Orthogonal Oligonucleotide Synthesis With Minimal Chemistry Cross Talk
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Solution Overview
Problem
Existing methods for simultaneous synthesis of multiple oligonucleotides face challenges in effectively addressing the coupling efficiency and cross talk between different chemistries, which are not efficiently addressed in existing technologies, particularly in the synthesis of DNA-encoded libraries (DEL) for biomedical applications such as biological-active oligonucleotides, such as an ASO, siRNA, mRNA, mRNA, LNA, gRNA for CRISPR/Cas9, CRISPR/Cas9, CRISPR/Cas13, or CRISPR/Cas7/11, and DNA origami, which require reliable synthesis processes with minimal cross talk between the synthesis processes.
Innovation Solution
A method for simultaneous synthesis of a plurality of oligonucleotides using nucleotides with orthogonal protective groups, such as DMTr and Fmoc, to maximize the usage of one optimized protective group and minimize cross talk, utilizing a split-pool process.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If multiple oligonucleotides are synthesized simultaneously using different chemistries, then productivity is improved, but cross talk between different chemistries occurs
Solution Approach 1:
The solid support is divided into multiple independently controllable reactive moieties, each capable of supporting different chemistries. This segmentation allows simultaneous synthesis of multiple oligonucleotides with different protective groups without cross talk, as each segment can be selectively activated and controlled separately.
Solution Approach 2:
Different regions of the solid support are assigned different local qualities - specific reactive moieties are designed to be compatible with particular chemistries (e.g., acid-labile, base-labile, UV-labile protective groups). This local differentiation enables simultaneous multi-chemistry synthesis while preventing cross talk between different regions.
2Reliability
If orthogonal protective groups are used for multiple oligonucleotides, then reliability is improved, but device complexity increases
Solution Approach 1:
The solid support is designed with universal reactivity - multiple types of reactive moieties are integrated into a single support structure that can accommodate different chemistries. This multi-functional design allows one solid support to simultaneously synthesize multiple oligonucleotides with different protective groups (DMTr, Fmoc, etc.) without requiring separate synthesis systems for each chemistry.
Solution Approach 2:
The solid support acts as an intermediary platform that mediates between different chemistries. By providing a common structural framework with multiple reactive moieties, it enables different protective groups to coexist and function independently, reducing the need for separate synthesis apparatuses while maintaining synthesis fidelity.
3Manufacturing precision
If one optimized protective group is maximized, then manufacturing precision is improved, but adaptability decreases
Solution Approach 1:
The synthesis system is segmented into multiple independent reactive moieties, each optimized for specific chemistries. This allows the DMTr chemistry to maintain its optimized coupling efficiency on dedicated reactive moieties while other moieties support different chemistries, thus preserving both precision and adaptability simultaneously.
Solution Approach 2:
Different reactive moieties are designed with specialized local qualities matched to specific protective groups. The DMTr-optimized reactive moieties provide maximum coupling efficiency for DMTr chemistry, while other moieties are tailored for Fmoc, Lev, or other protective groups, enabling the system to maintain high precision for each chemistry while overall adapting to multiple chemistries.
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 achieves the simultaneous synthesis of multiple oligonucleotides with orthogonal protective groups, such as DMTr and Fmoc, to maximize the usage of one optimized protective group and minimize cross talk, enabling efficient synthesis of multiple distinct oligonucleotides in a single reaction vessel.
Implementation Method 1
A method for simultaneous synthesis of a plurality of oligonucleotides using nucleotides with orthogonal protective groups, such as DMTr and Fmoc
Implementation Method 2
utilizing a split-pool process
Data Source
AI summary
Disclosed is a method and compounds useful for performing said method for simultaneous synthesis of a plurality of oligonucleotide molecules, and more specifically for orthogonal synthesis of at least two different oligonucleotide molecules at the same time with applications in combinatorial chemistry and DNA encoded libraries (DEL).