Mapping Targetable Sites on Human Telomerase RNA Pseudoknot/Template Domain Using 2′-OMe RNA-interacting Polynucleotide (RIPtide) Microarrays
Berkovitch, Shaunna S.
Santos, Webster L.
Kutchukian, Peter S.
Pawloski, Adam R.
Verdine, Gregory L.
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CitationGude, Lourdes, Shaunna S. Berkovitch, Webster L. Santos, Peter S. Kutchukian, Adam R. Pawloski, Robert Kuimelis, Glenn McGall, and Gregory L. Verdine. 2012. “Mapping Targetable Sites on Human Telomerase RNA Pseudoknot/Template Domain Using 2′-OMe RNA-Interacting Polynucleotide (RIPtide) Microarrays.” Journal of Biological Chemistry287 (22): 18843–53. https://doi.org/10.1074/jbc.M111.316596.
AbstractMost cellular RNAs engage in intrastrand base-pairing that gives rise to complex three-dimensional folds. This self-pairing presents an impediment toward binding of the RNA by nucleic acid-based ligands. An important step in the discovery of RNA-targeting ligands is therefore to identify those regions in a folded RNA that are accessible toward the nucleic acid-based ligand. Because the folding of RNA targets can involve interactions between nonadjacent regions and employ both Watson-Crick and non-Watson-Crick base-pairing, screening of candidate binder ensembles is typically necessary. Microarray-based screening approaches have shown great promise in this regard and have suggested that achieving complete sequence coverage would be a valuable attribute of a next generation system. Here, we report a custom microarray displaying a library of RNA-interacting polynucleotides comprising all possible 2'-OMe RNA sequences from 4- to 8-nucleotides in length. We demonstrate the utility of this array in identifying RNA-interacting polynucleotides that bind tightly and specifically to the highly conserved, functionally essential template/pseudoknot domain of human telomerase RNA and that inhibit telomerase function in vitro.
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