Thursday, February 12, 2009

A Synth Bio Challange: Make it through an advanced video discussing the need for Bio Brick Standards. You can do it!

I admit this video is not for beginners. It's an advanced Synth Bio video, but don't be scared. Take a look anyway, you probably won't understand most of the details, but you will understand some of the overall procedures and its good to start to see how the process works. Hang in there!

What is this video? It's a narrated slide show by Jason Kelly introducing and detailing proposed technical standard for measuring the activity of engineered transcription promoters and ribosome binding sites in bacteria.

Wait wait wait! Whats a transcription promoter?!

Wiki Entry: In order for transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences and response elements which provide a binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase.
  • In bacteria, the promoter is recognized by RNA polymerase and an associated sigma factor, which in turn are brought to the promoter DNA by an activator protein binding to its own DNA sequence nearby.
  • In eukaryotes, the process is more complicated, and at least seven different factors are necessary for the binding of an RNA polymerase II to the promoter.

Promoters represent critical elements that can work in concert with other regulatory regions (enhancers, silencers, boundary elements/insulators) to direct the level of transcription of a given gene.

OK. What are ribosome binding sites?

A ribosomal binding site (RBS) is a sequence on mRNA that is bound by the ribosome when initiating protein translation.It can be either the 5' cap of a messenger RNA in eukaryotes, a region 6-7 nucleotides upstream of the start codon AUG in prokaryotes (called the Shine-Dalgarno sequence), or an internal ribosome entry site (IRES) in viruses. The sequence is complementary to the 3' end of the rRNA. The ribosome searches for this site and binding to it (through base-pairing) begins the translation process, recruiting initiation factors.

This presentation was developed for the March 1 2008 BioBricks Foundation (BBF) Technical Standards Workshop held at UCSF.

For more information see:

BBF Synth Bio Notes
Notes from the BBF meeting (BBF = Biobricks Foundation)
Registry/Measurement kit

BBF Synth Bio Protocols
/Promoter characterization experiment (FACS)

Make sure to visit:

Thanks to Jason Kelly for this video! Don't know who Jason is? Here's his bio: Jason hung around MIT for almost a decade receiving B.S degrees in Chemical Engineering and Biology and a PhD in Biological Engineering. He has expertise in developing tools to support the directed evolution of genetic parts and in standardizing the measurement of parts. During his graduate work, he designed and distributed "measurement kits" that allow independent labs to report measured promoter and RBS activity in common units so these parts could be more easily re-used. Jason is a founder of OpenWetWare, a community of life sciences researchers exploring ways to conduct science more efficiently and openly. is a Founder of Ginkgo BioWorks and has a PhD in Biological Engineering @ MIT in the Endy Lab, (June 2008) You can contact him via talk page, blog, or email.

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