10.1016/s0303-2647(99)00050-7

Cited by 71 publications

(35 citation statements)

References 3 publications

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“…As described below, all of the enzymes used in the system are thermostable which allows the system to be thermal cycled. The DNA sequences for the system we are testing have been selected using the SCAN program [9] to search a large sequence space constrained by chosen mismatch geometry. SCAN chooses sequences that have optimum annealing properties, do not have harmful secondary structure, and do not form primer dimers.…”

Section: T1mentioning

confidence: 99%

“…As described in Chapter 1, we used SCAN [9] to choose particular sequences for the Unary Counter. We chose fairly strict thermodynamic constraints in order to prevent inappropriate binding of the rule oligonucleotides, as well as any undesirable interaction between primers.…”

Section: Sources Of Rewrite Rule Specificitymentioning

confidence: 99%

“…We used these primers to test the putative extension and ligation efficiencies of the proposed designs. We then used SCAN [9] to search for optimal oligonucleotides with the given mismatch geometry and a common set of thermodynamic constraints. It is interesting to note that the first design we proposed is the one we implemented in the laboratory.…”

Section: Sources Of Rewrite Rule Specificitymentioning

confidence: 99%

“…The author would like to thank Alexander J. Hartemink for utilizing SCAN [9] to search for the oligonucleotide primer sequences.…”

Section: Acknowledgmentsmentioning

confidence: 99%

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Design and implementation of computational systems based on programmed mutagenesis

Khodor

Gifford

1999

Biosystems

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We introduce programmed mutagenesis, a technique for rewriting DNA strands according to programmed rules. We present the Unary Counter-a simple computational system based on programmed mutagenesis.We present the experimental results of the first two cycles of the unary counter which show that string rewriting by programmed mutagenesis is possible. We discuss the two enzyme system which allows to implement programmed mutagenesis by thermocycling a single reaction in a single test tube.We discuss the sources of rewrite rule specificity within the framework of programmed mutagenesis and present experimental results which indicate that it is possible to guarantee the specificity of the rewrite rules, and thus the correctness of the computation.We demonstrate that two oligonucleotides annealing to the template next to each other can ligate and extend to form the correct product. We argue that the ability to have oligonucleotides in close proximity function properly, together with the MIMD nature of the programmed mutagenesis systems provides evidence that parallel and nondeterministic computations are possible with programmed mutagenesis.Finally, we discuss the significance of our results and outline directions for future work.

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Section: T1mentioning

confidence: 99%

Section: Sources Of Rewrite Rule Specificitymentioning

confidence: 99%

Section: Sources Of Rewrite Rule Specificitymentioning

confidence: 99%

“…The author would like to thank Alexander J. Hartemink for utilizing SCAN [9] to search for the oligonucleotide primer sequences.…”

Section: Acknowledgmentsmentioning

confidence: 99%

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Design and implementation of computational systems based on programmed mutagenesis

Khodor

Gifford

1999

Biosystems

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“…Wood [Woo98] considers the use of error correcting codes for word design and to decrease errors in BMC. Hartemink et al [HGL98] describes an automated constraint-based procedure for nucleotide sequence selection for BMC.…”

Section: Correcting Errors In Bmcmentioning

confidence: 99%

Alternative Computational Models: A Comparison of Biomolecular and Quantum Computation

Reif

1998

Lecture Notes in Computer Science

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Molecular Computation (MC) is massively parallel computation where data is stored and processed within objects of molecular size. Biomolecular Computation (BMC) is MC using biotechnology techniques, e.g. recombinant DNA operations. In contrast, Quantum Computation (QC) is a type of computation where unitary and measurement operations are executed on linear superpositions of basis states. Both BMC and QC may be executed at the micromolecular scale by a variety of methodologies and technologies. This paper surveys various methods for doing BMC and QC and discusses the considerable theoretical and practical advances in BMC and QC made in the last few years. We compare bounds on key resource such as time, volume (number of molecules times molecular density), energy and error rates achievable, taking particular note of the scalability of these methods with the size of the problem solved. In addition to NP search problems and database search problems, we enumerate a wide variety of further potential practical applications of BMC and QC.We observe that certain problems (e.g., NP search problems), if solved with polynomial time bounds, requires exponentially large volume for BMC, so BMC does not scale well to solve very large NP search problems. However, we describe a number of applications (e.g., search within large data bases and simulation of parallel machines) where the volume grows polynomial.Also, we note that the observation operation of QC, which is a fundamental operation of QC used for obtaining classical output, may potentially suffer from exponentially large volume requirements. Observation operations in quantum physics are generally done by a macroscopic measurement apparatus, and the original formulations of QC implicity assumed that macroscopic measurement apparatus would be used for QC. However, if the measurement apparatus is very small, it will be subject to quantum effects. At this time, no one has demonstrated or proved that the observation operation (for a quantum system with n entangled qubits) can even be approximated within a larger unitary quantum system in volume growing less than exponentially with n. Hence it is unknown whether QC (with the observation operation) scales to even moderate numbers of qubits within small volume. We pose a major open problem in QC: to determine (i.e., provide a formal proof) whether or not observation, in a closed quantum system, can be approximated in small volume: say, growing as a polynomial in the number of qubits.We also discuss techniques for decreasing errors in BMC (e.g., annealing errors) and QC (e.g., decoherence errors), and volume where possible, to insure the scalability of BMC and QC to problems of large input size. In addition, we consider how BMC might be used to assist QC (e.g., to do observation operations for Bulk QC) and also how quantum techniques might be used to assist BMC (e.g., to do exquisite detection of very small quantities of a molecule in solution within a large volume).

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Advancement of Computer‐Aided Design Software and Simulation Tools for Nucleic Acid Nanostructures and DNA Origami

Kawamata¹

2022

DNA Origami

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Automated constraint-based nucleotide sequence selection for DNA computation

Cited by 71 publications

References 3 publications

Design and implementation of computational systems based on programmed mutagenesis

Design and implementation of computational systems based on programmed mutagenesis

Alternative Computational Models: A Comparison of Biomolecular and Quantum Computation

Advancement of Computer‐Aided Design Software and Simulation Tools for Nucleic Acid Nanostructures and DNA Origami

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