RNA folding and hydrolysis terms explain ATP independence of RNA interference in human systems.
Although RNA interference (RNAi) has emerged as an important tool for studying the effects of gene knockdown, it is still difficult to predict the success of RNAi effectors in human systems. By examining the basic thermodynamic equations for RNA interactions in RNAi, we demonstrate how the free energies of RNA folding and phosphoester bond hydrolysis can drive RNAi without ATP. Our calculations of RNAi efficiency are close to actual values obtained from in vitro experimental data from 2 previous studies, for both silencing complex formation (2.50 vs. 2.40 for relative efficiency of RISC formation) and mRNA cleavage (0.50 vs. 0.56 for proportion cleaved). Our calculations are also in agreement with previous observations that duplex unwinding and target site folding are major energy barriers to RNAi.
Ali
Nicole
N
Department of Physics, Harvard University, Cambridge, Massachusetts. , Current affiliation: Yale School of Medicine, New Haven, Connecticut, USA.
Manoharan
Vinothan N
VN
D000255:Adenosine Triphosphate / Q000378:metabolism*; D001483:Base Sequence; D006801:Humans; D006868:Hydrolysis; D008954:Models, Biological; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D034622:RNA Interference / Q000502:physiology*; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034743:RNA-Induced Silencing Complex / Q000096:biosynthesis; D013816:Thermodynamics
D012333:RNA, Messenger; D034743:RNA-Induced Silencing Complex; D012313:RNA; D000255:Adenosine Triphosphate