Generating the databases of RNA helices and loops. A list of all possible helices of lengths from 3 to 10 bp, composed of only canonical A-U and G-C base pairs, was trimmed by removing helices with more than three consecutive base pair repeats, by removing helices with strands that form intramolecular pairs, and by removing helices with high ensemble defect. The list was trimmed further by removing helices with high propensity to cross-hybridize with other helices in the list. To generate a list of sequences to use as loops, a list of all possible sequences of lengths from 3 to 10 nt was trimmed by removing sequences with more than three consecutive repeating nucleotides, and by removing sequences that can form intramolecular pairs. The list was trimmed further by removing sequences with high propensity of forming pairs with the final helix list and by removing sequences that can form self-complementary duplexes. The list was trimmed further by removing sequences with high propensity to cross-hybridize.
