Multi-Fluorous Blockmers for Phase-Separation Oligonucleotide Purification
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Solution Overview
Problem
Conventional liquid-phase synthesis methods for oligonucleotides require numerous reaction steps and complex purification processes, including column chromatography, making it difficult to synthesize large amounts efficiently, and existing fluorous tags are costly and complicated.
Innovation Solution
The use of a multi-fluorous blockmer, represented by specific chemical structures, which incorporates fluorous tags to alter solubility and simplify purification, allowing for a more versatile and cost-effective oligonucleotide synthesis method.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional liquid-phase synthesis methods are used, then oligonucleotides can be synthesized, but the synthesis process requires dozens of reaction steps and complex purification processes making it difficult to synthesize large amounts efficiently
Solution Approach 1:
The invention divides the oligonucleotide synthesis into blockmer units (e.g., 6-mer blockmers) that are synthesized separately and then assembled. This segmentation reduces the number of purification steps required compared to synthesizing the entire oligonucleotide sequence step-by-step, thereby improving productivity and reducing purification complexity.
Solution Approach 2:
The fluorous tag acts as an intermediary that enables simplified purification through fluorous phase separation. By incorporating fluorous tags into the blockmer structures, the invention creates a system where purification can be achieved through phase separation rather than complex column chromatography, reducing both time and operational complexity.
2Ease of manufacture
If fluorous tags are applied to liquid-phase synthesis method, then purification can be simplified, but the fluorous tags have complicated structure and are not readily available resulting in high cost
Solution Approach 1:
The invention modifies the fluorous tag structure by changing parameters such as the length of the fluorous chain and the position of the fluorous tag on the nucleoside. These parameter changes simplify the fluorous tag structure while maintaining the purification benefit, making the tags more readily available and cost-effective.
Solution Approach 2:
Instead of using complex fluorous tags throughout the entire oligonucleotide, the invention applies fluorous tags locally at specific positions (e.g., on terminal nucleosides or at blockmer boundaries). This local application reduces the overall structural complexity while maintaining purification efficiency.
3Reliability
If conventional synthesis methods are used, then reaction steps can be performed, but purification is complicated requiring column chromatography in most steps
Solution Approach 1:
The invention utilizes phase transitions between fluorous and non-fluorous phases for purification. By incorporating fluorous tags, the reaction mixture can be separated into fluorous and non-fluorous phases, allowing rapid purification without time-consuming column chromatography. This maintains reaction reliability while significantly reducing purification time.
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 method reduces purification burdens and lowers costs by using readily available fluorous tags, enabling larger-scale synthesis of oligonucleotides with simplified purification processes.
Implementation Method 1
employing a fluorous tag (a substituent favoring fluorocarbon) to such a liquid-phase synthesis method
Data Source
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AI summary
Provided are a multi-fluorous blockmer using a readily available fluorous tag and capable of reducing burdens of purification, and an oligonucleotide synthesis method using the same. A multi-fluorous blockmer represented by the formula is synthesized: wherein B is a natural or modified nucleobase; R1 is a protecting group that can be removed for deprotection under acidic or neutral conditions; R3 is a protecting group for phosphate; Pro is unprotected, protected, or F-protector, wherein F-protector is O(CH2)n(CF2)mCF3 when the protected moiety of nucleoside base B is O, and is NH(C=O)(CH2)n(CF2)mCF3 when the protected moiety of nucleoside base B is N, wherein n is 1 or 2 and m is an integer of 1 to 20; X is O or S; 1 is an integer of 0 to 58; R7 is (C=O)(CH2)2(C=O)(CH2)n(CF2)mCF3 or a silyl protecting group, wherein n is 1 or 2 and m is an integer of 1 to 20.