Trans-Acting Functional Nucleic Acid for mRNA Translation

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Solution Overview

Problem

Current methods for enhancing protein translation in eukaryotes, such as using SINEUPs, rely on mouse-derived sequences that can retrotranspose and have limited translation enhancement effect, necessitating the development of trans-regulatory elements that are specific, efficient, and derived from non-mouse sequences to effectively up-regulate gene expression for therapeutic applications.

Innovation Solution

A trans-acting functional nucleic acid molecule comprising a target binding sequence and a regulatory IRES sequence, which hybridizes to specific mRNAs and enhances translation using IRES sequences from human viruses or genes, allowing for gene-specific translation up-regulation without affecting mRNA levels and avoiding retrotransposition risks.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If SINEUPs using mouse-derived sequences are used to enhance translation, then translation enhancement effect is achieved, but retrotransposition risks and limited specificity occur

Engineering Contradiction:

Improvetranslation enhancement effectVSAvoidretrotransposition risks

Core Design Contradiction:

ProductivityVSReliability

Solution Approach 1:

The patent extracts the problematic mouse-derived SINE element from the functional nucleic acid molecule and replaces it with human-derived IRES sequences. This removal eliminates the retrotransposition risk while preserving the translation enhancement function through the IRES element's ability to recruit ribosomes to target mRNAs.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent changes the origin parameter of the effector domain from mouse-derived to human-derived sequences. This parameter change maintains the functional capability for translation enhancement while eliminating the harmful retrotransposition activity associated with mouse SINE elements in human cells.

Inventive Principle:

Principle #35Parameter changes

2Productivity

If cis-regulation of translation enhancement is used, then specific gene translation up-regulation is achieved, but it cannot be used for endogenously expressed mRNAs

Engineering Contradiction:

Improvetranslation up-regulation of endogenous mRNAsVSAvoidapplicability to endogenous mRNAs

Core Design Contradiction:

ProductivityVSAdaptability or versatility

Solution Approach 1:

The patent inverts the regulatory approach from cis-regulation (modifying the mRNA itself) to trans-regulation (using separate functional nucleic acid molecules that bind to target mRNAs). This inversion enables the translation enhancement mechanism to work on endogenously expressed mRNAs without requiring prior modification of the endogenous transcripts.

Inventive Principle:

Principle #13The other way round (Inversion)

Solution Approach 2:

The patent introduces functional nucleic acid molecules as intermediary agents that mediate between the translation initiation machinery and endogenous mRNAs. These molecules bind to specific sequences on endogenous mRNAs and recruit ribosomes, thereby enhancing translation without direct modification of the endogenous transcripts.

Inventive Principle:

Principle #24Intermediary (Mediator)

3Productivity

If existing translation enhancement methods are used, then protein translation is enhanced, but the enhancement effect is limited in potency

Engineering Contradiction:

Improveprotein translation enhancementVSAvoidtranslation enhancement potency

Core Design Contradiction:

ProductivityVSQuantity of substance

Solution Approach 1:

The patent creates a composite functional nucleic acid molecule combining a binding domain (complementary to target mRNA) with an effector domain (human IRES sequence). This composite structure integrates the specificity of binding with the potent translation enhancement capability of human IRES elements, achieving superior translation enhancement compared to existing methods.

Inventive Principle:

Principle #40Composite materials

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 solution achieves higher and more specific protein translation enhancement compared to existing methods, with IRES sequences demonstrating increased potency and safety by avoiding mouse-derived sequences and retrotransposition risks, while maintaining a modular and efficient delivery mechanism.

Implementation Method 1

The functional nucleic acid molecule hybridizes to a target mRNA sequence

Methodology Applied

Scientific EffectHybridization:

Implementation Method 2

a structured RNA element termed Internal Ribosome Entry Site (IRES) recruits the 40S ribosomal subunit

Methodology Applied

Scientific EffectTranslation enhancement:

Data Source

PatentUS11649456B2Functional nucleic acid molecule and use thereof

Publication Date: 2023.05.16 S I S SCUOLA INTERNAZ SUPERIORE DI STUDI AVANZATI

AI summary

There is disclosed a trans-acting functional nucleic acid molecule comprising a eukaryotic target binding sequence comprising a sequence reverse complementary to a target mRNA sequence for which protein translation is to be enhanced, and a regulatory sequence comprising an internal ribosome entry site (IRES) sequence or an internal ribosome entry site (IRES) derived sequence and enhancing translation of the target mRNA sequence, wherein the regulatory sequence is located 3′ of the target binding sequence.