Construction of RNA hairpin-small molecule database to facilitate a rational and modular approach to target RNA
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RNA plays essential roles in many biological processes. Several screening methods are available to find small molecules that target on RNA 1,2 , but they fail to identify the motifs that small molecules prefer to bind and therefore do not provide enough information to rationally design small molecules targeting RNAs. A useful approach would be to construct an RNA-ligand database and then use it to search the biological systems. RNA internal loop or hairpin loop libraries can be screened to find the structures similar to those that appear in, for example, mRNAs or microRNAs. The database could then provide the information necessary to target a biologically important RNAs. The purpose of this study is to identify RNA hairpin loop motifs that prefer to bind to two aminoglycoside derivatives, 6'-N-5-hexynoate kanamycin A, 6'-N-5-hexynoate neamine, and a library of 109 peptoids. The RNA library used in this study is a six nucleotide hairpin loop library containing 4096 members. A series of 43 individual hairpins were indentified for binding to the kanamycin A derivative. A common motif was found containing A in position 1 and C in position 5 (two-tailed p -value is <0.0001). There were 35 hairpins identified for binding to the neamine derivative. A motif common to those was 5'GC and 5'CG steps (p-value is <0.0001). Finally, there were 13 hairpins identified for binding to the four peptoids, with 5'AU and 5'UA steps as the most occurring pattern.