Oligonucleotide Synthesis Using Aromatic Hydrocarbon Solvent Mixtures
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Solution Overview
Problem
Existing methods for producing oligonucleotides using the phosphoramidite method often result in low purity due to the presence of n-1 mer impurities, which are difficult to separate from the target oligonucleotides.
Innovation Solution
A production method for oligonucleotides that involves using a mixed solvent solution of acetonitrile and an aromatic hydrocarbon, such as benzene or its derivatives, to dissolve the 2'-OMe-U amidite, which reduces the n-1 mer impurities during the synthesis process.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If 2'-OMe-U amidite is dissolved in acetonitrile to improve solubility, then the solubility of 2'-OMe-U amidite is improved, but n-1 mer impurities are generated during synthesis
Solution Approach 1:
The invention changes the solvent composition parameter by adding aromatic hydrocarbons (toluene, xylene, or benzene) to the acetonitrile solution. This parameter modification allows the 2'-OMe-U amidite to maintain good solubility while significantly reducing the formation of n-1 mer impurities during oligonucleotide synthesis, thus resolving the contradiction between solubility and purity.
2Quantity of substance
If dichloromethane is added to acetonitrile to improve solubility of 2'-OMe-U amidite, then the solubility is improved, but the purity of oligonucleotide remains unsatisfactory due to n-1 mer impurities
Solution Approach 1:
The invention replaces dichloromethane with aromatic hydrocarbons (toluene, xylene, or benzene) in the solvent mixture. This parameter change maintains the solubility improvement effect while eliminating the harmful side effect of n-1 mer impurity formation, thereby achieving both good solubility and high purity.
Solution Approach 2:
The invention uses common, inexpensive aromatic hydrocarbons (toluene, xylene, benzene) as solvents that can be easily handled and disposed of. These solvents provide the necessary solubility enhancement without the persistent contamination issues of dichloromethane, aligning with the principle of using simple, readily available materials that serve their purpose effectively.
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 achieves high-purity oligonucleotides by significantly reducing n-1 mer impurities, thereby improving the efficiency and quality of oligonucleotide production.
Implementation Method 1
2'-OMe-U amidite is dissolved in a mixed solution containing acetonitrile and an aromatic hydrocarbon
Data Source
Figure 1
AI summary
The present invention relates to a production method of an oligonucleotide that includes a step of coupling a compound represented by formula (2) [wherein G2 represents a protecting group of a hydroxy group, Ba represents a nucleobase which may be protected by a protecting group, R represents a protected hydroxy group or the like, X represents an oxygen atom or the like, and the bond marked with * represents a bond to the 3' terminal side of a nucleic acid.] with 2'-OMe-U amidite represented by formula (4) [wherein G1 represents a protecting group of a hydroxy group.] in the presence of an activator, wherein the 2'-OMe-U amidite is dissolved in a mixed solution containing acetonitrile and an aromatic hydrocarbon represented by formula (3) [wherein Y1 to Y6 represent a hydrogen atom, a methyl group, or the like.].