title: Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays.
abstract: Most 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.
authors.affiliation: Departmens of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Lourdes
authors.initials: L
authors.lastname: Gude
authors.forename: Shaunna S
authors.initials: SS
authors.lastname: Berkovitch
authors.forename: Webster L
authors.initials: WL
authors.lastname: Santos
authors.forename: Peter S
authors.initials: PS
authors.lastname: Kutchukian
authors.forename: Adam R
authors.initials: AR
authors.lastname: Pawloski
authors.forename: Robert
authors.initials: R
authors.lastname: Kuimelis
authors.forename: Glenn
authors.initials: G
authors.lastname: McGall
authors.forename: Gregory L
authors.initials: GL
authors.lastname: Verdine
mesh_terms: D006801:Humans; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D019098:Telomerase / Q000235:genetics / Q000378:metabolism*
chemical_list: D012313:RNA; D019098:Telomerase