Difference between revisions of "Degradation of r-a"

Revision as of 23:41, 16 October 2015

[NOTE TO MARC: Can you check the parameter for this reaction? I assumed the mRNA complex half life to be 1 min, is it too slow?]

The mRNA complex of scbR-scbA degrades very soon after it's formation.

r-a\rightarrow \varnothing

r= d_{mAR}\cdot[r-a]

The parameter of this reaction is the degradation rate of the r-a complex $d_{mRA}$ .

Name	Value	Units	Value in previous GBL model ^[1]	Remarks-Reference
$d_{mRA}$	$0.03-0.4$ ^[2] ^[3]	$min^{-1}$	$0.01 s^{-1}$ ^[1] (Bistability range: and $0-1.24 s^{-1}$ )	In a study on the properties of antisense RNA and on the effect it has on gene regulation in bacteria, Georg et al. report that the antisense RNAs resulting from overlapping or divergent promoters (i.e. isiA/IsrR sense/antisense pair in Synechocystis PCC6803) that form a complex, co-degrade almost immediately. Georg et al. 2012^[3] This opinion is further supported by A.J. Carpousis who, in a review on gene regulation by antisense RNA and quantifies a short mRNA half-life as approximately $2 min$ . A.J. Carpousis 2003^[2] Therefore we can assume that the antisense RNA in the GBL system will follow a similar pattern and will rapidly degrade. The half-life should be kept under $2 min$ , therefore we can explore the range of values $0.01-2 min$ . From the antisense RNA half-life ( $t_{1/2}$ ) we calculated the degradation rate, as per $d_{mRA}= \frac{ln(2)}{t_{1/2}}$ , which resulted in a degradation rate constant value between $0.35-69.3 min^{-1}$ .

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 This opinion is further supported by A.J. Carpousis who, in a review on gene regulation by antisense RNA and quantifies a short mRNA half-life as approximately <math>2 min</math>.
-[[Image:DmRA-text2.png|center|thumb|300px|A.J. Carpousis 2003<ref name="Carpousis2003"></ref>]]
+[[Image:DmRA-text2.png|center|thumb|350px|A.J. Carpousis 2003<ref name="Carpousis2003"></ref>]]
 Therefore we can assume that the antisense RNA in the GBL system will follow a similar pattern and will rapidly degrade. The half-life should be kept under <math>2 min</math>, therefore we can explore the range of values <math>0.01-2 min</math>. From the antisense RNA half-life (<math>t_{1/2}</math>) we calculated the degradation rate, as per <math>d_{mRA}= \frac{ln(2)}{t_{1/2}}</math>, which resulted in a degradation rate constant value between <math>0.35-69.3 min^{-1} </math>.