The efficiency of sequence-specific
                    separation of DNA mixtures for biological
                    computing

Khodor, Julia; Gifford, David K.

doi:10.1090/dimacs/048/03

Cited by 8 publications

(5 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Despite optimism about future techniques, current techniques available for DNA-based combinatorial search are too slow and/or inaccurate to solve a problem of even moderate size. [10] …”

Section: Dna-based Methods For Combinatorial Searchmentioning

confidence: 99%

Design and implementation of computational systems based on programmed mutagenesis

Khodor

Gifford

1999

Biosystems

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…Despite optimism about future techniques, current techniques available for DNA-based combinatorial search are too slow and/or inaccurate to solve a problem of even moderate size. [10] …”

Section: Dna-based Methods For Combinatorial Searchmentioning

confidence: 99%

Design and implementation of computational systems based on programmed mutagenesis

Khodor

Gifford

1999

Biosystems

Self Cite

View full text Add to dashboard Cite

show abstract

“…Besides, all of the sequencing methods require DNA extraction and purification. Khodor and Gifford [13] had pointed out that the upper bound on the efficiency of separation of DNA mixtures using magnetic beads is less than 1% without homologous probes and targets. Thus currently it is almost impossible to precisely sequence such a small amount of unknown mixed, sequence-specific DNA.…”

Section: Preliminariesmentioning

confidence: 99%

DNA-chip-based dynamic broadcast encryption scheme with constant-size ciphertexts and decryption keys

Fang

Lai

2014

Sci. China Inf. Sci.

View full text Add to dashboard Cite

In this paper we present DNA-DBE, a DNA-chip-based dynamic broadcast encryption scheme. In our scheme, new users can join dynamically without modification of other users' decryption keys. Either the ciphertext or the decryption key is of constant-size. Backward secrecy is achieved in DNA-DBE: if new users join the system dynamically, they will not be able to retrieve past data. The security of our scheme relies on hard biological problems, which are immune to attacks of new computing technologies in the future. There exists a special feature in DNA-based cryptosystems, i.e. the set of encryption keys and the set of decryption keys have a many-to-many relationship. The implementation of more complicated DNA cryptosystems taking advantage of this special feature has been previously left as an open problem. Our DNA-DBE system is a solution to this open problem, which is also the first exploration of DNA based group-oriented encryption system.

show abstract

“…Previously, we have also used competitive hybridization reactions to implement a molecular pattern classifier (Lim et al, 2010). However, it required affinity bead separation to remove unbound probes before the final output detection, which was the main source of error and brought about a significant increase of overall computation time (Khodor and Gifford, 1997). Using molecular beacons helps us to overcome these drawbacks.…”

Section: Weighted Detection and Analysis Of Target Nucleic Acidsmentioning

confidence: 99%

Biomolecular computation with molecular beacons for quantitative analysis of target nucleic acids

Lim¹,

Lee²,

Yang³

et al. 2013

Biosystems

View full text Add to dashboard Cite

Molecular beacons are efficient and useful tools for quantitative detection of specific target nucleic acids. Thanks to their simple protocol, molecular beacons have great potential as substrates for biomolecular computing. Here we present a molecular beacon-based biomolecular computing method for quantitative detection and analysis of target nucleic acids. Whereas the conventional quantitative assays using fluorescent dyes have been designed for single target detection or multiplexed detection, the proposed method enables us not only to detect multiple targets but also to compute their quantitative information by weighted-sum of the targets. The detection and computation are performed on a molecular level simultaneously, and the outputs are detected as fluorescence signals. Experimental results show the feasibility and effectiveness of our weighted detection and linear combination method using molecular beacons. Our method can serve as a primitive operation of molecular pattern analysis, and we demonstrate successful binary classifications of molecular patterns made of synthetic oligonucleotide DNA molecules.

show abstract

The efficiency of sequence-specific separation of DNA mixtures for biological computing

Cited by 8 publications

References 0 publications

Design and implementation of computational systems based on programmed mutagenesis

Design and implementation of computational systems based on programmed mutagenesis

DNA-chip-based dynamic broadcast encryption scheme with constant-size ciphertexts and decryption keys

Biomolecular computation with molecular beacons for quantitative analysis of target nucleic acids

Contact Info

Product

Resources

About