pH-Based Electrode Controlled Oligonucleotide Assembly
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for synthesizing oligonucleotides, such as the phosphoramidite process and enzymatic synthesis, are complex, generate hazardous waste, and suffer from issues like homopolymer creation, making them inefficient for DNA data storage and gene assembly.
Innovation Solution
The use of pH-based electrode-controlled hybridization on a microelectrode array to assemble oligonucleotide complexes into long oligonucleotides, where negative voltages create a basic environment to control hybridization and prevent unwanted extension at activated electrodes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If phosphoramidite process is used for oligonucleotide synthesis, then oligonucleotides can be synthesized, but the process becomes complex and generates hazardous organic waste
Solution Approach 1:
The patent changes the chemical environment parameter from organic solvent-based to aqueous-based synthesis. The electrode-controlled enzymatic synthesis operates in water or aqueous buffers, eliminating the need for acetonitrile and other hazardous organic solvents used in phosphoramidite chemistry, thus resolving the contradiction between manufacturability and harmful waste generation
Solution Approach 2:
The patent replaces the chemical synthesis mechanism (phosphoramidite chemistry) with an electrochemical control mechanism. Instead of using chemical reagents and protecting groups, the invention uses electrodes to control enzymatic activity through electrical signals, substituting a chemical process with an electrochemical one that is environmentally friendly
2Ease of manufacture
If TdT enzyme is used for enzymatic synthesis, then oligonucleotides can be synthesized without protecting groups, but uncontrolled homopolymers are created
Solution Approach 1:
The patent implements feedback control through electrode monitoring. The system continuously monitors the synthesis state and uses electrode signals to regulate TdT enzyme activity in real-time. When a nucleotide is added, the electrode detects the change and controls subsequent enzyme activity to prevent uncontrolled homopolymer formation, ensuring precise sequence assembly
Solution Approach 2:
The patent introduces dynamic control to the enzymatic synthesis process. Instead of static enzymatic reactions, the system dynamically adjusts enzyme activity through electrical signals from electrodes. The TdT enzyme activity is modulated in real-time based on synthesis progress, allowing precise control over nucleotide addition and preventing homopolymer errors
3Ease of manufacture
If phosphoramidites with protecting groups are used, then synthesis can proceed, but expensive modified nucleotides create artifacts and increase cost
Solution Approach 1:
The patent extracts and removes the problematic protecting groups from the synthesis process. By using electrode-controlled enzymatic synthesis, the invention eliminates phosphoramidites and their protecting groups entirely, using natural nucleotides instead. This extraction of harmful components resolves the contradiction between manufacturability and application reliability
Solution Approach 2:
The patent replaces expensive modified nucleotides (phosphoramidites with protecting groups) with cheap, natural nucleotides. The electrode-controlled enzymatic system can efficiently incorporate standard nucleotides without requiring costly modifications, reducing both material cost and the risk of artifacts in final applications
4Manufacturing precision
If multiple techniques are used to limit homopolymer creation in enzymatic synthesis, then sequence control improves, but device complexity increases
Solution Approach 1:
The patent creates a universal electrode control system that performs multiple functions: it monitors synthesis progress, regulates enzyme activity, controls nucleotide incorporation, and prevents homopolymer formation. This single multi-functional electrode system replaces multiple separate control techniques, resolving the contradiction between precision and complexity
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 method enables controlled, parallel writing of information-encoding oligonucleotides, avoiding the limitations of existing synthesis techniques by reducing waste and preventing homopolymer formation, thus enhancing efficiency and precision in DNA data storage and gene assembly.
Implementation Method 1
Switching on electrodes to negative voltages can generate a sufficiently basic local environment to prevent oligonucleotide hybridization
Implementation Method 2
The negative voltage reduces water molecules in proximity to the electrodes raising the pH and creating a localized basic environment
Implementation Method 3
The environment is sufficiently basic (e.g., above about pH 9) such that double-stranded oligonucleotides de-hybridize
Data Source
AI summary
Electrode controlled hybridization is used to change local pH and selectively assemble oligonucleotide complexes on the surface of a microelectrode array. The oligonucleotide complexes have sticky ends that provide locations for subsequent oligonucleotide complexes to hybridize. The order in which specific oligonucleotide complexes are joined together encodes information. Controlled activation of individual electrodes in the microelectrode array creates negative voltages that reduces a buffer solution and raises the pH in proximity to the electrodes. At higher pH levels double-stranded oligonucleotides de-hybridize. Nicks between oligonucleotide complexes and oligonucleotides anchored to the microelectrode array are closed creating covalent attachments. De-hybridized single-stranded oligonucleotides are removed leaving only the oligonucleotides connected to microelectrode array. Thus, during a given round of synthesis, oligonucleotide complexes are added only to the locations on the microelectrode array where the electrodes are not activated.