AbstractsBiology & Animal Science

Part I: Targeting RNA Duplexes with Modified Triplex-Forming Oligonucleotides Triplex is emerging as an important RNA tertiary structure motif, in which consecutive base triples form between a duplex and a third strand. RNA duplex region is also often functionally important site for protein binding. Thus, Triplex-Forming Oligonucleotides (TFOs) may be developed to regulate various biological functions involving RNA such as viral ribosomal frame-shifting and reverse transcription. How chemical modification in TFOs affects RNA triplex stability, however, is not well understood. Here, we incorporated Locked Nucleic Acid (LNA), 2-thio U, and 2′-O methyl modified residues in a series of all pyrimidine RNA TFOs, and studied the binding to two RNA hairpin structures. 12-Base-triple major-groove pyrimidine•purine-pyrimidine triplex structures form between the RNA/DNA hairpins and the complementary RNA TFOs. UV-absorbance-detected thermal melting studies reveal that the LNA and 2-thio U modifications in TFOs strongly…