104. Which of the following mRNA molecules would form the most stable stem-loop structure?
(A) 5'...GGCUU......UUCGG...3'
(B) 5'...GGCUU......AAGCC...3'
(C) 5'...GGCUU......GGCUU...3'
(D) 5'...GGCUU......CCGAA...3'
(E) 5'...AAGCC......AAGCC...3'
Answer
First of all, stem-loops are formed by so-called inverted repeats. Is est, one strand of loop is complement to the other:
5'-...GGGCCC... (small loop here)
3'-...CCCGGG...
If this sequence is linearized now, we will get
5'-...GGGCCC......GGGCCC...-3' strand
Stem is that paired part of looped RNA.
Any mismatches (when, e.g. G is opposed by A) are called bulges.
So, hairpin (synonym of stem-loop) stability is defined by number of mismatches and stability of each base pair in the stem. That one arise from the fact that A have 2 hydrogen bonds with U (or T in DNA) and G have 3 hydrogen bonds with C, so GC pair is much more stable.
From first fact we can eliminate answer choices A, C, D and E, since neither A binds to C, nor U to U or A to U (just compare two nucleotides on the inner edges of uncovered sequences). Lets check answer B to be sure.
5'-...GGCUU...(loop)
3'-...CCGAA...
Should be stable!
This question is from easiest ones, so should not take a lot of time, which we are short of.
Yes, and I am back, will try to complete this blog during preparation.
