Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study.
In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us to study the potency difference between 2-nt 3' overhangs against blunt-ended siRNA molecules in an RNA interference (RNAi) system. The rate constant predicted by this model was fed into a stochastic simulation of the RNAi system (using the Gillespie stochastic simulator) to study the overall potency effect. We observed that the stochasticity in the transcription/translation machinery has no observable effects in the RNAi pathway. Sustained gene silencing using siRNAs can be achieved only if there is a way to replenish the dsRNA molecules in the cell. Initial findings show about 1.5 times more blunt-ended molecules will be required to keep the mRNA at the same reduced level compared to the 2-nt overhang siRNAs. However, the mRNA levels jump back to saturation after a longer time when blunt-ended siRNAs are used. We found that the siRNA-RISC complex formation reaction rate was 2 times slower when blunt-ended molecules were used pointing to the fact that the presence of the 2-nt overhangs has a greater effect on the reaction in which the bound RISC complex cleaves the mRNA.
Ghosh
Preetam
P
School of Computing, The University of Southern Mississippi, Hattiesburg, MS 39406, USA. preetam.ghosh@usm.edu
Dullea
Robert
R
Fischer
James E
JE
Turi
Tom G
TG
Sarver
Ronald W
RW
Zhang
Chaoyang
C
Basu
Kalyan
K
Das
Sajal K
SK
Poland
Bradley W
BW
D019295:Computational Biology; D003198:Computer Simulation; D008956:Models, Chemical; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D034741:RNA, Small Interfering / Q000737:chemistry*; D034743:RNA-Induced Silencing Complex / Q000737:chemistry*; D049490:Systems Biology
D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex