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An Extended Dot-Bracket-Notation for Functional Nucleic Acids

An Extended Dot-Bracket-Notation for Functional Nucleic Acids
An Extended Dot-Bracket-Notation for Functional Nucleic Acids
Functional nucleic acids are an attractive substrate for molecular computing. A nucleic acid molecule is a linear chain of covalently bound building blocks assembled in arbitrary order from a set of typically four nucleotides. Certain pairs of nucleotides weakly attract each other through short-range electrostatic interaction and, accordingly, complementary sequences of nucleotides can bind to each other. The complementary stretches of nucleic acids that attract each other can be part of two different molecules or two parts of a single molecule. Binding within a single molecule leads to a folding of the linear chain. This so called secondary structure is of great importance for the function of nucleic acids. The present paper is concerned with the representation of this secondary structure. We propose an extension for the syntax of the standard dot-bracket notation to increase its convenience and expressive power for both its use to communicate nucleic acid secondary structures among humans and machines. The extensions reflect our own requirements for the representation of nucleic acids for molecular computation, but should be useful for functional nucleic acids in general.
978-3-85403-244-1
75-86
Oesterreichische Computer Gesellschaft
Ramlan, Effirul I.
74dbdb29-5071-4b5c-87a1-b511e7b17383
Zauner, Klaus-Peter
c8b22dbd-10e6-43d8-813b-0766f985cc97
Csuhaj-Varj{\'u}, E.
Freund, R.
Oswald, M.
Salomaa, K.
Ramlan, Effirul I.
74dbdb29-5071-4b5c-87a1-b511e7b17383
Zauner, Klaus-Peter
c8b22dbd-10e6-43d8-813b-0766f985cc97
Csuhaj-Varj{\'u}, E.
Freund, R.
Oswald, M.
Salomaa, K.

Ramlan, Effirul I. and Zauner, Klaus-Peter (2008) An Extended Dot-Bracket-Notation for Functional Nucleic Acids. In, Csuhaj-Varj{\'u}, E., Freund, R., Oswald, M. and Salomaa, K. (eds.) International Workshop on Computing with Biomolecules, Wien, Austria, August 27, 2008. Oesterreichische Computer Gesellschaft, pp. 75-86.

Record type: Book Section

Abstract

Functional nucleic acids are an attractive substrate for molecular computing. A nucleic acid molecule is a linear chain of covalently bound building blocks assembled in arbitrary order from a set of typically four nucleotides. Certain pairs of nucleotides weakly attract each other through short-range electrostatic interaction and, accordingly, complementary sequences of nucleotides can bind to each other. The complementary stretches of nucleic acids that attract each other can be part of two different molecules or two parts of a single molecule. Binding within a single molecule leads to a folding of the linear chain. This so called secondary structure is of great importance for the function of nucleic acids. The present paper is concerned with the representation of this secondary structure. We propose an extension for the syntax of the standard dot-bracket notation to increase its convenience and expressive power for both its use to communicate nucleic acid secondary structures among humans and machines. The extensions reflect our own requirements for the representation of nucleic acids for molecular computation, but should be useful for functional nucleic acids in general.

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Published date: 2008
Organisations: Agents, Interactions & Complexity

Identifiers

Local EPrints ID: 267292
URI: http://eprints.soton.ac.uk/id/eprint/267292
ISBN: 978-3-85403-244-1
PURE UUID: 1d72a7dc-cfa8-49b2-b3d9-07c8f6d84ae5

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Date deposited: 23 Apr 2009 17:29
Last modified: 26 Jun 2020 16:45

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Contributors

Author: Effirul I. Ramlan
Author: Klaus-Peter Zauner
Editor: E. Csuhaj-Varj{\'u}
Editor: R. Freund
Editor: M. Oswald
Editor: K. Salomaa

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