Sulfur-Based Oligonucleotide Protection for Mild Deprotection
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Solution Overview
Problem
Existing oligonucleotide synthesis technologies cannot incorporate sensitive functional groups due to the use of harsh conditions that destroy these groups, limiting their application in molecular biology, biomedical research, and medicine.
Innovation Solution
Utilization of sulfur-based protecting groups and linkers that remain stable during synthesis and can be efficiently cleaved under nearly neutral and non-nucleophilic conditions, allowing for the incorporation of sensitive groups like esters and alkyl halides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional acyl group-based protecting groups and linkers are used in oligonucleotide synthesis, then the synthesis process can be completed using standard conditions, but the sensitive functional groups (esters, alkyl halides, etc.) cannot survive the harsh cleavage conditions required to remove the protecting groups
Solution Approach 1:
The patent changes the chemical parameters of the protecting groups from traditional acyl groups to sulfur-based groups (such as phenylthio, methylthio, ethylthio). These sulfur-based groups have different chemical stability properties that allow them to withstand the harsh basic and nucleophilic conditions used in oligonucleotide synthesis while still enabling removal under controlled conditions, thus resolving the contradiction between stability and manufacturability
Solution Approach 2:
The sulfur-based protecting groups act as intermediaries that bridge the conflicting requirements: they are stable enough to protect sensitive groups during synthesis but can be removed under conditions that are mild enough to preserve the sensitive functional groups. The sulfur atom serves as a mediator between the harsh synthesis environment and the delicate sensitive groups
2Productivity
If harsh nucleophilic and basic conditions are used to cleave protecting groups, then the protecting groups can be removed efficiently, but the sensitive functional groups are destroyed
Solution Approach 1:
The patent changes the deprotection mechanism by using sulfur-based groups that can be removed under milder conditions. The sulfur-based protecting groups undergo cleavage through mechanisms that do not require the same harsh nucleophilic and basic conditions as traditional acyl groups, thus maintaining productivity while eliminating the harmful effect on sensitive groups
Solution Approach 2:
The patent converts the potential harm of needing harsh conditions for deprotection into a benefit by designing sulfur-based groups that inherently allow milder removal conditions. The sulfur atom's unique chemical properties enable selective cleavage that protects sensitive groups while still achieving efficient deprotection
3Adaptability or versatility
If conventional protecting groups are used, then standard synthesis procedures can be applied, but sensitive functional groups cannot be incorporated into oligonucleotides
Solution Approach 1:
The patent changes the chemical parameters of the protecting groups to sulfur-based variants that are compatible with sensitive functional groups. This parameter change enables the incorporation of esters, alkyl halides, and other sensitive groups into oligonucleotides while maintaining their stability throughout the synthesis and purification processes
Solution Approach 2:
The sulfur-based protecting groups provide universal compatibility with multiple types of sensitive functional groups. A single protecting group system can protect both amino groups and preserve sensitive groups like esters and alkyl halides, enabling versatile synthesis of oligonucleotides with various sensitive modifications
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
Enables the synthesis of oligonucleotides containing sensitive groups without premature deprotection, enhancing their application in molecular biology, biomedical research, and medicine.
Implementation Method 1
sulfur-based protecting groups and linkers that remain stable during synthesis and can be efficiently cleaved under nearly neutral and non-nucleophilic conditions
Data Source
AI summary
Embodiments for the synthesis of sensitive oligonucleotides as well as insensitive oligonucleotides are provided. Sulfur-based groups are used for the protection of exo-amino groups of nucleobases, phosphate groups and 2′-OH groups, and as cleavable linker for linking oligonucleotides to a support. Oligonucleotide syntheses are achieved under typical conditions using phosphoramidite chemistry with important modifications. To prevent replacing sulfur-based protecting groups by acyl groups via cap-exchange, special capping agents are used. To retain hydrophobic tag to assist RP HPLC purification, special phosphoramidites are used in the last synthetic cycle. With the sulfur-based groups for protection and linking, oligonucleotide deprotection and cleavage are achieved via oxidation followed by beta-elimination under mild conditions. Therefore, besides for insensitive oligonucleotide synthesis, the embodiments of the invention are capable for the synthesis of oligonucleotide analogs containing sensitive functional groups that cannot survive the harsh conditions used in prior art oligonucleotide synthesis technologies.