Final answer:
RNA-RNA rearrangements often require sequences to be read multiple times due to the complex three-dimensional structures formed by extensive base pairing, with sequence conservation affecting active site formation. Repetitions in reading help in accurately determining the correct, functional conformations and may provide insights into genetic code evolution.
Step-by-step explanation:
Many of the sequences are read more than once during RNA-RNA rearrangements because RNA molecules have a tendency to fold into complex three-dimensional structures essential for their function. This intensive intramolecular base pairing leads to multiple configurations, some of which are more stable or functional than others, and thus multiple readings can lead to different structural interpretations of the RNA sequence. Moreover, evolutionary processes such as sequence variation and conservation of nucleotides in these sequences can affect the frequency and formation of active sites in RNA, which can be essential for its binding affinity and function. Therefore, duplications, deletions, and rearrangements must be read multiple times to ensure that the most suitable structure for a particular function is obtained.
For example, in the case of the Ile RNA binding site, partial conservation of nucleotides around a more conserved internal loop is necessary to form an active site. However, as RNA sequences become longer, they might fall into 'conformer hell', where the frequency of an ideal site forming decreases because of the increased possibility of alternative conformers. This necessitates repeated reading to determine the correct conformation which is functional. Additionally, repetition allows for the evaluation of RNA sequences that may have a relevant relation to the genetic code, which can be significant in understanding the evolutionary events that led to the formation of the amino acid code.