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Team:Newcastle/Promoter Library
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==Introduction== | ==Introduction== | ||
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| + | In order to effectively model genetic circuits, databases of parts with known characteristics are essential. Without such databases, computationally designed circuits may not be feasible to implement ''in vivo''. Unfortunately, parameters such as promoter strength, RBS affinity, transcription, translation and decay rates are hard to find in the literature, and those which do exist are rarely measured under standardised conditions. | ||
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| + | Several efforts to produce parts libraries are currently underway.As part of our contribution to synthetic biology, we decided to create a promoter library for ''B. subtilis''. | ||
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==Novelty in this sub-project== | ==Novelty in this sub-project== | ||
A library of promoters with different strengths would be very useful for engineering biological devices. | A library of promoters with different strengths would be very useful for engineering biological devices. | ||
Revision as of 21:06, 21 October 2009
Project
Sub-projects
Wet Lab
Meetings
Planning
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Promoter Library
Introduction
In order to effectively model genetic circuits, databases of parts with known characteristics are essential. Without such databases, computationally designed circuits may not be feasible to implement in vivo. Unfortunately, parameters such as promoter strength, RBS affinity, transcription, translation and decay rates are hard to find in the literature, and those which do exist are rarely measured under standardised conditions.
Several efforts to produce parts libraries are currently underway.As part of our contribution to synthetic biology, we decided to create a promoter library for B. subtilis.
Novelty in this sub-project
A library of promoters with different strengths would be very useful for engineering biological devices. Promoters' strength can be compared with their PoPS values. However measuring the PoPS is not a trivial process. We can instead meausure their strengths relatively.
Design
Template used to create the promoter sequences: Prefix...UpSpacer...-35...PromSpacer...-10...DownSpacer..Suffix
- BBPrefix - StandardBioBrickPrefix EcoR1 and Xba1 - gaattcgcggccgcttctagag
- UpSpacer - attta - consensus sigA 5 bases 5'
- -35 - TTGACA
- PromSpacer - length 17 - consensus ttttatttaaattatga
- -10 - TATAAT
- DownSpacer (from ackA)- ggaaaag
- BBSuffix - Standard BioBrick suffix Spe1 and Pst1 - tactagtagcggccgctgcag
Variances
We designed three variances to create library of promoters with different strengths.
- Degenerating -35 and -10 sequences.
BBPrefix...UpSpacer...N-35... PromSpacer...N-10...DownSpacer..BBSuffix
- BBPrefix...UpSpacerNN...-35...NNPromSpacerNN...-10...NNDownSpacer..BBSuffix
- BBPrefix...UpSpacer...-35... 18N’s...-10...DownSpacer..BBSuffix
Variance 1
In this variance we only degenerate -35 and -10 sequences.
Variance 2
Variance 3
Lab Work Strategies
Other Presentations and Diagrams
News
Events
- 20 – 21 June 2009 - Europe workshop (London)
- 23 – 24 June 2009 - UK iGEM meetup (Edinburgh)
- 23 October Practice Presentation (Newcastle)
- 23 October T-shirts are ready
- 27 October Practice Presentation (Sunderland)
- 27 October Poster is ready
- 30 October – 2 November 2009 - Jamboree (Boston)
Social Net
- Newcastle iGEM Twitter
- [http://www.facebook.com/home.php#/group.php?gid=131709337641 Newcastle on Facebook]
- [http://www.youtube.com/user/newcastle2009igem Newcastle Youtube Channel]
