Q: \"Here we show that freezing stimulates the self-ligation (circularization) o
ID: 145580 • Letter: Q
Question
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.
Explanation / Answer
Ans 1) The author suggest by changing the solvent, the RNA enzyme function and it even starts to favor the joining or ligation reaction. One of the examples in this is the use of ethanol as the solvent which helps in favoring the HPR ligation process and activity. On using evaporation of solvent or ethanol at 25° degrees, it was found that HRP ligation was obtained in a M2+ independent process. Ethanol was found to promote HPR ligation in unfrozen solution in presence of Mg2+ and it helps in 40% faster rapid circularization. It was also found at for unfrozen solution; the ethanol induced ligation can also take place in presence of EDTA without Mg2+. This is because it promotes rapid aggregation and precipitation of the RNA. The dissolved salt fails to precipitate or concentrate in aqueous solution which helps in the ligation process. In case of ethanol, one of the most important factors for it to promote ligation is dehydration of RNA by use of concentrated salt as it leads to evaporation of the aqueous solvent. It helps in stabilizing folded RNA molecules by promoting the A-form helices formation.
Ans 2) The way a RNA find its native state in an environment is different from how protein finds its native state because of the application of the Chargaff’s rule. It states that DNA from all cells must have 1:1 ratio of pyrimidine and purine bases i.e equal amount of guanine and cytosine and adenine and thymine for the base pairing. It is because in RNA it attains the stable state only when there is 1:1 ratio of purine : pyrimidine which is not the requirement when it comes to formation of the polypeptide chain for protein formation.
Ans 3) According to the RNA world hypothesis, RNA is responsible for two things which are the storage of the genetic information along with catalysis of the chemical reactions in the primitive cells. According to the theory, it was RNA which came first and proposes earlier life forms may have used only RNA for genetic material storage. It states that the DNA became the genetic material later as a result of evolution as RNA was sort of unstable. The hypothesis was postulated due to the fact that RNA has the capability of self replication. According to the RNA world hypothesis, the freezing based ligation is a great mechanism adopted by the complex RNA to evolve under situations when they needed to be protected against dehydration. They sort of agree with the hypothesis due to the finding that ribozyme catalysis which is ligation of the linear RNA in frozen state can be directly connected to the hypothesis. RNA with its ability to create circularization and carry the genetic information along with serving as template for the rolling circle replication is a strong reason to agree with the hypothesis.
Related Questions
Navigate
Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.