Measuring the activity of BioBrick promoters using an in vivo reference standard

Kelly, Jason R.; Rubin, Adam J.; Davis, Joseph H.; Ajo-Franklin, Caroline M.; Cumbers, John; Czar, Michael J.; de Mora, Kim; Glieberman, Aaron L.; Monie, Dileep D.; Endy, Drew

Measuring the activity of BioBrick promoters using an in vivo reference standard

dc.contributor.author	Kelly, Jason R.	en
dc.contributor.author	Rubin, Adam J.	en
dc.contributor.author	Davis, Joseph H.	en
dc.contributor.author	Ajo-Franklin, Caroline M.	en
dc.contributor.author	Cumbers, John	en
dc.contributor.author	Czar, Michael J.	en
dc.contributor.author	de Mora, Kim	en
dc.contributor.author	Glieberman, Aaron L.	en
dc.contributor.author	Monie, Dileep D.	en
dc.contributor.author	Endy, Drew	en
dc.date.accessioned	2012-08-24T11:40:51Z	en
dc.date.available	2012-08-24T11:40:51Z	en
dc.date.issued	2009-03-20	en
dc.date.updated	2012-08-24T11:40:51Z	en
dc.description.abstract	Background The engineering of many-component, synthetic biological systems is being made easier by the development of collections of reusable, standard biological parts. However, the complexity of biology makes it difficult to predict the extent to which such efforts will succeed. As a first practical example, the Registry of Standard Biological Parts started at MIT now maintains and distributes thousands of BioBrick™ standard biological parts. However, BioBrick parts are only standardized in terms of how individual parts are physically assembled into multi-component systems, and most parts remain uncharacterized. Standardized tools, techniques, and units of measurement are needed to facilitate the characterization and reuse of parts by independent researchers across many laboratories. Results We found that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments. We choose one promoter (BBa_J23101) to serve as an in vivo reference standard for promoter activity. We demonstrated that, by measuring the activity of promoters relative to BBa_J23101, we could reduce variation in reported promoter activity due to differences in test conditions and measurement instruments by ~50%. We defined a Relative Promoter Unit (RPU) in order to report promoter characterization data in compatible units and developed a measurement kit so that researchers might more easily adopt RPU as a standard unit for reporting promoter activity. We distributed a set of test promoters to multiple labs and found good agreement in the reported relative activities of promoters so measured. We also characterized the relative activities of a reference collection of BioBrick promoters in order to further support adoption of RPU-based measurement standards. Conclusion Relative activity measurements based on an in vivoreference standard enables improved measurement of promoter activity given variation in measurement conditions and instruments. These improvements are sufficient to begin to support the measurement of promoter activities across many laboratories. Additional in vivo reference standards for other types of biological functions would seem likely to have similar utility, and could thus improve research on the design, production, and reuse of standard biological parts.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	Journal of Biological Engineering. 2009 Mar 20;3(1):4	en
dc.identifier.doi	https://doi.org/10.1186/1754-1611-3-4	en
dc.identifier.uri	http://hdl.handle.net/10919/18869	en
dc.language.iso	en	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Jason R Kelly et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	Measuring the activity of BioBrick promoters using an in vivo reference standard	en
dc.title.serial	Journal of Biological Engineering	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en