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Team:Warsaw/Stage1/Modeling
From 2010.igem.org
Modeling
Durig the brainstorm period of our project we came up with many interesting ideas and we tried to find a way to squeeze all those ideas into one E.Coli Cell. It lead us to one generel dilema. How many different genes can we insert into our Coli at one time andd how precisly regulate their dosage. We decides to use different RBS sequences to controol gene exporession. We knew from the registry that B0033 is weak and for strong expresssion we should use B0034, but also we have learned that those RBSes were measures in one seup with standard promoter and GFP reporter gene. We faced two ganeral questios:
1) Are those 5 measured RBSes in the registry enaugh? Does it make sense to to use any other RBSes?
2) RBSes were measured with GFP reporter. Are these RBS measurements universal. Would RBS behave differently if we pout our favourite gene uinstead of GFP?
We went downstairs, ordered lots of coffe, switched on the laptops and asked google scholar for help. We came acrooss a nature paper abut stadarisation of synthetic biological parts and devices []. The parts' evolutionary reliability measurement was perticulary interesting for us. Paper suggest that after 74 culture doubling the measured part mutated and wasn't fuctional anymore. System failiure resulted from deletion bethween repeated DNA sequences due to recombination. In that specific system it occured because terminator B0015 was used 2 times.
This scenario would be probably repeated if we used the same RBS parts. However teh experiment was performed in the recA+ strain - in other words a strain thet recombinates.2009 Warsaw team used B0032 many times to obtain moderate gene expression, because Top10 (recA-) strain was used there were no recobination events.In the light of these evidence we wanted to refine our design and avoid repeated sequences to make our system portable. This is a problem if you want to use RBSes of similar strength, because there is seldom more than one characterised.
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