The ribosome binding site calculator

Research output: Chapter in Book/Report/Conference proceedingChapter

188 Citations (Scopus)

Abstract

The Ribosome Binding Site (RBS) Calculator is a design method for predicting and controlling translation initiation and protein expression in bacteria. The method can predict the rate of translation initiation for every start codon in an mRNA transcript. The method may also optimize a synthetic RBS sequence to achieve a targeted translation initiation rate. Using the RBS Calculator, a protein coding sequence's translation rate may be rationally controlled across a 100,000+ fold range. We begin by providing an overview of the potential biotechnology applications of the RBS Calculator, including the optimization of synthetic metabolic pathways and genetic circuits. We then detail the definitions, methodologies, and algorithms behind the RBS Calculator's thermodynamic model and optimization method. Finally, we outline a protocol for precisely measuring steady-state fluorescent protein expression levels. These methods and protocols provide a clear explanation of the RBS Calculator and its uses.

Original languageEnglish (US)
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Pages19-42
Number of pages24
DOIs
StatePublished - Jan 1 2011

Publication series

NameMethods in Enzymology
Volume498
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Fingerprint

Ribosomes
Binding Sites
Translational Peptide Chain Initiation
Proteins
Initiator Codon
Biotechnology
Metabolic Networks and Pathways
Thermodynamics
Bacteria
Messenger RNA
Networks (circuits)

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

Salis, H. M. (2011). The ribosome binding site calculator. In Methods in Enzymology (pp. 19-42). (Methods in Enzymology; Vol. 498). Academic Press Inc.. https://doi.org/10.1016/B978-0-12-385120-8.00002-4
Salis, Howard M. / The ribosome binding site calculator. Methods in Enzymology. Academic Press Inc., 2011. pp. 19-42 (Methods in Enzymology).
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Salis, HM 2011, The ribosome binding site calculator. in Methods in Enzymology. Methods in Enzymology, vol. 498, Academic Press Inc., pp. 19-42. https://doi.org/10.1016/B978-0-12-385120-8.00002-4

The ribosome binding site calculator. / Salis, Howard M.

Methods in Enzymology. Academic Press Inc., 2011. p. 19-42 (Methods in Enzymology; Vol. 498).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Salis HM. The ribosome binding site calculator. In Methods in Enzymology. Academic Press Inc. 2011. p. 19-42. (Methods in Enzymology). https://doi.org/10.1016/B978-0-12-385120-8.00002-4