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21 May 2018

Q: "Here we show that freezing stimulates the self-ligation (circularization) of linear forms of the hairpin ribozyme (HPR) containing 2',3'-cyclic phosphate and 5'-OH termini. Divalent metal ions (M2+) are not required, but monovalent cations and anions at millimolar concentrations can have various effects on this reaction depending on the specific ion. Under optimal conditions, the observed rate of M2+-independent self-ligation reaches a peak (0.04 min(-1)) at -10 degrees C with a yield of -60% after 1 h. In contrast, no ligation occurs either at above 0 degrees C or in solutions that remain unfrozen when supercooled to subzero temperatures. Under freezing conditions, the cleavage-ligation equilibrium strongly favors ligation. Besides freezing, evaporation of the aqueous solvent as well as the presence of ethanol at levels of 40% or above can also induce M2+-independent HPR ligation at 25 degrees C. We argue that partial RNA dehydration, which is a common feature of freezing, evaporation, and the presence of ethanol, is a key factor supporting HPR ligation activity at both above- and below-freezing temperatures. In the context of the RNA world hypothesis, freezing-induced ligation is an attractive mechanism by which complex RNAs could have evolved under conditions in which RNA was relatively protected against degradation."
--Kasakov et al. (2006) RNA 12(3):446-456.
1. The authors suggest that by changing the solvent, the RNA enzyme function changes to favor the ligation (joining) reaction. Give an example of how the DNA structure can change in different solvents that might support that model for RNA.
2. The solvent is important in determining the native state (lowest energy/most stable) 3-D structure of a protein. In a sentence or two, explain why the way an RNA finds its native state in a particular environment is different from the way a protein finds its native state (hint: Chargaff's rules do not apply to single-stranded RNA, but are more relevant in RNA than in protein).
3. What is the RNA world hypothesis? Briefly explain why you agree or disagree with the statement made by the authors that their findings support the RNA world hypothesis.

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Casey Durgan
Casey DurganLv2
22 May 2018

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