Synthetic Circular RNA IRES Design for Cap-Independent Expression

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Solution Overview

Problem

Existing gene therapies using DNA face risks of genomic integration and limited protein expression due to dependency on transcription factors, while natural IRES elements are lengthy, complex, and prone to immune rejection, lacking systematic methods for efficient cap-independent protein expression.

Innovation Solution

Development of synthetic IRES elements and circular RNA polynucleotides with engineered IRES-like sequences for controlled protein expression, using constructs like Formulae I-IV, and methods to identify and optimize these sequences for therapeutic applications.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If natural IRES elements are used for cap-independent translation, then protein expression is enabled, but the sequence length becomes excessively large and complex secondary structures form

Engineering Contradiction:

Improveprotein expression efficiencyVSAvoidIRES sequence length

Core Design Contradiction:

ProductivityVSLength of stationary object

Solution Approach 1:

The patent segments the traditional long IRES element into a shortened synthetic sequence that retains essential functional motifs. By identifying and preserving only the critical nucleotide regions required for ribosome binding and cap-independent translation initiation, the design achieves functional equivalence with natural IRES while reducing sequence length and structural complexity.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent modifies key parameters of the IRES sequence including nucleotide composition, length, and secondary structure characteristics. By optimizing these parameters—specifically reducing length while maintaining or enhancing ribosome accessibility—the synthetic IRES achieves efficient cap-independent translation without the excessive length and complex folding of natural elements.

Inventive Principle:

Principle #35Parameter changes

2Productivity

If natural IRES elements are used, then cap-independent translation is achieved, but host cell immune rejection occurs

Engineering Contradiction:

Improvetranslation efficiencyVSAvoidimmune rejection

Core Design Contradiction:

ProductivityVSObject-affected harmful factors

Solution Approach 1:

The patent creates a synthetic copy of the IRES function using artificially designed sequences that mimic the essential features of natural IRES elements without containing the full native sequence. This synthetic copy enables cap-independent translation while avoiding immune recognition, as the shortened and modified sequence does not trigger the host cell's immune response mechanisms that natural viral or cellular IRES elements would activate.

Inventive Principle:

Principle #26Copying

3Stability of the object's composition

If DNA is used for gene therapy, then stability and ease of manipulation are achieved, but genomic integration and anti-DNA antibody generation occur

Engineering Contradiction:

Improvenucleic acid stabilityVSAvoidgenomic integration risk

Core Design Contradiction:

Stability of the object's compositionVSObject-generated harmful factors

Solution Approach 1:

The patent employs RNA as a temporary, non-integrating carrier for gene delivery. Unlike DNA which can persist and integrate into the genome, the RNA-based circular polynucleotide is designed to be transient—it performs its function of encoding and translating the therapeutic protein then degrades naturally without long-term persistence. This disposable approach eliminates genomic integration risks while maintaining sufficient stability for therapeutic efficacy.

Inventive Principle:

Principle #27Cheap short-living objects (Disposable)

4Adaptability or versatility

If DNA transcription is dependent on transcription factors, then specific gene regulation is achieved, but protein expression becomes limited when factors are absent

Engineering Contradiction:

Improvegene expression controlVSAvoidprotein expression level

Core Design Contradiction:

Adaptability or versatilityVSProductivity

Solution Approach 1:

The patent inverts the traditional transcription-dependent expression paradigm by using a cap-independent translation mechanism. Instead of relying on transcription factors to initiate gene expression at the DNA level, the system uses an internal ribosome entry site that directly recruits ribosomes to the mRNA template, bypassing the need for transcriptional activation. This inversion enables constitutive protein expression regardless of the presence or absence of specific transcription factors.

Inventive Principle:

Principle #13The other way round (Inversion)

Data Source

PatentUS20250320519A1Synthetic circular RNA compositions and methods of use thereof

Publication Date: 2025.10.16 SHANGHAI CIRCODE BIOMED CO LTD

AI summary

The present disclosure relates to compositions, methods, processes, kits and devices for the selection, design, preparation, manufacture, formulation, and/or use of a polynucleotide having an Internal Ribosome Entry Site (IRES) sequence, an IRES-like sequence or a combination thereof. In particular, the present disclosure relates to compositions, methods, processes, kits and devices for the selection, design, preparation, manufacture, formulation, and/or use of a circular polynucleotide (e.g., a circular RNA). The present disclosure also relates to a method of improving expression, functional stability, immunogenicity, ease of manufacturing and/or half-life of a therapeutic product encoded by the circular RNA.