title: Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function.
abstract: We demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally substitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement of a duplex stem with unstructured oligo-T/U strands, which are bPNA binding sites. Functional rescue was observed on refolding of the oligo-T/U strands into bPNA triplex hybrid stems. Bifacial PNA binding was thus used to allosterically switch-on protein and small-molecule binding in DNA and RNA aptamers, as well as catalytic bond scission in a ribozyme. Duplex stems that support the catalytic site of a minimal type I hammerhead ribozyme were replaced with oligo-U loops, severely crippling or ablating the native RNA splicing function. Refolding of the U-loops into bPNA triplex stems completely restored splicing function in the hybrid system. These studies indicate that bPNA may have general utility as an allosteric trigger for a wide range of functions in non-coding nucleic acids.
authors.affiliation: Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States.
authors.forename: Xin
authors.initials: X
authors.lastname: Xia
authors.forename: Xijun
authors.initials: X
authors.lastname: Piao
authors.forename: Dennis
authors.initials: D
authors.lastname: Bong
mesh_terms: D000494:Allosteric Regulation; D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D015394:Molecular Structure; D020135:Peptide Nucleic Acids / Q000737:chemistry / Q000378:metabolism*; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*
chemical_list: D052157:Aptamers, Nucleotide; D020135:Peptide Nucleic Acids; D016337:RNA, Catalytic