Single-Strand Nucleic Acid Molecule for Gene Expression Control

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Solution Overview

Problem

Current methods for inhibiting gene expression, such as RNA interference, face challenges including low manufacturing efficiency for siRNA and difficulties in synthesizing circular RNA molecules, as well as laborious conditions required for maintaining siRNA stability within cells.

Innovation Solution

A single-stranded RNA molecule with a specific structure comprising a 5' side region, an inner region with an expression inhibitory sequence, and a 3' side region, linked via non-nucleotide residues, allowing for efficient production and intramolecular folding without the need for annealing, thereby inhibiting gene expression.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If siRNA is used to inhibit gene expression, then gene expression inhibition is achieved, but manufacturing efficiency is low due to separate synthesis and hybridization of sense and antisense strands

Engineering Contradiction:

Improvemanufacturing efficiencyVSAvoidprocess complexity

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent combines the sense and antisense strands into a single-stranded RNA molecule that contains both sequences. The molecule includes a 5' region with sense sequence, a middle region, and a 3' region with antisense sequence, all connected in one continuous strand. This eliminates the need for separate synthesis and hybridization steps, directly resolving the manufacturing efficiency problem.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The single-stranded RNA is segmented into functional regions: a 5' region (sequence A), a middle region (sequence B), and a 3' region (sequence C). Each region has specific length requirements (A: 1-10 nt, B: 10-30 nt, C: 1-10 nt) that enable the molecule to form secondary structures for gene silencing while simplifying production.

Inventive Principle:

Principle #1Segmentation

2Reliability

If siRNA is administered to cells, then gene expression inhibition is achieved, but laborious conditions are required to maintain stability and prevent dissociation to single-stranded RNAs

Engineering Contradiction:

ImprovesiRNA stabilityVSAvoidhandling complexity

Core Design Contradiction:

ReliabilityVSEase of operation

Solution Approach 1:

The single-stranded RNA molecule is designed to self-fold into stable secondary structures through intramolecular base pairing between the 5' region and 3' region. This self-structuring capability eliminates the need for external stabilization measures or complex handling conditions, as the molecule maintains its functional conformation autonomously within cells.

Inventive Principle:

Principle #25Self-service

3Reliability

If circular RNA molecules are used for gene expression inhibition, then partial double-stranded structure is achieved through intermolecular annealing, but synthesis is difficult

Engineering Contradiction:

Improvedouble-stranded structure formationVSAvoidsynthesis difficulty

Core Design Contradiction:

ReliabilityVSEase of manufacture

Solution Approach 1:

Instead of using circular RNA that requires intermolecular annealing of separate strands, the patent inverts the approach by using a single-stranded RNA that forms intramolecular double-stranded regions through internal base pairing. This inversion simplifies synthesis while achieving the same functional double-stranded structure needed for gene silencing.

Inventive Principle:

Principle #13The other way round (Inversion)

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 single-stranded RNA molecule effectively inhibits gene expression by a mechanism similar to RNA interference, offering improved manufacturing efficiency and stability within cells, reducing off-target effects and simplifying production processes.

Implementation Method 1

a double strand is formed by fold-back of the region (Xc) towards the region (X) and self annealing of the regions (Xc) and (X)

Methodology Applied

Scientific EffectSelf-annealing:

Implementation Method 2

a double strand is formed by fold-back of the region (Yc) towards the region (Y) and self annealing of the regions (Yc) and (Y)

Methodology Applied

Scientific EffectSelf-annealing:

Data Source

PatentEP2933333B1Single-strand nucleic acid molecule for controlling gene expression

Publication Date: 2018.02.21 BONAC CORP

Figure 1A~2B
Figure 3A~3D
Figure 4~5

AI summary

Provided is a novel nucleic acid molecule capable that can inhibit the expression of a gene and can be produces easily and efficiently. The nucleic acid molecule contains is a single-stranded nucleic acid molecule including an expression inhibitory sequence that inhibits expression of a target gene. The single-stranded nucleic acid molecule includes, in sequence from the 5' side to the 3' side: a 5' side region (Xc); an inner region (Z); and a 3' side region (Yc). The inner region (Z) is composed of an inner 5' side region (Xc) and an inner 3' side region (Y) that are linked to each other. The 5' side region (Xc) is complementary to the inner 5' side region (X). The 3' side region (Yc) is complementary to the inner 3' side region (Y). A linker region (Lx) is present between the 5' side region (Xc) and the inner 5' side region (X). The 5' side region (Xc) and the inner 5' side region (X) are linked to each other via the linker region (Lx). The linker region (Lx) comprises a non-nucleotide residue. At least one of the inner region (Z), the 5' side region (Xc), and the 3' side region (Yc) includes the expression inhibitory sequence. According to this single-strand nucleic acid molecule, it is possible to inhibit the expression of the target gene.