Long non-coding RNAs (lncRNAs) are functional yet non-protein-coding RNAs that have crucial roles in many disease processes. For example, an 8 kb lncRNA MALAT1 is known to regulate alternative splicing and tumor progression in several cancer types. Inter-species sequence conservation at its 3’-end indicated a high degree of functionality, and a short triple helix structural domain in this region was found to be pivotal in enabling stability and consequent nuclear accumulation of this RNA. However, the interactions and dynamics of this domain in the context of the longer conserved region as well as its importance in driving oncogenic phenotypes is currently unknown. Given the growing precedence of small molecules being able to recognize RNA structural elements, this work aims to develop small molecule chemical probes to study the disease-related functions of MALAT1 structural motifs. Towards this goal, we first optimized a short synthesis of a 33-member small molecule library that was then screened against the MALAT1 triple helix domain. We obtained several ligands with sub-micromolar EC50 values towards this target, as well as modest to excellent selectivity over the non-triple helix-forming construct and general DNA and RNA controls. Next, we conducted thermal melting experiments of select ligands to determine the effect of the ligands on the triple helix stability and observed stabilizing effects. Concurrently, we are developing a high-throughput screening method to quickly identify ligands that induce different thermodynamically stable species in the context of the triple helix alone as well as potential alternative structures that may exist within the conserved region. Ultimately, this work will yield chemical probes that can be utilized for studying the individual roles of 3’-end structural elements that enable oncogenic phenotypes induced by MALAT1 in several human cancers.

Utilizing small molecule tools to identify and target structural motifs in an oncogenic long non-coding RNA

256th National Meeting (2018)

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