29

Perform RNA folding with RNAfold using the following sequence (https://rna.tbi.uni­

vie.ac.at/cgi-­bin/RNAWebSuite/RNAfold.cgi):

> RNAsecondary structure

A T A A G A G A C C A C A A G C G A C C C G C A G G G C C A G A C G T T C T T C G C C G A G A G T C G T C G G G

G T T T C C T G C T T C A A C A G T G C T T G G A C G G A A C C C G G C G C T C G T T C C C C A C C C C G G C

CGGCCGCCCATAGCCAGCCCTCCGTCACCTCTTCACCGCACCCTCGGACTGCCCCAA

G G C C C C C G C C G C C G C T C C A G C G C C G C G C A G C C A C C G C C G C C G C C G C C G C C T C T C

C T T A G T C G C C G C C A T G A C G A C C G C G T C C A C C T C G C A G G T G C G C C A G A A C T A C C A C C

AGGACTCAGAGGCCGCCATCAACCGCCAGATCAACCTGGAGCTCTACGCCTCCTACG

TTTACCTGTCCATGTCTTACTACTTTGACCGCGATGATGTGGCTTTGAAGAACTTTGC

C A A A T A C T T T C T T C A C C A A T C T C A T G A G G A G A G G G A A C A T G C T G A G A A A C T G A T

G A A G C T G C A G A A C C A A C G A G G T G G C C G A A T C T T C C T T C A G G A T A T C A A G A A A C C A G

A C T G T G A T G A C T G G G A G A G C G G G C T G A A T G C A A T G G A G T G T G C A T T A C A

T T T G G A A A A A A A T G T G A A T C A G T C A C T A C T G G A A C T G C A C A A A C T G G C C A C T G A

C A A A A A T G A C C C C C A T T T G T G T G A C T T C A T T G A G A C A C A T T A C C T G A A T G A G

CAGGTGAAAGCCATCAAAGAATTGGGTGACCACGTGACCAACTTGCGCAAGATGGGAGC

GCCCGAATCTGGCTTGGCGGAATATCTCTTTGACAAGCACACCCTGGGAGACAGTGATAA

TGAAAGCTAAGCCTCGGGCTAATTTCCCCATAGCCGTGGGGTGACTTCCCTGGTCACCAAGGC

A G T G C A T G C A T G T T G G G G T T T C C T T T A C C T T T T C T A T A A G T T G T A C C A A A A C A T

CCACTTAAGTTCTTTGATTTGTACCATTCCTTCAAATAAAGAAATTTGGTACCCAGG

TGTTGTCTTTGAGGTCTTGGGATGAATCAGAAATCTATCCAGGCTATCTTCCAGATTCCTT

AAGTGCCGTTGT

1. Which of the following statements about RNA folding is correct (multiple answers

possible)?

(A)

An RNA secondary structure should always have a very high folding energy,

then it is most stable.

(B)

RNAfold does not find a possible secondary structure for the exercise

example.

(C)

For the exercise example, RNAfold calculates a minimum free energy (fold­

ing energy) of −360.20 kcal/mol.

(D)

RNA folding (also bioinformatically predicted) is, from this point of view, a

very simple process, since there is only one linear structure.

(E)

RNA folding (also bioinformatically predicted) is a complex process from

this point of view, since there are, for example, several secondary structural

forms (e.g. stem- and hairpin-loop).

2. Create a short random RNA sequence (approx. 20–25 nucleotides) and let RNAfold

fold it. Subsequently, double the sequence length and fold it again.

How do the amounts of the released energies of the short and long sequence relate to

each other?

2.3  Exercises for Chap. 2