RNA secondary structure prediction with RNAfold.
In the double-helical structure of the DNA molecule, two complementary nucleotide strands are held together with hydrogen bonds between the Waston-Crick pairs A-T and C-G. RNA molecules usually come as single strands but left in their environment they fold themselves in their tertiary structure because of the same hydrogen bonding mechanism. Helices, also known as stems, are formed intra-molecularly.
There are 16 possible base pairings, however, of these, only six (AU, GU, GC, UA, UG, CG) are stable enough to form actual base pairs. The rest are called mismatches and occur at very low frequencies in helices. RNA molecules, such as ribosomal RNAs and transfer RNAs, have an important role. Their structure cannot easily be disrupted without impact on their function and lethal consequences and selection are acting to maintain the secondary structure. Yet, the primary structure of the stems (i.e., their nucleotide sequence) can still vary and in fact, we observe that RNA helical regions are quite variable in sequence. The nature of the bases is not important and substitutions are possible as long as they preserve the secondary structure. One could model the evolution of stems using the DNA models described above but there may be a substantial bias in results because paired substitutions would seem far less probable than they are in reality. Statistics become invalid and it can have an effect on inferred phylogenies.
The secondary structure is left unchanged when complementary substitutions occur in the DNA gene coding for the RNA molecule.
ncbi#dbj#bii#
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