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Team:TU-Eindhoven/Protocols
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<p>In the lab we used many standard protocols, however, some of were modified from literature. The reasons for modification are indicated briefly below.</p> | <p>In the lab we used many standard protocols, however, some of were modified from literature. The reasons for modification are indicated briefly below.</p> | ||
| - | <h3>BioBrick construction</h3> | + | <h3>BioBrick<sup>TM</sup> construction</h3> |
| - | <p>Many protcols for assembling BioBricks<sup>TM</sup> are already available, like Standard Assembly and 3A-assembly. These are suited for the assembly of standardized bricks, however, we created our BioBricks<sup>TM</sup> out of non-standard material and when working with yeast we used non-standard vectors to carry the protein coding sequences. In other words, most of our cloning steps had to be done the old-fashioned way and consequently the yields were lower than with standard assembly. The solution was to use more DNA and longer incubation for digestion. This guaranteed a proper yield at the end of the process. The detail can be found in our [[File:BioBrick_construction|high-efficiency BioBrick assembly protocol]]</p> | + | <p>Many protcols for assembling BioBricks<sup>TM</sup> are already available, like Standard Assembly and 3A-assembly. These are suited for the assembly of standardized bricks, however, we created our BioBricks<sup>TM</sup> out of non-standard material and when working with yeast we used non-standard vectors to carry the protein coding sequences. In other words, most of our cloning steps had to be done the old-fashioned way and consequently the yields were lower than with standard assembly. The solution was to use more DNA and longer incubation for digestion. This guaranteed a proper yield at the end of the process. The detail can be found in our [[File:BioBrick_construction|high-efficiency BioBrick<sup>TM</sup> assembly protocol]]</p> |
<h3>Yeast transformation</h3> | <h3>Yeast transformation</h3> | ||
Revision as of 15:05, 25 September 2012
Standard protocols and modifications
In the lab we used many standard protocols, however, some of were modified from literature. The reasons for modification are indicated briefly below.
BioBrickTM construction
Many protcols for assembling BioBricksTM are already available, like Standard Assembly and 3A-assembly. These are suited for the assembly of standardized bricks, however, we created our BioBricksTM out of non-standard material and when working with yeast we used non-standard vectors to carry the protein coding sequences. In other words, most of our cloning steps had to be done the old-fashioned way and consequently the yields were lower than with standard assembly. The solution was to use more DNA and longer incubation for digestion. This guaranteed a proper yield at the end of the process. The detail can be found in our high-efficiency BioBrickTM assembly protocol
Yeast transformation
The principal protocol for yeast transformation was Gietz and Schiestl (2007)[1]. It promised high transformation efficiency, however, in combination with our yeast the yield was a factor thousand lower than expected. The solution was to increase the amount of DNA used for transformation up to a whopping 3 ug and to work with freshly cultured yeast in mid-log phase instead of vials of frozen competent cells. For more details, please refer to the File:Yeast transformation.pdf.
References
- [1]Gietz and Schiestl, ''High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method'', Nature Protocols (2007) vol. 2, issue 1, pp. 31-34
