Team:Newcastle/Promoter Library

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==Introduction==
==Introduction==
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As a part of our project we wish to create a library of SigmaA promoters and characterise them based on their stregnths.
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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


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

Team Newcastle iGEM Promoter Library1.png

Team Newcastle iGEM Promoter Library2.png


  • 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.

  1. Degenerating -35 and -10 sequences.
 BBPrefix...UpSpacer...N-35... PromSpacer...N-10...DownSpacer..BBSuffix
  1. BBPrefix...UpSpacerNN...-35...NNPromSpacerNN...-10...NNDownSpacer..BBSuffix
  2. BBPrefix...UpSpacer...-35... 18N’s...-10...DownSpacer..BBSuffix

Variance 1

In this variance we only degenerate -35 and -10 sequences.

Team Newcastle iGEM Promoter Library3.png

Team Newcastle iGEM Promoter Library4.png

Variance 2

Team Newcastle iGEM Promoter Library5.png

Variance 3

Team Newcastle iGEM Promoter Library6.png

Lab Work Strategies

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