Rapid UnyLinker Cleavage via Ammonium Hydroxide
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Solution Overview
Problem
Current methods for cleaving oligonucleotides from solid supports, such as those using UnyLinker, are inefficient, requiring extended times and temperatures for complete deprotection and cleavage, especially when using 3′ oxy-LNA nucleosides.
Innovation Solution
Treating oligonucleotides bound to a solid support with a concentrated ammonium hydroxide solution for at least 30 minutes to no longer than 6 hours, where the 3′ nucleoside is a LNA nucleoside covalently attached, facilitates rapid and effective cleavage and deprotection, allowing for efficient release of oligonucleotides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional cleavage methods are used on UnyLinker solid support, then complete deprotection and cleavage is achieved, but the process requires extended time (8 hours at 55°C) and elevated temperature
Solution Approach 1:
The patent changes the chemical structure parameter of the nucleoside at the 3′ position to LNA (locked nucleic acid), which fundamentally alters the cleavage kinetics. This structural modification enables the cleavage reaction to proceed rapidly at room temperature without requiring extended time or elevated temperature, thus resolving the contradiction between reliable cleavage and processing time
Solution Approach 2:
The LNA nucleoside is pre-installed at the 3′ position before oligonucleotide assembly, creating a built-in feature that predisposes the molecule for rapid cleavage. This preliminary structural preparation eliminates the need for subsequent optimization of cleavage conditions, achieving both high efficiency and speed
2Reliability
If conventional cleavage methods are used on UnyLinker solid support, then complete deprotection is achieved, but elevated temperature (55°C) is required
Solution Approach 1:
By changing the nucleoside structure to LNA at the 3′ position, the patent modifies the chemical reactivity parameters of the system. This structural change enables complete deprotection to occur at room temperature, eliminating the need for elevated temperature while maintaining complete deprotection efficiency
3Productivity
If LNA nucleoside is used at 3′ position, then rapid cleavage occurs, but the method is specific to LNA modifications
Solution Approach 1:
The patent demonstrates that while LNA provides rapid cleavage, the UnyLinker platform itself remains universally applicable. The rapid cleavage is achieved through the specific LNA-UnyLinker combination, but the UnyLinker support can still be used with various nucleoside modifications, maintaining platform versatility while offering an optimized pathway for LNA-containing oligonucleotides
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
This method enables rapid and efficient cleavage and deprotection of LNA oligonucleotides from solid supports, achieving high yields and minimizing processing time, with up to 99% cleavage efficiency within 30 minutes to 6 hours, even at room temperature.
Implementation Method 1
treating the oligonucleotide bound to the solid support with a concentrated ammonium hydroxide solution for a period of at least about 30 minutes and no longer than about 6 hours
Data Source
AI summary
Methods for cleaving oligonucleotides from a solid support are described as are methods for synthesizing an oligonucleotide on a solid support and subsequently cleaving the oligonucleotide from the solid support. In the methods, the 3′ nucleoside of the oligonucleotide attached to the solid support is a LNA nucleoside. The method entail treating the bound oligonucleotide with a concentrated ammonium hydroxide solution for about 30 minutes to about 6 hours.