Team:TUDelft/Lock/Key library

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Latest revision as of 00:42, 22 October 2009

Lock/Key library

As mentioned in preliminary approaches in the section RNA-based Delay: Biosynthetic AND gate, our design was based on the previous work of Isaacs F. 2004, [http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley iGEM 2006], [http://openwetware.org/wiki/IGEM:Caltech/2007 Caltech iGEM 2007] and Peking iGEM 2007. However, we found that these projects were done using the "normal" RBS ([http://partsregistry.org/Part:BBa_B0034 B0034]). The registry of biobricks has several RBS, besides, as a advice from our modeling team, the RBS present in our constructs should be one with low affinity or “weak” in order to avoid leakage problems. Therefore, we constructed an algorithm based on the previous works which allows us to generate pairs of locks and keys for any RBS (in or outside the registry).

Lock/Key library: Algorithm

Based on the various above mentioned studies on the locks and keys, we have developed an algorithm, which has led us to develop a simple web based tool to help in generating the DNA sequences of locks and keys for a chosen Ribosome Binding Site (RBS) DNA sequence. Click here for more information.

Lock/Key generator

You can also directly visit the web based Lock/Key generator page by clicking here.

Lock/Key library: New Biobricks Design

We want to test if the algorithm delivers functional locks and keys. In order to do that, we plan to characterize two locks and keys generated by our algorithm. The RBS’s chosen were the weak and medium (biobricks) from the registry. The DNA sequences of these new parts are... more

Results

Main results

Construction of an algorithm capable to generate locks (cis regulation) for different ribosome binding sites (RBS’s) and their correspond key (trans).
Online lock and key generator derived from the algorithm.
Construction of four DNA sequences in biobrick format and [http://partsregistry.org/wiki/index.php?title=Part:BBa_pSB1A3 pSB1A3] plasmid backbone which encode lock for medium RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175031 K175031]), key for the lock of medium RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175032 K175032]), lock for weak RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175029 K175029]) or key for the lock of weak RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175030 K175030]).
Assembly of two composed biobricks ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175034 K175034] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K175035 K175035]), designed to test the functionality of the lock/key pairs constructed.
Assembly of two GFP generators under the control of PLacI with weak RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175033 K175033]) or medium RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175048 K175048])... more

Home

Retrieved from "http://2009.igem.org/Team:TUDelft/Lock/Key_library"

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-{{Template:TUDelftiGEM2009}}
+{{Template:TUDelftiGEM2009_menu_M3_Time}}
-''This page is still under construction''
-<br>
 ='''Lock/Key library'''=
-As mentioned in preliminary approaches in the section RNA-based Delay: Biosynthetic AND gate, our design was based on the previous work of [https://2009.igem.org/Team:TUDelft/References Isaacs F. 2004], [http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley iGEM 2006], [http://openwetware.org/wiki/IGEM:Caltech/2007 Caltech iGEM 2007] and [http://parts.mit.edu/igem07/index.php/Peking Peking iGEM 2007].However, we found that these projects were done using a single RBS. The registry of biobricks has several RBS, besides, as a advice from our modeling team, the RBS present in our constructs should be one with low affinity or “weak” in order to avoid leaky problems. Therefore, we constructed an algorithm based in the previous works which allows us to generate pairs of locks and keys for any RBS (in or outside the registry).
+As mentioned in preliminary approaches in the section RNA-based Delay: Biosynthetic AND gate, our design was based on the previous work of [https://2009.igem.org/Team:TUDelft/Module_3_References Isaacs F. 2004], [http://openwetware.org/wiki/IGEM:UC_Berkeley/2006 Berkeley iGEM 2006], [http://openwetware.org/wiki/IGEM:Caltech/2007 Caltech iGEM 2007] and [https://2007.igem.org/Peking Peking iGEM 2007]. However, we found that these projects were done using the "normal" RBS ([http://partsregistry.org/Part:BBa_B0034 B0034]). The registry of biobricks has several RBS, besides, as a advice from our modeling team, the RBS present in our constructs should be one with low affinity or “weak” in order to avoid leakage problems. Therefore, we constructed an algorithm based on the previous works which allows us to generate pairs of locks and keys for any RBS (in or outside the registry).
+=='''Lock/Key library: Algorithm'''==
+Based on the various above mentioned studies on the locks and keys, we have developed an algorithm, which has led us to develop a simple web based tool to help in generating the DNA sequences of locks and keys for a chosen Ribosome Binding Site (RBS) DNA sequence. Click [[Team:TUDelft/Algorithm |here]] for more information.
+=='''Lock/Key generator'''==
+You can also directly visit the web based '''Lock/Key generator page''' by clicking [https://2009.igem.org/Team:TUDelft/RiboKeyLock_Generator here].
-*[[Team:TUDelft/Algorithm | Lock/Key library: Algorithm]]
+=='''Lock/Key library: New Biobricks Design'''==
+We want to test if the algorithm delivers functional locks and keys. In order to do that, we plan to characterize two locks and keys generated by our algorithm. The RBS’s chosen were the weak and medium (biobricks) from the registry. The DNA sequences of these new parts are...[[Team:TUDelft/New_Lock_Key_Biobricks | more]]
-*[[Team:TUDelft/New Biobricks | Lock/Key library: New Biobricks Design]]
+=='''Results'''==
-*[[Team:TUDelft/Results3 | Results]]
+'''''Main results'''''
+* Construction of an algorithm capable to generate locks (cis regulation) for different ribosome binding sites (RBS’s) and their correspond key (trans).
+* Online [https://2009.igem.org/Team:TUDelft/RiboKeyLock_Generator lock and key generator] derived from the algorithm.
+* Construction of four DNA sequences in biobrick format and [http://partsregistry.org/wiki/index.php?title=Part:BBa_pSB1A3 pSB1A3] plasmid backbone which encode lock for medium RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175031 K175031]), key for the lock of medium RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175032 K175032]), lock for weak RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175029 K175029]) or key for the lock of weak RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175030 K175030]).
+* Assembly of two composed biobricks ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175034 K175034] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K175035 K175035]), designed to test the functionality of the lock/key pairs constructed.
+* Assembly of two GFP generators under the control of PLacI with weak RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175033 K175033]) or medium RBS ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K175048 K175048])...[[Team:TUDelft/Results3 | more]]
 [https://2009.igem.org/Team:TUDelft Home]
 <br>
 {{Template:TUDelftiGEM2009_end}}