Field programmable chemistry: Integrated chemical and electronic processing of informational molecules towards electronic chemical cells

Wagler, Patrick F.; Tangen, Uwe; Maeke, Thomas; McCaskill, John S.

doi:10.1016/j.biosystems.2012.01.005

Cited by 13 publications

(28 citation statements)

References 42 publications

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“…As already mentioned in Section 1 (see references given there), candidates for chemtainers investigated in MATCHIT are vesicles and oil droplets (in water) for which a range of functionalities relevant to the implementation of an MA have been demonstrated. Together with novel types of MEMS devices also resulting from MATCHIT [15], a physical implementation of an MA may be within reach in the near future.…”

Section: Discussionmentioning

confidence: 99%

“…In the context of the chemtainers, we reported the first DNA-computation operations on the surface of artificial giant unilamellar vesicles (GUVs), DNA-mediated self-assembly [9, 10] and controlled fusion [11–13] of GUVs and oil-in-water droplets, and increase in the complexity of available soft colloid chemtainers by preparing hierarchically organized GUVs [14]. The research efforts of integrating chemical and electronic systems in a MEMS device resulted in unconventional embedded computation systems that performed complex nanoscale chemical tasks autonomously [15]. Traditional computer science was not only used for programing the MEMS devices.…”

Section: Introductionmentioning

confidence: 99%

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The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

Weyland

Fellermann

Hadorn

et al. 2013

Computational and Mathematical Methods in Medicine

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We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

Weyland

Fellermann

Hadorn

et al. 2013

Computational and Mathematical Methods in Medicine

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“…We introduce eight such operations, responsible for feeding and moving of chemtainers and tags, controlled fusion of chemtainers, encapsulation of material into chemtainers, chemtainer bursting and flushing of content. Our exact transitions are motivated by the functionalities of the underlying microfluidics architecture [20], but they also serve as a guideline as to how alternative transitions in other hardwares can be codified. The impact of the exact instruction set on the constructive capabilities of the resulting calculus will be discussed in §3.…”

Section: Induced Transitionsmentioning

confidence: 99%

“…Whereas natural cells ultimately employ genomic information to regulate the resulting material production network, we envision programmable electronic control by embedding chemtainers into mechanoelectronic microsystems [19,20]. In such devices, dedicated microfluidic channels can be designed for vesicle generation [21], DNA tag insertion, tag and chemtainer trafficking [22], specific or unspecific fusion [23], vesicle rapture and encapsulation [24].…”

Section: Introductionmentioning

confidence: 99%

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Programming chemistry in DNA-addressable bioreactors

Fellermann

Cardelli

2014

J. R. Soc. Interface.

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We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by stateof-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis.

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DNA mit 3′‐5′‐Disulfid‐Verknüpfung – schnelle chemische Ligation durch isosteren Ersatz

2014

Self Cite

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Die Bemühungen, die chemische Ligation von Oligonukleotiden ohne biochemische Enzyme zu etablieren, haben zu einer Vielzahl an synthetischen Analoga geführt und damit die Oligomer-Ligation um neue Oligonukleotide, Peptide und Hybride, wie PNA, bereichert. [1] Wichtigste Anforderungen an potenzielle PCR-freie Diagnosewerkzeuge sind eine schnelle templatierte chemische DNA-Ligation mit hoher Paarungsselektivität, sowie eine empfindliche Detektionsmethode. Hier berichten wir über eine Oligonukleotid-Festphasensynthese von 5'-oder 3'-Mercapto-didesoxynukleotiden. Die chemische Ligation liefert 3'-5'-Disulfid-Bindungen anstelle der 3'-5'-Phosphordiester-Bindung. Unter Verwendung einer Fluoreszenzmethode beschreiben wir eine der schnellsten Ligationsreaktionen mit Halbwertszeiten in der Grçßenordnung von Sekunden. Durch die Wahl der DNA-Modifikation und der 3'-5'-Orientierung der Aktivierung wird die nicht templatierte Ligation effektiv unterdrückt. Der Temperatureinfluss auf die templatierte Ligation wir aufgezeigt.

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Field programmable chemistry: Integrated chemical and electronic processing of informational molecules towards electronic chemical cells

Cited by 13 publications

References 42 publications

The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

Programming chemistry in DNA-addressable bioreactors

DNA mit 3′‐5′‐Disulfid‐Verknüpfung – schnelle chemische Ligation durch isosteren Ersatz

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