Oligonucleotide Extraction via Laser Ablation and Sequencing Mapping
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Solution Overview
Problem
Current methods for synthesizing DNA in synthetic biology face challenges with high costs and low purity, particularly in assembling long DNA sequences, and existing techniques like pick-and-place methods are time-consuming and prone to cross-contamination.
Innovation Solution
A method involving a sequencing substrate with a clonal library of oligonucleotides on a solid support, where measured location data is mapped with pixel data to precisely extract and amplify high-purity oligonucleotides using a pulsed laser, enabling rapid and accurate extraction and replication of desired DNA sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If conventional chemical synthesis is used to assemble DNA sequences, then the purity of synthesized DNA is maintained, but the cost increases and the sequence length is limited
Solution Approach 1:
The invention divides the DNA synthesis process into two distinct stages: (1) microarray-based parallel synthesis of multiple DNA sequences simultaneously, and (2) post-synthesis purification through next-generation sequencing and pick-and-place retrieval. This segmentation allows high-throughput production while maintaining purity by separating the synthesis and purification functions.
Solution Approach 2:
The invention performs preliminary sequencing of all synthesized DNA molecules on the microarray before retrieval. By using next-generation sequencing to identify and locate specific DNA sequences in advance, the system ensures that only correctly synthesized sequences are selected for amplification, thereby guaranteeing high purity in the final product.
2Quantity of substance
If microarray synthesis with pick-and-place method is used, then the cost of DNA is reduced, but the time required increases and cross-contamination occurs
Solution Approach 1:
The invention replaces manual or mechanical pick-and-place operations with an automated system that uses next-generation sequencing data to guide laser-based or robotic retrieval. The sequencing information provides precise location data, allowing automated systems to extract specific DNA sequences without manual intervention, thereby reducing time and eliminating human error.
Solution Approach 2:
The invention implements a feedback loop where next-generation sequencing results are used to identify the exact locations of desired DNA sequences on the microarray. This feedback mechanism enables precise, automated retrieval of only the correct sequences, eliminating cross-contamination and reducing extraction time through targeted processing.
3Quantity of substance
If microarray synthesis is used to synthesize millions of DNA sequences, then the price of DNA is dramatically reduced, but the purity of synthesized DNA decreases
Solution Approach 1:
The invention introduces next-generation sequencing as an intermediary step between microarray synthesis and final DNA retrieval. The sequencing process acts as a quality control mediator that identifies and locates correctly synthesized DNA sequences, ensuring that only high-purity sequences are selected for amplification, even when millions of sequences are synthesized in parallel.
Solution Approach 2:
The system uses sequencing data as feedback to guide the retrieval process. By analyzing sequencing results, the system can identify which microarray positions contain the desired high-purity sequences and retrieve only those, maintaining high purity standards despite high-throughput parallel synthesis.
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 allows for the rapid and precise extraction and amplification of high-purity nucleotides, overcoming the limitations of existing methods by reducing extraction time and preventing cross-contamination, thus facilitating cost-effective and efficient DNA synthesis for genome-level research.
Implementation Method 1
separating the solid support from the sequencing substrate and transferring it to the matching substrate
Data Source
AI summary
Provided is a method of mass-producing high-purity nucleotides including providing a sequencing substrate having a clonal library of oligonucleotides on a solid support, sequencing the clonal library, obtaining measured location data of the solid support on the sequencing substrate, mapping pixel data of a signal generated from the solid support given as a result of the sequencing with the measured location data, extracting the solid support having a desired base sequence from the sequencing substrate using the mapping result, and amplifying an oligonucleotide on the extracted solid support to replicate on a large scale.