Content area

Abstract

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology.

Details

1009240
Title
Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars: e1000529
Publication title
Volume
5
Issue
10
Pages
e1000529
Publication year
2009
Publication date
Oct 2009
Section
Research Article
Publisher
Public Library of Science
Place of publication
San Francisco
Country of publication
United States
Publication subject
ISSN
1553734X
e-ISSN
15537358
Source type
Scholarly Journal
Language of publication
English
Document type
Journal Article
Accession number
19816554
ProQuest document ID
1312449130
Document URL
https://www.proquest.com/scholarly-journals/modeling-structure-function-relationships/docview/1312449130/se-2?accountid=208611
Copyright
© 2009 Cai et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLoS Comput Biol 5(10): e1000529. doi:10.1371/journal.pcbi.1000529
Last updated
2024-10-04
Database
ProQuest One Academic