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Described in reference 1. An unexpected pattern has been discovered in ribosomal RNA sequences, in which certain sub-structures also have certain biases in their nucleotide composition. Thus, for example, internal loops have certain reproducible tendencies that are different from helices or junctions. These compositional biases appear to come from the folding process itself. This should help recognize the correct structures for new RNAs whose 3D structure is, as yet, unknown.

Described in reference 2. Surprisingly, simple sequences do not become more and more frequent as RNAs of randomized sequence get longer and longer. Instead, small active sequence motifs are optimally present (and in numbers in agreement with theoretical predictions) in populations of RNA with random tracts 50 to 70 nucleotides in length. This is important because the shorter, more useful molecules are those that might have been expected in a prebiotic ancient population.

Described in reference 3. Abundance of active molecules of specified structure can be predicted in randomized RNA sequence populations, using new approximations and algorithms. This is clearly important to the study of the probability of emergence of complex molecular function from such random sequence populations as might have happened in an RNA world. This is true even if the probability, not only of the presence of the correct sequences, but the probabilities that they fold into the active motif, are taken into account.

Described in reference 4. The genetic code minimizes the damage done by mutations and mistakes by maximizing the relation between the codons for chemically similar amino acids. The genetic code also forms binding sites of RNA for amino acids by selectively using codons and anticodons in the binding site sequences for amino acids. It was shown here that these two properties are independent; that is, though they co-exist in the modern code and are consistent, they do not imply each other.

Described in reference 5. The genetic code’s sequences for L-histidine selectively recur within the active sites of RNAs selected to bind L-histidine.