L-RNA Aptamer Targeting APP 3′-UTR G4 Structure
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Solution Overview
Problem
Current G4-targeting tools lack sufficient selectivity to distinguish between different G-quadruplex (G4) structures, limiting their precision in targeting specific G4 motifs associated with diseases like Alzheimer's.
Innovation Solution
Development of a novel L-RNA aptamer specific to the 3′-UTR of APP mRNA, characterized by a loop region that recognizes and binds to the G4 structure at the 3′-UTR of APP mRNA, enhancing binding specificity and efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional G4-targeting tools (chemicals or antibodies) are used, then binding preference to G4 motifs is achieved, but selectivity to distinguish between different G4s is insufficient
Solution Approach 1:
The patent segments the G4-targeting approach by developing aptamers that recognize specific structural features of particular G4s (such as loop sequences or stacking patterns) rather than using generic G4-binding tools. This allows differentiation between various G4 types (e.g., APP 3'UTR G4 versus other G4s) while maintaining binding preference.
Solution Approach 2:
The aptamers are designed to bind to specific local regions or structural motifs within G4 structures (such as particular loop sequences or stacking configurations) rather than binding uniformly to all G4s. This local specificity enables the tools to distinguish between different G4s based on their unique structural characteristics.
2Strength
If L-RNA aptamers are developed using standard SELEX, then binding affinity is achieved, but binding specificity is non-ideal due to off-target binding
Solution Approach 1:
The patent employs modified SELEX conditions and criteria to select aptamers with enhanced specificity. By adjusting selection stringency, using structured target sequences, and applying computational filtering, the process identifies aptamers that maintain high binding affinity while minimizing off-target binding to non-G4 structures or other G4s.
Solution Approach 2:
The SELEX process incorporates feedback mechanisms where binding assays continuously evaluate aptamer performance against both target and non-target sequences. This feedback loop allows iterative refinement of the aptamer pool to eliminate off-target binders while preserving affinity for the intended target.
3Productivity
If existing G4-targeting tools are used to control APP expression, then APP translation is inhibited, but precision targeting of APP 3'UTR G4 is not achieved
Solution Approach 1:
The patent segments the APP mRNA 3'UTR region to specifically target the G4 structure located in this region, rather than using broad-spectrum G4 inhibitors that affect multiple genes. This localized targeting precision ensures that APP translation is inhibited without off-target effects on other proteins.
Solution Approach 2:
The aptamers serve as intermediary molecules that specifically bind to the APP 3'UTR G4 structure, blocking the translation process. This intermediary approach provides precise control over APP expression by directly interfering with the specific G4 structure required for translation, rather than using non-specific inhibition methods.
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
The novel L-RNA aptamer effectively binds to the APP 3′-UTR G4 structure, demonstrating improved specificity and affinity compared to existing tools, and has the potential to alleviate symptoms associated with Alzheimer's disease by regulating APP expression.
Implementation Method 1
L-RNA aptamers are composed of L-RNA (enantiomeric form of naturally occurring D-RNA) that is unnatural, so they cannot be recognized by nucleases and cannot not trigger immunogenicity
Implementation Method 2
Guanine (G)-rich sequences in DNA and RNA can form into nucleic acid structure motifs referred to as G-quadruplex (G4) structures, which are assembled by two or more G-tetrads that are connected by loop nucleotides
Data Source
AI summary
Disclosed herein is an L-RNA aptamer specific to 3′-untranslated region (3′-UTR) of amyloid precursor protein (APP) messenger RNA (mRNA). According to some embodiments of the present disclosure, the L-RNA comprises the nucleotide sequence of SEQ ID NO: 1. Also disclosed herein are a recombinant polynucleotide derived from the L-RNA aptamer, and uses of the L-RNA aptamer in treating Alzheimer's disease (AD).