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Revision as of 12:54, 10 August 2010 (view source) Hugo 87 (Talk | contribs) (→RBS Characterization) ← Older edit		Revision as of 12:59, 10 August 2010 (view source) Hugo 87 (Talk | contribs) (→RBS Characterization) Newer edit →
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	=RBS Characterization=		=RBS Characterization=
	For our RBS characterization project, 5 different RBS sequences from the [http://partsregistry.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Anderson Anderson RBS family] (J61100, J61101, J61107, J61117, J61127) and one known RBS ([http://partsregistry.org/Part:BBa_B0032 B0032]) where placed in front of GFP and measured over 18 hours using a Gen5 fluorenscence and absorbance plate reader. The general map of the construction is shown below, where the RBS is displayed in fucsia.		For our RBS characterization project, 5 different RBS sequences from the [http://partsregistry.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Anderson Anderson RBS family] (J61100, J61101, J61107, J61117, J61127) and one known RBS ([http://partsregistry.org/Part:BBa_B0032 B0032]) where placed in front of GFP and measured over 18 hours using a Gen5 fluorenscence and absorbance plate reader. The general map of the construction is shown below, where the RBS is displayed in fucsia.
-	[[Image:RBS1.jpg|center|600px]]	+	[[Image:RBS1.jpg|left|500px]]
		+	{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"
		+	|'''Feature'''
		+	|'''Function'''
		+	|-
		+	|[http://partsregistry.org/Part:BBa_E0040 E0040]
		+	|GFP
		+	|-
		+	|[http://partsregistry.org/Part:BBa_J61101 J61101]
		+	|0.119831
		+	|-
		+	|[http://partsregistry.org/Part:BBa_J61107 J61107]
		+	|0.065454
		+	|-
		+	|[http://partsregistry.org/Part:BBa_J61117 J61117]
		+	|0.038518
		+	|-
		+	|[http://partsregistry.org/Part:BBa_J61127 J61127]
		+	|0.087334
		+	|-
		+	|[http://partsregistry.org/Part:BBa_B0032 B0032]
		+	|0.300000
		+	|}
	[[Image:26_07_2010_Rbs.png|center]]		[[Image:26_07_2010_Rbs.png|center]]

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Revision as of 12:59, 10 August 2010

RBS Characterization

For our RBS characterization project, 5 different RBS sequences from the Anderson RBS family (J61100, J61101, J61107, J61117, J61127) and one known RBS (B0032) where placed in front of GFP and measured over 18 hours using a Gen5 fluorenscence and absorbance plate reader. The general map of the construction is shown below, where the RBS is displayed in fucsia.

Feature	Function
E0040	GFP
J61101	0.119831
J61107	0.065454
J61117	0.038518
J61127	0.087334
B0032	0.300000

Strength was calculated by taking the mean of the ratio between the expression of known RBS (B0032) and expression of Anderson RBS over some time. Expression being the measured fluorescence divided by measured biomass (absorbance, OD). The measurements where taken from the part of the curve where optimal growth can be assumed, so from 0:40 until 2:30 The result is a simple characterization of the Anderson RBS sequences in relation to the known RBSes. The given strengths are given in comparison with the iGEM RBS standard B0034.

RBS	Strength
J61100	0.047513
J61101	0.119831
J61107	0.065454
J61117	0.038518
J61127	0.087334
B0032	0.300000

We've also looked at mRNA folded shapes using mfold to see if there was a common pattern in the Anderson RBS shapes. This might have been usable in predicting RBS strength for the other untested Anderson RBS sequences. Unfortunately, this didn't seem to be the case, as all the tried RBS sequences had very different mfold shapes.