Dr. Bicardi is wanting to discover the Kd (equilibrium dissociation
constant) for the interaction between a protein (YFP) and an RNA molecule (RO1) that folds the stem-loop when it binds to the protein.
The sequence of RO1 is:
5' - CCUUGAUAGUUAUUGCGGAAGGGGCAAUAACUAAUCAAGG - 3'
(a) Make a diagram, like the roadkill map, to determine the loop structure that forms when the oligonucleotide RO1 is folded. Be sure to indicate the 5' and 3' ends and the base pairings in the drawing.
(b) As the protein is absent, the RO1 molecule can form an intermolecular complex that contains 2 RO1 molecules when the concentration is high. Which structure would you expect to see from the described intermolecular complex? Draw the structure.
(c) RNA can be labeled by using an enzyme (nucleotide kinase) to catalyze the transfer of the phosphate that contains the radioactive isotope of the phosphorus 32P from ATP to the 3' OH of the RNA molecule. Initially, the scientist wanted to label the RNA molecule with this method, however, he added sodium hydroxide to the solution containing RO1 and it hydrolyzes to its component monomers. Draw the chemical structure of the nucleotide that contains the isotope after the hydrolysis with the position. Remember to show all of the bonds.
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