Combigen Oligonucleotide Discovery via Defined Secondary Structures
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Solution Overview
Problem
The existing SELEX method for discovering high-affinity nucleic acid ligands is cumbersome, prone to errors, expensive, and time-consuming, often resulting in large aptamers lacking defined secondary structures, which limits their utility and requires iterative processes to carve out minimal tight-binding cores.
Innovation Solution
The method, referred to as Combigen, uses a library of oligonucleotides with known primary and secondary structures, eliminating the need for enzymatic amplification and sequencing, and allows for direct classification of binding affinity, enabling the identification of combimers with desired binding properties without separating species based on affinity, and incorporating non-nucleic acid components.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If SELEX method is used to discover high-affinity nucleic acid ligands, then binding affinity can be achieved, but the process becomes cumbersome, time-consuming, and expensive
Solution Approach 1:
The patent pre-defines the secondary structure of oligonucleotides before synthesis, allowing direct creation of functional candidates without iterative selection cycles. This preliminary structural design eliminates the need for time-consuming SELEX cycles while maintaining binding affinity through structured aptamer cores with defined hairpin loops and stems.
Solution Approach 2:
The patent segments the oligonucleotide into functional regions: a defined secondary structure core (hairpin loop with stem) and variable regions. This segmentation allows independent optimization of binding affinity in the core while maintaining structural integrity, reducing the search space and time required for discovery.
2Reliability
If SELEX method is used, then high-affinity sequences can be discovered, but the resulting aptamers lack defined secondary structures
Solution Approach 1:
The patent incorporates pre-defined secondary structures directly into the oligonucleotide sequences before synthesis. The hairpin loop structures with specific stem configurations are built-in from the start, ensuring that candidate molecules have both binding affinity and defined three-dimensional shapes without requiring post-discovery structural characterization.
3Reliability
If SELEX method is used, then aptamers can be discovered, but they are larger than minimal tight-binding sequences
Solution Approach 1:
The patent divides the oligonucleotide into essential core regions (hairpin loop with minimal stem) and optional flanking regions. This segmentation allows identification of minimal tight-binding cores that maintain affinity while reducing overall length, eliminating the need to carve out minimal sequences from larger SELEX products.
4Reliability
If SELEX method is used, then sequences can be discovered through iterative selection, but the process is prone to errors and expensive to automate
Solution Approach 1:
The patent performs sequence design and structural definition before synthesis, eliminating the need for iterative sequencing and selection steps. This preliminary approach reduces automation complexity by replacing multiple manual intervention steps (sequencing, purification, selection) with a single synthesis process using pre-designed templates.
5Reliability
If SELEX method is used, then high-affinity sequences can be enriched through multiple cycles, but the process requires expensive robotic equipment with frequent human interaction
Solution Approach 1:
The patent segments the discovery process into independent design modules that can be automated. The pre-defined secondary structures serve as templates for automated synthesis, eliminating the need for robotic equipment to handle multiple selection cycles. Human interaction is reduced to initial design and final verification steps.
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 enables rapid discovery of nucleic acid oligomers with high affinity and specificity for proteins and cellular targets, facilitating their incorporation into sensors and other applications, such as air, food, and water quality control, medical diagnostics, and drug discovery, with improved stability and reduced costs.
Implementation Method 1
nucleic acid ligands with high affinity for target species
Data Source
AI summary
A method is disclosed to obtain oligonucleotide sequences with high affinity to target molecules. By design, the oligonucleotides have a defined primary and secondary structure. The affinity for binding to target species is classified or quantified by assay measurements using physical measurements rather than being based primarily on separations. Targets include but are not limited to proteins, polymers, biological membranes including cells and organelles and small molecules.