Cell-Based RNA Perturbation Screening Platform
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for screening small molecules against RNA structures lack a systematic approach to modulate RNA within a cellular context, failing to consider native cellular functions and structures, and are laborious for high-throughput screening across multiple targets.
Innovation Solution
A nucleic acid construct with reporter genes and RNA secondary structures is used to create a cell-based screening platform, allowing for the study of chemical or genetic perturbations on RNA structures within their endogenous genomic context, enabling multiplexed RNA structure small molecule screening.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If biochemical assays (microarray, ASMS, Alphascreen) are used to screen small molecules against RNA structures, then large chemical libraries can be screened against RNA targets, but the native cellular RNA functions and structures are not considered
Solution Approach 1:
The patent introduces a cellular intermediary system (cells expressing RNA structures with reporter genes) that mediates between small molecule screening and native RNA function assessment. This allows chemical libraries to be screened while maintaining cellular context, as the cells serve as an intermediary that preserves native RNA structures and functions during screening.
Solution Approach 2:
The patent creates a universal cell-based platform that can screen against multiple different RNA structures simultaneously. The same cellular system can be used to assess various RNA targets (G-quadruplexes, stem-loops, etc.) while maintaining native cellular context, making the system universally applicable to different RNA screening needs.
2Reliability
If cellular systems are used to screen small molecules that bind to RNA structures within cellular context, then native RNA structure is maintained, but high throughput screening across multiple targets is laborious and requires building multiple chemical libraries
Solution Approach 1:
The patent merges multiple screening capabilities into a single cell-based platform. By expressing multiple different RNA structures within the same cellular system, the patent combines what would otherwise require separate screening experiments into one unified high-throughput assay, thereby maintaining native RNA structure while enabling productive multi-target screening.
Solution Approach 2:
The patent adds a new dimension to RNA screening by moving from traditional biochemical assays to a cellular dimension. This dimensional shift allows simultaneous maintenance of native RNA structure and enabling of high-throughput capability, as the cellular environment provides both structural authenticity and scalability for multi-target screening.
3Measurement precision
If existing methods are used to identify single RNA targets, then specific RNA structures can be studied, but the effect of perturbations on large numbers of RNA structures cannot be studied systematically
Solution Approach 1:
The patent creates a universal screening platform that maintains the precision of single-target identification while adding the versatility to study multiple RNA structures systematically. The cell-based system can precisely measure effects on individual RNA targets while simultaneously enabling comparative studies across many different RNA structures through high-throughput capability.
Data Source
AI summary
This invention features nucleic acid constructs which comprises reporter genes and a query sequence, wherein the query sequences encode or are RNA folded into a secondary structure and or RNA regulatory elements. These nucleic acid constructs can be used in massively parallel assay methods for perturbation profiling also disclosed herein. Such methods provide the ability to study the effect of chemical or genetic perturbations to modulate RNA within an intracellular context.