In 1989 the Noble Prize in Chemistry was awarded for the discovery of catalytic
ID: 175642 • Letter: I
Question
In 1989 the Noble Prize in Chemistry was awarded for the discovery of catalytic properties of RNA. Since then, some exciting work has been done on the folding of these RNAs. In one set of experiments, the folding of RNA as a function of magnesium concentration was monitored via catalytic activity (Figure 1). The equilibrium folding of the same RNA was also monitored by CD and UV absorbance (Figure 2, solid and open circles, respectively). Why does the UV absorbance decrease with increasing [Mg^2+]? Is there any significance to the fact that the CD and UV curves intersect at a different [Mg^2+] than the midpoint of the activity plot (Figure 1)? What is the significance, or why isn't it significant? What is the main "take-home" message from these plots? Free energy contour plots for the folding of the same ribozyme as a function of [Mg^2+] is shown below. These plots were calculated from FRET experiments in which the donor and acceptor pair (Fluorescein/Cy3) is located in a region that normally forms a tertiary contact in the native RNA structure. What can you conclude from these plots? Is this information consistent with the CD and UV data, above? Explain why or why not.Explanation / Answer
Increasing the magnesium concentration causes into increase in binding with negative charged RNA molecule. RNA and DNA are negative charge molecules. So if there negative group are attached with Mg2+ ions, they cannot absorb the UV light more.
No there will no other intersect can occur in between UV and CD curve because UV is inversely dependent to Mg concentration and CD is directly. More open frame of molecule results into more planar polarization in CD.
Yes these plots are significant, these show that increasing concentration of Mg2+ ions decrease efficiency of RNA molecule to be translated.
Mg2+ ions quench the absorbance. During 0.1 mM concentration it doesn’t open the RNA fragment and thus the FRET data has 0.2efficiency. But increasing the Mg2+ ions concentration leads to open the RNA fragment i.e. linearizing. Now the efficiency is increasing with the decreasing distance between donor and acceptor chromophores. At last the RNA segment opened and chromophores get fully attach to RNA and thus radiation is readily absorbed. That’s increase the efficiency of FRET.