Oligonucleotide Binding-Element Development via Ligase Ligation
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Solution Overview
Problem
Current methods for developing nucleic acid binding-elements are labor-intensive, time-consuming, and expensive, with limited specificity and selectivity, particularly when screening against molecules with similar structures to the target molecules.
Innovation Solution
A method involving a mixture of target protein molecules, oligonucleotides, and a ligase is used to form oligonucleotides-target molecule complexes, which are then ligated to create binding-elements with enhanced specificity and selectivity for target protein molecules, utilizing techniques such as CircLigase for efficient ligation and subsequent purification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional SELEX process is used to discover binding-elements, then binding-elements with desired affinity can be obtained, but the process becomes labor-intensive, time-consuming and expensive
Solution Approach 1:
The patent applies preliminary action by pre-synthesizing a diverse library of oligonucleotide sequences before the selection process. This pre-prepared library is then directly used in the binding-element discovery process, eliminating the need for time-consuming iterative synthesis and selection cycles of traditional SELEX methods.
Solution Approach 2:
The patent uses copying by creating multiple copies of target-bound oligonucleotides through PCR amplification. The enriched binding-elements are copied and amplified to generate sufficient quantities for further analysis and application, replacing the labor-intensive manual handling of individual binding events.
2Reliability
If traditional SELEX process is used to discover binding-elements, then binding-elements with desired affinity can be obtained, but the process becomes labor-intensive and expensive
Solution Approach 1:
The patent employs copying through PCR amplification to multiply the bound oligonucleotides, replacing manual operations. This automated copying process reduces labor intensity and cost while maintaining the ability to select high-affinity binding-elements.
Solution Approach 2:
The patent replaces manual mechanical operations with automated molecular biology techniques. The mechanical process of manual selection and analysis is substituted with enzymatic amplification (PCR) and automated sequencing, reducing labor intensity and cost.
3Reliability
If binding-elements are selected from large library through multiple selection processes, then adequate target affinity can be achieved, but specificity against similar molecules is limited
Solution Approach 1:
The patent applies local quality by using a focused library of oligonucleotides with specific local sequence characteristics optimized for the target protein. Rather than using a completely diverse library, the approach concentrates selection power on sequences with local features that specifically recognize the target, improving specificity against similar molecules.
Solution Approach 2:
The patent changes parameters by modifying the oligonucleotide library composition and selection conditions to enhance specificity. The process uses controlled variations in sequence composition and binding conditions to distinguish the target from similar molecules, achieving higher manufacturing precision in binding specificity.
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 produces binding-elements with higher specificity and selectivity for target protein molecules, suitable for affinity purification and suitable for applications like diagnostics and chromatographic processes, reducing the complexity and cost of the discovery process.
Implementation Method 1
ligating the oligonucleotides bound to the target protein molecules to form the binding-element
Data Source
Figure 1I~1III
Figure 2
AI summary
Methods for developing a binding-element are provided. A mixture comprising a target molecule, a plurality of oligonucleotides and a ligase is provided, followed by binding the oligonucleotides to the target molecule to form an oligonucleotides-target molecule complex. The oligonucleotides bound to the target molecule are ligated to form the binding-element. The binding-elements are separated from the mixture.