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

E. Ramlan, Klaus Peter Zauner

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

LanguageEnglish
Article number22
JournalJournal of Cheminformatics
Volume5
Issue number5
DOIs
Publication statusPublished - 7 May 2013

Fingerprint

Nucleic acids
nucleic acids
information processing
Nucleic Acids
Macromolecules
macromolecules
candidacy
information technology
paradigm
ribonucleic acids
present
ability
Silicon
Biological systems
RNA
organisms
Self assembly
Information technology
self assembly
Thermodynamic properties

Keywords

  • Functional nucleic acids
  • Molecular logic gates
  • Nucleic acids computer
  • Ribozymes

Cite this

@article{a86aba2b21214ae09aa531f05e9fa37c,
title = "In-silico design of computational nucleic acids for molecular information processing",
abstract = "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.",
keywords = "Functional nucleic acids, Molecular logic gates, Nucleic acids computer, Ribozymes",
author = "E. Ramlan and Zauner, {Klaus Peter}",
year = "2013",
month = "5",
day = "7",
doi = "10.1186/1758-2946-5-22",
language = "English",
volume = "5",
journal = "Journal of Cheminformatics",
issn = "1758-2946",
publisher = "Chemistry Central",
number = "5",

}

In-silico design of computational nucleic acids for molecular information processing. / Ramlan, E.; Zauner, Klaus Peter.

In: Journal of Cheminformatics, Vol. 5, No. 5, 22, 07.05.2013.

Research output: Contribution to journalArticle

TY - JOUR

T1 - In-silico design of computational nucleic acids for molecular information processing

AU - Ramlan, E.

AU - Zauner, Klaus Peter

PY - 2013/5/7

Y1 - 2013/5/7

N2 - 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.

AB - 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.

KW - Functional nucleic acids

KW - Molecular logic gates

KW - Nucleic acids computer

KW - Ribozymes

UR - http://www.scopus.com/inward/record.url?scp=84879933953&partnerID=8YFLogxK

U2 - 10.1186/1758-2946-5-22

DO - 10.1186/1758-2946-5-22

M3 - Article

VL - 5

JO - Journal of Cheminformatics

T2 - Journal of Cheminformatics

JF - Journal of Cheminformatics

SN - 1758-2946

IS - 5

M1 - 22

ER -