Modified ds Oligonucleotides for Stable RNAi Delivery
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Solution Overview
Problem
Existing double-stranded oligonucleotides face limitations in therapeutic, diagnostic, and research applications due to susceptibility to nucleases and suboptimal properties such as stability and delivery efficiency.
Innovation Solution
The introduction of controlled structural elements, including backbone phosphoryl guanidine chiral centers in the Sp configuration and modified sugars, enhances the properties and activities of double-stranded oligonucleotides, such as improved stability and cellular delivery.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If naturally-occurring nucleic acids are used, then the oligonucleotides can be easily synthesized and incorporated, but they are susceptible to endo- and exo-nucleases resulting in poor stability
Solution Approach 1:
The patent applies parameter changes by modifying the chemical structure of nucleic acids through various modifications including base modifications (e.g., 5-methylcytosine), sugar modifications (e.g., 2'-O-methyl ribose, Locked Nucleic Acids), and backbone modifications (e.g., phosphorothioate linkages, morpholino backbones). These structural parameter changes confer resistance to nucleases while maintaining synthesizability, directly resolving the contradiction between ease of manufacture and stability.
Solution Approach 2:
The patent employs composite materials by creating hybrid oligonucleotide structures that combine modified and unmodified nucleotides within the same sequence. For example, certain positions may contain 2'-O-methyl ribose modifications while others contain standard ribose, or phosphorothioate linkages may be strategically placed within an otherwise DNA backbone. This composite approach optimizes both stability and manufacturability by placing modifications only where necessary.
2Reliability
If chemical modifications are introduced to improve stability, then resistance to nucleases increases, but the complexity of synthesis and characterization increases
Solution Approach 1:
The patent applies local quality by implementing modifications at specific, strategically chosen positions within the oligonucleotide sequence rather than uniformly throughout. For example, phosphorothioate linkages may be placed at the 5' and 3' ends where they provide maximum protection against exonucleases, while internal positions may use different modifications or remain unmodified. This localized approach minimizes synthesis complexity while maximizing stability benefits.
Solution Approach 2:
The patent applies partial action by introducing a limited number and type of modifications rather than comprehensively modifying every nucleotide. The modifications are applied selectively at key positions to achieve sufficient stability and functionality without the excessive complexity that would result from full modification of the entire oligonucleotide sequence.
3Reliability
If stereochemical control is implemented at backbone chiral centers, then unexpected properties and activities are achieved, but the manufacturing precision requirements increase
Solution Approach 1:
The patent applies parameter changes by controlling the stereochemistry at backbone chiral centers, specifically using Sp configuration at the phosphorothioate chiral center. This stereochemical parameter change confers unexpected improvements in stability and activity, including enhanced resistance to nucleases and improved binding affinity, while the synthesis methodology maintains reasonable manufacturing precision through established asymmetric synthesis techniques.
Data Source
AI summary
The present disclosure provides double stranded oligonucleotides, compositions, and methods relating thereto. The present disclosure encompasses the recognition that structural elements of double stranded oligonucleotides, such as base sequence, chemical modifications (e.g., modifications of sugar, base, and/or internucleotidic linkages) or patterns thereof, and/or stereochemistry (e.g., stereochemistry of backbone chiral centers (chiral internucleotidic linkages), and/or patterns thereof, can have significant impact on oligonucleotide properties and activities, e.g., RNA interference (RNAi) activity, Ago2 loading, thermal stability, in vivo stability, delivery to tissues and into cells, etc. The present disclosure also provides methods for treatment of diseases, e.g., hepatic diseases, central nervous system (CNS) diseases, etc., using provided double stranded oligonucleotide compositions, for example, in RNA interference.