Nucleic Acids Enzymes: The Fusion of Self-assembly and Conformational Computing

E. Ramlan, Klaus Peter Zauner

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Macromolecules are the predominant physical substrate supporting information processing in organisms. Two key characteristics—conformational dynamics and self-assembly properties—render macromolecules unique in this context. Both characteristics have been investigated for technical applications. In
nature’s information processors self-assembly and conformational switching commonly appear in combination and are typically realised with proteins. At the current state of biotechnology the best candidates for implementing artifical molecular information processing systems that utilise the combination self-assembly and conformational switching are functional nucleic acids. The increasingly realised prevalence of oligonucleotides in intracellular control points towards potential applications. The present paper reviews approaches to integrating the selfassembly and the conformational paradigm with allosterically controlled nucleic acid enzymes. It also introduces a new computational workflow to design functional nucleic acids for information processing.
LanguageEnglish
Title of host publicationUnconventional Computing 2007
EditorsAndrew Adamatzky, Larry Bull, Benjamin De Lacy Costello, Susan Stepney, Christof Teuscher
Place of PublicationFrome BA11 6TT United Kingdom
Pages68-94
Number of pages26
ISBN (Electronic)978-1905986057
Publication statusPublished - 1 Jun 2007

Fingerprint

Self assembly
Nucleic Acids
Fusion reactions
Macromolecules
Enzymes
Biotechnology
Oligonucleotides
Substrates
Proteins

Keywords

  • Molecular computing
  • RNA
  • DNA
  • Allosteric nucleic acids
  • Ribozymes

Cite this

Ramlan, E., & Zauner, K. P. (2007). Nucleic Acids Enzymes: The Fusion of Self-assembly and Conformational Computing. In A. Adamatzky, L. Bull, B. D. L. Costello, S. Stepney, & C. Teuscher (Eds.), Unconventional Computing 2007 (pp. 68-94). Frome BA11 6TT United Kingdom.
Ramlan, E. ; Zauner, Klaus Peter. / Nucleic Acids Enzymes: The Fusion of Self-assembly and Conformational Computing. Unconventional Computing 2007. editor / Andrew Adamatzky ; Larry Bull ; Benjamin De Lacy Costello ; Susan Stepney ; Christof Teuscher. Frome BA11 6TT United Kingdom, 2007. pp. 68-94
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Ramlan, E & Zauner, KP 2007, Nucleic Acids Enzymes: The Fusion of Self-assembly and Conformational Computing. in A Adamatzky, L Bull, BDL Costello, S Stepney & C Teuscher (eds), Unconventional Computing 2007. Frome BA11 6TT United Kingdom, pp. 68-94.

Nucleic Acids Enzymes: The Fusion of Self-assembly and Conformational Computing. / Ramlan, E.; Zauner, Klaus Peter.

Unconventional Computing 2007. ed. / Andrew Adamatzky; Larry Bull; Benjamin De Lacy Costello; Susan Stepney; Christof Teuscher. Frome BA11 6TT United Kingdom, 2007. p. 68-94.

Research output: Chapter in Book/Report/Conference proceedingChapter

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N2 - Macromolecules are the predominant physical substrate supporting information processing in organisms. Two key characteristics—conformational dynamics and self-assembly properties—render macromolecules unique in this context. Both characteristics have been investigated for technical applications. Innature’s information processors self-assembly and conformational switching commonly appear in combination and are typically realised with proteins. At the current state of biotechnology the best candidates for implementing artifical molecular information processing systems that utilise the combination self-assembly and conformational switching are functional nucleic acids. The increasingly realised prevalence of oligonucleotides in intracellular control points towards potential applications. The present paper reviews approaches to integrating the selfassembly and the conformational paradigm with allosterically controlled nucleic acid enzymes. It also introduces a new computational workflow to design functional nucleic acids for information processing.

AB - Macromolecules are the predominant physical substrate supporting information processing in organisms. Two key characteristics—conformational dynamics and self-assembly properties—render macromolecules unique in this context. Both characteristics have been investigated for technical applications. Innature’s information processors self-assembly and conformational switching commonly appear in combination and are typically realised with proteins. At the current state of biotechnology the best candidates for implementing artifical molecular information processing systems that utilise the combination self-assembly and conformational switching are functional nucleic acids. The increasingly realised prevalence of oligonucleotides in intracellular control points towards potential applications. The present paper reviews approaches to integrating the selfassembly and the conformational paradigm with allosterically controlled nucleic acid enzymes. It also introduces a new computational workflow to design functional nucleic acids for information processing.

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KW - RNA

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Ramlan E, Zauner KP. Nucleic Acids Enzymes: The Fusion of Self-assembly and Conformational Computing. In Adamatzky A, Bull L, Costello BDL, Stepney S, Teuscher C, editors, Unconventional Computing 2007. Frome BA11 6TT United Kingdom. 2007. p. 68-94