RNA Computing in a Living Cell

Shapiro, Ehud; Gil, Binyamin

doi:10.1126/science.1165665

Cited by 28 publications

(16 citation statements)

References 14 publications

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“…This would require appropriate sensors to detect cell state, for example the pH-sensitive DNA nanomachine recently reported by Modi et al [36]. This may result in new methods for smart diagnosis and treatment using DNA signal translators [37][38][39].…”

Section: Discussion and Related Workmentioning

confidence: 99%

DNA Reservoir Computing: A Novel Molecular Computing Approach

Goudarzi

Lakin

Stefanović

2013

Lecture Notes in Computer Science

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Abstract. We propose a novel molecular computing approach based on reservoir computing. In reservoir computing, a dynamical core, called a reservoir, is perturbed with an external input signal while a readout layer maps the reservoir dynamics to a target output. Computation takes place as a transformation from the input space to a high-dimensional spatiotemporal feature space created by the transient dynamics of the reservoir. The readout layer then combines these features to produce the target output. We show that coupled deoxyribozyme oscillators can act as the reservoir. We show that despite using only three coupled oscillators, a molecular reservoir computer could achieve 90% accuracy on a benchmark temporal problem.

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Section: Discussion and Related Workmentioning

confidence: 99%

DNA Reservoir Computing: A Novel Molecular Computing Approach

Goudarzi

Lakin

Stefanović

2013

Lecture Notes in Computer Science

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“…From the engineered DNA and RNA logic gates [14,15] to the development of synthetic RNA devices [5-7,35], the type of molecules that are of interest for information processing tasks have a number of meta-stable conformations representing their change of folding with regard to the changes in their environments. For instance, an allosterically controlled hammerhead ribozyme imitating the AND logic operator [15] has four different meta-stable conformations.…”

Section: Methodsmentioning

confidence: 99%

In-silico design of computational nucleic acids for molecular information processing

Ramlan

Zauner

2013

J Cheminform

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Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing.

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“…Owing to the high specific affinity of an aptamer to its target, it is thought to resemble chemical antibodies, with the dissociation constants ranging from the nanomolar to picomolar level (Iliuk, Hu, and Tao 2011). Since then, people have begun to study how to utilize the advantages of aptamers, and the applications of aptamers remains dynamic in such fields as disease diagnosis (Nimjee, Rusconi, and Sullenger 2005;Gubala et al 2012;Liu et al 2009), drug screening (Missailidis and Hardy 2009), bioseparation and bioanalysis applications (de-los-Santos-Á lvarez et al 2008;Mairal et al 2008;Smith et al 2007), and even RNA computing (Shapiro and Gil 2008). Furthermore, the binding system of aptamer-target will be destructed when some negative conditions were introduced, such as high-temperature or denaturing agents.…”

Section: Introductionmentioning

confidence: 99%

Rapid and Efficient Proteolysis for Protein Analysis by an Aptamer-Based Immobilized Chymotrypsin Microreactor

Xiao

Man

et al. 2013

Analytical Letters

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Efficient protein digestion is a key step for successful mass spectrometry identification. However, traditional in-solution digestion suffers some drawbacks, such as autolysis of protease, long analysis times and lack of control. Recently, specific single-stranded nucleic acids, aptamers, screened from random sequence pools, have been performed high affinity for targets. In this paper, we have developed a novel enzyme reactor, which immobilized chymotrypsin based on aptamer-grafted silica beads. Mixed proteins, which consist of bovine serum albumin, myoglobin, and cytochrome c, were used as samples, to evaluate the digestion performance of the enzymatic reactor. With the use of this novel tool, proteins were digested in 40 min to an extent similar to that achieved with soluble enzyme at 37 C after 16 h. Moreover, enzymatic reactor regeneration was carried out through chymotrypsin elution and re-immobilization. The advanced characteristics of the aptamer-based chymotrypsin reactor demonstrated that aptamers could serve as novel materials for rapid and efficient enzyme immobilization and application in protein studies.

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RNA Computing in a Living Cell

Cited by 28 publications

References 14 publications

DNA Reservoir Computing: A Novel Molecular Computing Approach

DNA Reservoir Computing: A Novel Molecular Computing Approach

In-silico design of computational nucleic acids for molecular information processing

Rapid and Efficient Proteolysis for Protein Analysis by an Aptamer-Based Immobilized Chymotrypsin Microreactor

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