PMC:1459172 / 15272-16634 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1459172","sourcedb":"PMC","sourceid":"1459172","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1459172","text":"Let us now consider the algorithmic details of folding two concatenated RNA sequences. The missing backbone edge between the last nucleotide of the first molecule, position n1 in the concatenated sequence, and the first nucleotide of the second molecule (now numbered n1+1) will be referred to as the cut c. In each dimeric structure there is a unique loop Lc that contains the cut c. If c lies in the external loop of a structure S then the two molecules A and B do no interact in this structure. Algorithmically, Lc is either a hairpin loop, interior loop, or multibranch loop. From an energetic point of view, however, Lc is an exterior loop, i.e., it does not contribute to the folding energy (relative to the random coil reference state). For example, an interior loop (i, j; k, l) does not contribute to the energy if either i ≤ n1 \u003ck or l ≤ n1 \u003cj. Naturally, dangling end contributions must not span the cut, either. Hairpin loops and interior loops (including the special cases of bulges and stacked pairs) can therefore be dealt with by a simple modification of the energy rules. In the case of the multiloop there is also no problem as long as one is only interested in energy minimization, since multiloops are always destabilizing and hence have strictly positive energy contribution. Such a modified MFE algorithm has been described already in [41].","tracks":[]}