Final Report Summary - NONCODOWN (Optimizing Antisense Oligonucleotides for Efficient and Specific Knockdown of Nuclear Non-Coding RNA)
The past decade has seen a dramatic increase in discovery of noncoding RNA with functional regulatory roles in the nucleus of mammalian cells. Yet tools to manipulate these nuclear noncoding RNAs remain inadequate. This project has taken a multi-pronged approach to technology development for silencing nuclear RNAs. (1) We have developed a series of optimized antisense oligonucleotides for targeting and degrading structured RNAs by containing a partial sequence of PNA and part of DNA, joined by a conformationally locked nucleotide. (2) We have compared a number of chemical designs for silencing a nuclear-retained RNA transcript, including siRNAs, single-stranded siRNAs, and LNA-modified antisense oligonucleotides (ASOs). We found that the ASOs were by far the most potent for this task. (3) We have screened chemically modified oligonucleotides, including Locked Nucleic Acid and Peptide Nucleic Acid, for blocking the action of a bacterial regulatory ncRNA, and identified potent inhibitors.