Nucleic Acids Research Advance Access published online on June 26, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp549
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Discovering ligands for a microRNA precursor with peptoid microarrays
Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9185, USA
*To whom correspondence should be addressed. Tel: +214 648 4054; Fax: +214 648 4156; Email: Kevin.Luebke{at}utsouthwestern.edu
Received May 19, 2009. Revised June 10, 2009. Accepted June 11, 2009.
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 µM 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.