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1. Finding runs of complementary sequence.
  1. Look for runs of complementary A/U and G/C base pairs (we will ignore G/U for simplicity) when the RNA molecule AGCCAUUUUUUGGCU is folded back on itself.
  2. Show that the molecule can form a stem-and-loop structure. Using the base-stacking energy values and destabilizing energy values of loops provided in Table 8.2, what will be the energy of the molecule?

2. This question illustrates a way of finding runs of complementary sequence in the same RNA molecule used in Question 1 (i.e., regions that can potentially base-pair) by using a dot matrix approach. This type of matrix is made by mfold for predicting RNA secondary structure. The following matrix shows the sequence of the above RNA molecule both across the top of the matrix and down the side:
  1. Make a copy of the matrix in a text file or on a piece of ruled graph paper. Place an X at each position where the bases across the top are capable of base-pairing with those down the side (i.e., G/C and A/U base pairs).
  2. Look for a diagonal row of X's running from the upper right of the matrix to the lower left.
  3. What is the longest run of X's? Describe any symmetry in the matrix. What is the significance of this run?

3. Michael Zuker's mfold (multiple foldings of RNA) is used to find the minimum energy structure of an RNA molecule. Please check with the instructor before going to the RNA analysis page at Use of this Web site must be spread out because the analysis is very computer intensive.
  1. Copy and paste the potato spindle tuber viroid sequence (GenBank accession no. AY360446) into the input window of mfold.
  2. Using the program parameters provided, the immediate option, click the fold RNA box, and wait for the results.
  3. In the output, click on structures 1, 2, 3, etc. to view the alternative structures.
  4. Describe the first structure reported and the energy of this structure.


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