Finderons and methods of their preparation and use

A method of site-specifically cleaving a single-stranded, RNA-containing substrate, comprising the step of contacting the RNA-containing substrate with a finderon for a time sufficient for the finderon to hybridize to and cleave the RNA containing substrate, the finderon comprising:

• (a) a first flanking region comprising from four to fifteen contiguous, covalently-linked nucleotides, at least a portion of the first flanking region being complementary to a first target region located at a 3' position of a cleavage site on a substrate RNA molecule;
• (b) a second flanking region comprising from four to fifteen contiguous, covalently-linked nucleotides, at least a portion of the second flanking region being complementary to a second target region located at a 5' position of the cleavage site;
• and
• (c) a rigid linker covalently bound to a 3' terminus of the first flanking region and to a 5' terminus of the second flanking region, the linker comprising from one to twelve non-nucleotidic units maintaining the cleavage site in a trigonal bipyramidal transition state conformation, and wherein the non-nucleotidic unit is selected from the group consisting of a cyclohexane diol, asteroid, a lupene diol, an isosorbide, and combinations thereof and a linear distance of about 15 to 30 Angstroms is established between the first and second flanking regions.