If you want to design puzzles based on naturally-occurring RNAs, consider searching for a sequence in one of the online secondary structure databases listed below. You may have to break pseudoknots to create your puzzle. For structures represented in dot-bracket notation, this can be done by substituting a "." for symbols other than parentheses.
| Name | Description |
| RNA STRAND | Over 4000 secondary structures from a variety of sources. Structures available in dot-bracket notation. |
| Rfam | A collection of RNA families. Secondary structures must be saved through the VARNA applet. |
| fRNAdb | A database of noncoding RNAs. |
| Subviral RNA Database | A database of subviral agents. |