RNA ligation by hammerhead ribozymes and DNAzyme in plausible prebiotic conditions

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Lie, Lively
Wartell, Roger M.
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This work is focused on the ligation activity of the hammerhead ribozyme and DNAzymes in plausible prebiotic conditions. Before the Great Oxidation Event, RNA may have interacted with soluble Fe2+, as a replacement or in combination with Mg2+. Divalent metal cations are sometimes necessary in ribozyme activity by interacting with mostly phosphates to influence the tertiary structure of an RNA. In some cases, these metal cations help in the acid/base chemistry in catalytic cores. Chapter 2 reveals the benefits and drawbacks of hammerhead ribozyme ligation with Fe2+. Both ligation and cleavage of the hammerhead is enhanced, but an unexpected problem arose, RNA aggregation that is difficult to denature. Chapter 3 and 4 focuses on the hammerhead ligation in ice. Freeze-induced ligation frees the hammerhead from divalent metal requirements and when combined with heat-freeze cycles to mimic day and night, yield reaches 60%. Freezing the reaction mixture also reduces sequence specificity between enzyme and substrates. Chapter 5 reveals a RNA-cleaving DNAzyme that can ligate cleaved RNA substrates when the reaction mixture is frozen. The significance behind this chapter is that previous ligating DNAzymes require high-energy triphosphates and instead uses a 2’3’-cyclic phosphate. This 2’3’-cyclic phosphate is already a product of the cleavage reaction of the DNAzyme and the cleavage/ligation reaction is in effect recycling the same materials.
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