Bicyclic Nucleoside Coupling Protocol Optimization
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Solution Overview
Problem
The synthesis of oligomeric compounds containing bicyclic nucleosides has consistently yielded lower efficiencies compared to those without cEt nucleosides due to suboptimal coupling in standard protocols, particularly in solid phase oligonucleotide synthesis.
Innovation Solution
Modified coupling protocols for bicyclic nucleosides in solid phase synthesis, involving a higher percentage of activator solution and adjusted delivery times and recirculation, enhance coupling efficiency and yield, specifically using a 70% activator and 30% phosphoramidite solution with 1.4 to 1.75 equivalents of bicyclic nucleosides based on initial loading, and incorporating diisopropylcyanoethoxy phosphoramidite groups.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If standard coupling protocols with 50% activator solution are used for bicyclic nucleosides, then the synthesis process is simple and fast, but the coupling efficiency and yield are low
Solution Approach 1:
The patent modifies the coupling protocol by changing the activator solution concentration from 50% to 70%, and adjusts the recirculation time from 30 seconds to 45 seconds. These parameter changes directly address the low coupling efficiency of bicyclic nucleosides while maintaining protocol simplicity and automation compatibility.
2Reliability
If standard coupling protocols are used, then the procedure is straightforward, but the yield of oligomeric compounds containing bicyclic nucleosides is consistently lower
Solution Approach 1:
The patent implements specific parameter changes including increasing activator solution concentration to 70% and extending recirculation time to 45 seconds. These changes reliably improve synthesis yield for bicyclic nucleosides while being easily implemented in automated synthesizers without complicating the operational procedure.
3Productivity
If more equivalents of bicyclic nucleosides are used to improve yield, then the coupling efficiency increases, but the cost and complexity of the synthesis increases
Solution Approach 1:
The patent achieves improved coupling efficiency through changing the activator solution concentration to 70% and recirculation time to 45 seconds, allowing the use of standard equivalents (1.5-2.0) of bicyclic nucleosides. This approach improves productivity without increasing the quantity of reagents required.
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 modified protocols significantly improve coupling efficiency and overall yield for bicyclic nucleosides in solid phase synthesis, maintaining the same number of equivalents while optimizing the solid support-bound hydroxyl group interactions.
Implementation Method 1
coupling monomer subunits to the free hydroxyl groups, wherein each monomer subunit comprises a phosphoramidite group and a blocked hydroxyl group to provide phosphite triester linked monomer subunits
Implementation Method 2
oxidizing or sulfurizing the phosphite triester linked monomer subunits to provide phosphate triester or thiophosphate triester linked monomer subunits
Data Source
AI summary
Provided herein are methods for the synthesis of oligomeric compounds wherein the standard coupling protocols are modified when coupling bicyclic nucleosides of Formula I. More particularly, the modified coupling protocols provide for a decrease in the ratio of phosphoramidite solution to activator solution in the coupling reagent with an increased contact time. The modified coupling protocols provide for oligomeric compounds having comparable yields to similar oligomeric compounds having modified nucleosides other than bicyclic nucleosides of Formula I.