RNA folding and hydrolysis terms explain ATP-independence of RNA interference in human systems

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Original Entry: Tom Dimiduk APPHY 225 Fall 2010 [RNA folding and hydrolysis terms explain ATP-independence of RNA interference in human systems http://www.liebertonline.com/doi/pdf/10.1089/oli.2009.0186]

Keywords

Free Energy, Self Assembly, RNA

Summary

The authors show how the process of RNA interference (RNAi) [figure 1] can proceed without any energy input. They use [DINAMelt http://dinamelt.bioinfo.rpi.edu/hybrid2.php] a web server which does RNA energy calculations, and known energies the chemical bonds in the RNA to compute the free energy in all stages of the operation of RNAi. They choose to examine the version of RNAi that uses the RNA-induced silencing complex (RISC) because it is well understood and they believe it is important in most applications of RNAi.

The reaction equations they solve are:

folded template RNA precursor -> unfolded template RNA precursor
unfolded template RNA precursor -> unfolded template RNA + unfolded template compliment strand + unfolded loop fragment
template RNA + inactive RNAi complex -> active RISC 
unfolded template compliment strind + unfolded loop fragment -> folded template compliment strand + folded loop fragment
Figure 1: Schematic of the process of RNAi going through the activation of the RNAi complex (RISC) (steps 1-3) and targeted destruction of messenger RNA (mRNA) (steps 4-6). (1) binding a template RNA (2), cleaving (if necessary) the template RNA (3) releasing the uneeded complimentary strand, (4) binding to a target mRNA, (5) unfolding the target mRNA, and (6) cleaving the mRNA

Understanding the free energy of each state of the reaction lets them calculate equilibrium constants and compare to experiment. They are able to make parameter free predictions which line up well with several experiments. They correctly compute that using a loop precursor will yeild more effective silencing (by a factor of 2.56 compared to the experimental value of 2.4) because it provides two extra phosphodiester bonds to cleave adding 6.2 kJ/mole to the reaction, a significant fraction of the free energy. The also are able to predict the degree of mRNA knockdown with good accuracy, predicting a remaining fraction of 0.56 for an experiment which actually left a fraction of 0.5.

Thus these simple thermodynamic calculations can show how a complicated biological system works, and lend great support to the experimentally suggested hypothesis that this complex can proceed without added energy (ATP).

Soft Matter Discussion

This can sort of be considered a self assembly process, though self disassembly might a be more accurate term, because the process proceeds without added energy. Being a biological system, it is somewhat more complicated than many of the self assembly systems studied in soft matter, but yet it is still amenable to a relatively full thermodynamic analysis.