Sunday, February 06, 2011

Synbio update: reference standards, protein fusions, and bioscaffolds

One of the core tools developed and used by synthetic biologists is the Registry of Standard Biological Parts which has over 5,000 available parts (paper). A contemporary research focus is on improving methods for working with the standardized parts. Three recent innovations are described below.

1. In vivo reference standards
One advance is in establishing in vivo reference standards for the different biological parts. For example, the absolute activity of different promoters (gene transcription regulators) varies across experimental conditions and measurement instruments. Variation in promoter activity was reduced 50% by using a selected promoter as an in vivo reference standard against which other promoters were measured (paper).

2. Construction of protein fusions
Another advance is in allowing the construction of protein fusions. This is not feasible in the current assembly standard due to an unfavorable scar sequence that encodes an in-frame stop codon. Restriction enzymes BglII and BamHI are employed in a new assembly standard that replaces the scar sequence with a generally innocuous glycine-serine peptide linker (paper).

3. Rapid circuit generation with BioScaffolds
A third advance is in the creation of a new part, a BioScaffold, that can be used in the rapid generation of synthetic biological circuits. The BioScaffold can be inserted into cloning vectors and excised from them to leave a gap into which other DNA elements can be placed. Targeted circuit modification simplifies and speeds up the iterative design-build-test process through the direct reuse of existing circuits (paper).

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