DNA-Encoded Library Synthesis via Split-and-Pool and Enzymatic Ligation
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for producing combinatorial libraries, especially DNA-encoded libraries, face challenges in synthesizing vast numbers of compounds efficiently and identifying active molecules due to the complexity of the libraries, which lowers the concentration of individual members and complicates identification.
Innovation Solution
A method utilizing a 'split and pool' strategy to synthesize libraries with encoding oligonucleotide tags, where a solution with an initiator linked to an oligonucleotide is divided, reacted with unique building blocks, and then pooled, allowing for the incorporation of multiple unique molecules through repeated cycles, enabling the synthesis of libraries with a high number of distinct members.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If the number of distinct members within the library is increased to achieve greater complexity, then the probability of containing active molecules is improved, but the concentration of any particular library member is lowered which complicates identification
Solution Approach 1:
The patent uses DNA tags as information copies that identify each library member's chemical structure. Instead of physically separating and identifying each compound individually, the DNA tag serves as a replicable information carrier that can be amplified and sequenced to reveal the identity of the parent compound, solving the identification problem in high-complexity libraries
Solution Approach 2:
The patent introduces DNA tags as an intermediary between the chemical compound and its identification. The DNA tag is covalently linked to each library member and serves as a mediator that carries structural information, allowing indirect identification of compounds through sequencing rather than direct physical analysis
2Measurement precision
If DNA tags are used to identify library members, then the identification capability is improved, but the synthesis methods for producing very large libraries have not yet been demonstrated
Solution Approach 1:
The patent segments the synthesis process into discrete cycles where DNA tags and chemical moieties are added in separate, repeatable steps. Each cycle involves tagging with a specific DNA sequence followed by chemical coupling, allowing the process to be scaled to produce very large libraries through multiple iterative cycles
Solution Approach 2:
The patent employs periodic action through repeated synthesis cycles, where the same basic operations (tagging, coupling, pooling) are performed iteratively. This periodic repetition of the synthesis protocol enables the accumulation of library complexity while maintaining control over the process
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 approach facilitates the synthesis of large libraries with a high-fidelity incorporation of oligonucleotide tags, allowing for multiple rounds of selection and subsequent amplification and sequencing of active molecules, enhancing the efficiency of identifying compounds with desired biological activities.
Implementation Method 1
reacting the initial oligonucleotide with an incoming oligonucleotide which identifies the building block of step (b) in the presence of an enzyme which catalyzes ligation of the initial oligonucleotide and the incoming oligonucleotide
Data Source
AI summary
The present invention provides methods of synthesizing a molecule comprising a functional moiety which is operatively linked to an encoding oligonucleotide. The methods include providing an initiator compound comprising an initial functional moiety comprising n building blocks, wherein the initial functional moiety comprises at least one reactive group, and is operatively linked to an initial oligonucleotide; reacting the initiator compound with a building block comprising at least one complementary reactive group, under conditions suitable for reaction of the complementary reactive group to form a covalent bond; and reacting the initial oligonucleotide with an incoming oligonucleotide corresponding to the building block in the presence of an enzyme which catalyzes ligation of the initial oligonucleotide and the incoming oligonucleotide, under conditions suitable for ligation of the incoming oligonucleotide and the initial oligonucleotide to form an encoding oligonucleotide.