Shape RNA Structure Analysis for Drug Discovery and Translational Research

DESCRIPTION provided by applicant Roughly of the human genome is transcribed into RNA and in most of these RNAs complex higher order structures underlie or fundamentally affect critical biological processes RNA structures are the targets of many antibiotics and RNA structure should be further exploited in small molecule drug discovery efforts For example structures in the genomes of RNA viruses like HIV and influenza are essential for viral replication and pathogenesis Half of the single nucleotide polymorphisms that are most strongly associated with human diseases occur in non coding regions and are likely associated with abnormal RNA structures Many nucleic acid based therapeutics including clinically important antisense and siRNA approaches only work when exceedingly rare high affinity and structurally accessible sites are targeted The Weeks laboratory has developed a chemical probing strategy called SHAPE MaP that accurately reports on RNA structure in physiologically relevant contexts This technology enables nucleotide resolution RNA structure analysis information to be read out by massively parallel sequencing Although independent groups describe SHAPE as the andquot gold standardandquot of RNA structure analysis in its current form SHAPE MaP represents a cutting edge but research grade technology The long term vision of Ribometrix is to make SHAPE MaP a platform technology with applications in drug discovery translational research and basic biological discovery In this work we will conduct proof of concept studies to solve impediments to adoption of SHAPE MaP by non expert laboratories via two aims to create and experimentally validate diagnostic controls to enable efficient evaluation and troubleshooting of a prototype SHAPE MaP RNA structure analysis pipeline by non expert users and to examine and optimize formulation of SHAPE reagents for consistent handling Progress to Phase will be justified by data showing that novice users are able to implement and diagnose RNA structure probing experiments using easily handled long lifetime reagents consistent with quantitative benchmarks In Phase Ribometrix will automate the downstream computational steps required to fully interpret SHAPE MaP experiments and will create complete industrialized reagent platforms for use by pharmaceutical and academic customers and collaborators Successful development of a user friendly SHAPE technology platform will enable researchers in all areas of biomedical science to perform robust quantitative experiments that explore the fundamental role of RNA in biology and that facilitate creation of RNA based and RNA directed therapeutics PUBLIC HEALTH RELEVANCE To explore the fundamental role of RNA in biology and to facilitate creation of RNA based and RNA directed therapeutics it is essential to understand the complex higher order structures of RNA transcripts To enable accurate analysis of RNA structure in physiologically relevant contexts Ribometrix proposes to develop a user friendly SHAPE MaP technology platform that allows novice users to implement RNA structure probing experiments using easily handled long lifetime reagents Widespread and robust access to SHAPE technology will transform design of mRNA and antisense therapeutics discovery of novel RNA targets and analysis and validation of small molecule RNA interactions