Discovering ligands for a microRNA precursor with peptoid microarrays.
We have screened peptoid microarrays to identify specific ligands for the RNA hairpin precursor of miR-21, a microRNA involved in cancer and heart disease. Microarrays were printed by spotting a library of 7680 N-substituted oligoglycines (peptoids) onto glass slides. Two compounds on the array specifically bind RNA having the sequence and predicted secondary structure of the miR-21 precursor hairpin and have specific affinity for the target in solution. Their binding induces a conformational change around the hairpin loop, and the most specific compound recognizes the loop sequence and a bulged uridine in the proximal duplex. Functional groups contributing affinity and specificity were identified, and by varying a critical methylpyridine group, a compound with a dissociation constant of 1.9 microM for the miR-21 precursor hairpin and a 20-fold discrimination against a closely-related hairpin was created. This work describes a systematic approach to discovery of ligands for specific pre-defined novel RNA structures. It demonstrates discovery of new ligands for an RNA for which no specific lead compounds were previously known by screening a microarray of small molecules.
Chirayil
Sara
S
Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9185, USA.
Chirayil
Rachel
R
Luebke
Kevin J
KJ
D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D035683:MicroRNAs / Q000737:chemistry*; D046228:Microarray Analysis / Q000379:methods*; D034444:Peptoids / Q000737:chemistry*; D012322:RNA Precursors / Q000737:chemistry*
D008024:Ligands; D035683:MicroRNAs; D034444:Peptoids; D012322:RNA Precursors; D008274:Magnesium