Autonomous DNA Computing Machine Based on Photochemical Gate Transition

Ogasawara, Shinji; Ami, Takehiro; Fujimoto, Kenzo

doi:10.1021/ja802583z

Cited by 27 publications

(19 citation statements)

References 17 publications

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“…DNA molecules have been extensively used as a highly versatile construction material to build nanomechanical devices such as DNA machines 1 2 3 4 , motors 5 6 7 8 , walkers 9 10 11 12 and robots 13 14 . Moreover, DNA is also useful for assembling molecular computing units including logic gates 15 16 17 18 , circuits 19 20 21 , calculators 20 22 23 , and automatons 24 25 . Recently, these two fields of application were linked by designing a DNA origami-based nanorobot guided by an aptamer-encoded logic gate 14 , highlighting an emerging interest to integrate DNA-made mechanical nanodevices with molecular computing.…”

mentioning

confidence: 99%

Interlocked DNA nanostructures controlled by a reversible logic circuit

Lohmann

Famulok

2014

Nat Commun

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DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.

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confidence: 99%

Interlocked DNA nanostructures controlled by a reversible logic circuit

Lohmann

Famulok

2014

Nat Commun

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“…The binary digit additions are carried out by onetime irradiation at 366 nm in the single test tube. The fluorescence readout by the DNA chip was in good agreement with the correct answer of binary digit additions (Ogasawara et al, 2008).…”

Section: Autonomous Dna Computationmentioning

confidence: 53%

“…But they're largely uncontrolled by humans. We cannot, for example, program a tree to calculate the digits of pi (Melkikh, 2008;Ogasawara et al, 2008;Watson et al, 1987). The idea of using DNA to store and process information took off in 1994 when a California scientist fi rstly used DNA in a test tube to solve a simple mathematical problem (Stryer, 1995).…”

Section: Introductionmentioning

confidence: 99%

DNA Computation: Applications and Perspectives

Tagore¹,

Bhattacharya²,

Islam³

et al. 2010

J Proteomics Bioinform

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The computational capability of living systems has intrigued researchers for years. Primarily, the focus has been on implementing aspects of living systems in computational devices. Computer literal peoples expand their hand to the molecular biologist and chemist to explore the potential for computation of biological molecules line Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) which are information carrying molecules. In this context, DNA computation is basically a collection of specially selected DNA strands whose combinations will result in the solution to some problems. DNA computation rather DNA-based computing is at the intersection of several threads of research. Main advantages of DNA computation are miniaturization and parallelism over conventional silicon-based machines. The informationbearing capability of DNA molecules is a cornerstone of modern theories of genetics and molecular biology. In this paper we have tried to focus on some key issues regarding the used and implementation DNA-based devices in life science fi eld. We have also tried to suggest its advantage over silicon computers.

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“…There are several valuable approaches to full-adders based on oligonucleotides, [126][127][128][129][130][131] silver clusters, [132] and bifluorophoric molecules. [133][134] Another approach, albeit a simulation, uses a photochemical technique.…”

Section: Other Logic Arraysmentioning

confidence: 99%

Molecular Logic Gate Arrays

Silva¹

2011

Chemistry An Asian Journal

165

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Chemists are now able to emulate the ideas and instruments of mathematics and computer science with molecules. The integration of molecular logic gates into small arrays has been a growth area during the last few years. The design principles underlying a collection of these cases are examined. Some of these computing molecules are applicable in medical- and biotechnologies. Cases of blood diagnostics, 'lab-on-a-molecule' systems, and molecular computational identification of small objects are included.

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Autonomous DNA Computing Machine Based on Photochemical Gate Transition

Cited by 27 publications

References 17 publications

Interlocked DNA nanostructures controlled by a reversible logic circuit

Interlocked DNA nanostructures controlled by a reversible logic circuit

DNA Computation: Applications and Perspectives

Molecular Logic Gate Arrays

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