Modified dsRNA with Nucleotide Overhangs for Serum Stability

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Solution Overview

Problem

Current RNA interference methods using double-stranded RNA (dsRNA) face challenges due to instability in bodily fluids, leading to low efficacy and rapid degradation, which limits their bioavailability and effectiveness in silencing target genes.

Innovation Solution

Development of modified dsRNA with a nucleotide overhang of 1 to 4 nucleotides and chemically modified nucleotides, specifically designed to enhance stability and bioavailability by increasing resistance to chemical and enzymatic degradation, allowing for improved serum stability and targeted gene silencing.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If standard dsRNA is used for RNA interference, then gene silencing can be achieved, but the dsRNA is rapidly degraded by nucleases in serum and cells, resulting in low bioavailability and reduced effectiveness

Engineering Contradiction:
ImprovedsRNA stabilityVSAvoiddsRNA half-life in serum
Core Design Contradiction:
ReliabilityVSDuration of action of moving object

Solution Approach 1:

The patent applies parameter changes by modifying the chemical structure of nucleotides within the dsRNA molecule. Specifically, it incorporates nucleotides with 2′-O-alkyl modifications (such as 2′-O-methyl, 2′-O-ethyl, 2′-O-propyl groups) and locked nucleotide analogs that alter the sugar pucker and conformational flexibility. These chemical parameter modifications increase resistance to nucleases while maintaining RNAi activity, thereby improving stability and half-life in serum without sacrificing gene silencing effectiveness

Inventive Principle:
Principle #35Parameter changes

Solution Approach 2:

The patent employs composite materials by creating dsRNA molecules that combine modified nucleotides with unmodified nucleotides in specific ratios and positions. The composite structure includes 2′-O-alkyl modified nucleotides, locked nucleotide analogs, and natural nucleotides arranged to optimize both stability and RNAi function. This composite approach allows the molecule to benefit from the enhanced nuclease resistance of modified components while retaining the functional capabilities of natural RNA structures

Inventive Principle:
Principle #40Composite materials

2Reliability

If chemically modified nucleotides are incorporated into dsRNA to increase stability, then resistance to degradation improves, but the complexity of synthesis and manufacturing increases

Engineering Contradiction:
ImprovedsRNA nuclease resistanceVSAvoiddsRNA synthesis complexity
Core Design Contradiction:
ReliabilityVSEase of manufacture

Solution Approach 1:

The patent applies local quality by strategically placing modified nucleotides at specific positions within the dsRNA sequence rather than uniformly modifying all nucleotides. The modifications are concentrated at the 3′ ends of the strands and at positions most susceptible to nuclease attack, while internal regions may use unmodified or less complex modifications. This localized approach maximizes protective effect while minimizing synthesis complexity and cost

Inventive Principle:
Principle #3Local quality

Solution Approach 2:

The patent implements partial action by incorporating modified nucleotides at specific percentages (e.g., 1-10 modified nucleotides per 22-nucleotide strand) rather than full modification. This partial modification approach provides sufficient nuclease resistance to achieve the desired stability improvement while keeping synthesis procedures manageable and costs acceptable for therapeutic development

Inventive Principle:
Principle #16Partial or excessive action

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 modified dsRNA demonstrates increased stability and bioavailability, enabling more effective silencing of target genes with reduced dosages, thus offering a promising therapeutic approach for diseases caused by abnormal gene expression.

Implementation Method 1

double-stranded RNA molecules (dsRNA) have been shown to block gene expression by virtue of a highly conserved regulatory mechanism known as RNA interference (RNAi)

Methodology Applied
Scientific EffectRNA interference (RNAi):

Implementation Method 2

the RNA III Dicer enzyme processes dsRNA into small interfering RNA (siRNA) of approximately 22 nucleotides

Methodology Applied
Scientific EffectEnzymatic degradation: Enzyme

Implementation Method 3

One strand of the siRNA (the 'complementary strand') then serves as a guide sequence to induce cleavage of messenger RNAs (mRNAs) comprising a nucleotide sequence which is at least partially complementary to the sequence of the complementary strand by an RNA-induced silencing complex (RISC)

Methodology Applied
Scientific EffectEnzymatic cleavage: Enzyme

Data Source

PatentUS7786290B2Double-stranded ribonucleic acid with increased effectiveness in an organism
Publication Date: 2010.08.31 ALNYLAM PHARMACEUTICALS INC
  • US7786290B2 patent drawing
  • US7786290B2 patent drawing
  • US7786290B2 patent drawing

AI summary

The present invention relates to a method for the targeted selection of a double-stranded ribonucleic acid (dsRNA) consisting of two single strands that exhibits increased effectiveness in inhibiting the expression of a target gene by means of RNA interference, wherein at least end of the dsRNA comprises a nucleotide overhang of 1 to 4 unpaired nucleotides in length; wherein the unpaired nucleotide adjacent to the terminal nucleotide pair comprises a purine base; and wherein the terminal nucleotide pair on both ends of the dsRNA is a G-C pair, or at least two of the last four consecutive terminal nucleotide pairs are G-C pairs.