RNA Higher-Order Structure Analysis via Hoogsteen Base Pair Targeting
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Solution Overview
Problem
Current methods for detecting RNA higher-order structures, such as those involving Watson-Crick base pairs, struggle to identify non-Watson-Crick base-paired structures like G4, and existing techniques are inefficient in obtaining information from multiple modification sites within a single RNA molecule, leading to incomplete structure representation.
Innovation Solution
A method utilizing reactive OFF-ON type alkylating agents covalently bonded to low molecular weight compounds for mutational profiling, which involves contacting the agent with RNA, determining the nucleotide sequence, and identifying interaction regions to efficiently detect a wider range of RNA higher-order structures, including non-Watson-Crick base-paired ones.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If Watson-Crick base pair focused methods are used, then standard RNA structure detection is achieved, but non-Watson-Crick base-paired structures like G4 cannot be identified
Solution Approach 1:
The patent changes the detection parameter from Watson-Crick base pair specificity to Hoogsteen base pair specificity. By using Hoogsteen base pair-specific modifying molecules that react with Hoogsteen base pairs, the method enables detection of non-Watson-Crick structures like G4 while maintaining reliable identification through sequence information preservation.
Solution Approach 2:
The patent introduces Hoogsteen base pair-specific modifying molecules as intermediaries. These molecules selectively bind to and modify Hoogsteen base pairs, serving as mediators that enable the detection of non-Watson-Crick structures without interfering with the underlying sequence information.
2Loss of information
If existing modification reactions are used, then structure information is obtained, but sequence information is lost
Solution Approach 1:
The patent segments the RNA molecule into modified regions (where Hoogsteen base pairs are targeted) and unmodified regions (where sequence information is preserved). By selectively modifying only specific base pairs while leaving the rest of the sequence intact, both structure and sequence information can be obtained simultaneously.
Solution Approach 2:
The patent creates a copy of the RNA sequence through cDNA synthesis that preserves the original sequence information even at modified positions. The Hoogsteen base pair modification affects structure detection but does not alter the underlying sequence, allowing the sequence to be copied and analyzed intact.
3Productivity
If multiple modification sites are analyzed, then comprehensive structure information is obtained, but analysis efficiency decreases
Solution Approach 1:
The patent makes the Hoogsteen base pair-specific modifying molecule universal for detecting various types of non-Watson-Crick structures. A single modifying molecule can target multiple Hoogsteen base pairs throughout the RNA molecule, enabling simultaneous detection of multiple structural features without requiring separate analysis for each site.
Solution Approach 2:
The patent merges the detection of multiple Hoogsteen base pair modifications into a single analytical process. By using parallel sequencing to detect all modification sites simultaneously, the method combines multiple structure detection tasks into one efficient analysis, maintaining complete structure representation while improving productivity.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach allows for the precise and efficient detection of various RNA higher-order structures, including those formed by Hoogsteen base pairs, without losing sequence information, enabling a more comprehensive understanding of RNA structures and their functions.
Implementation Method 1
reactive OFF-ON type alkylating agents covalently bonded to low molecular weight compounds
Implementation Method 2
reactive OFF-ON type alkylating agents in which the small molecule compound remains a stable precursor until it is in proximity to the target DNA or RNA and is activated at the target site
Data Source
AI summary
The present disclosure provides a technique for efficiently detecting a wider variety of RNA higher-order structures including non-Watson-Crick base pair-type higher order structures. The method for analyzing the RNA higher-order structure according to the present disclosure comprises the steps of providing a compound in which a target-binding moiety Sm and an RNA-modifying moiety Y are linked by a linker L; contacting the compound and one or a plurality of RNAs; determining a nucleotide sequence of the RNA after contacting with the compound; and determining a position and/or a region on the RNA that interacts with the target binding moiety of the compound, based on the nucleotide sequence.