Heterologous DNA Barcoding via Microwell Array Assembly
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Solution Overview
Problem
Traditional DNA barcoding methods are costly and labor-intensive due to the need for constructing and ligating multiple DNA oligos, which requires significant time and materials for analyzing large amounts of gene samples in a parallel manner.
Innovation Solution
A heterologous DNA barcoding method using a DNA microarray with barcode sequences and a microwell array, where the DNA microarray is assembled with the microwell array to form micro reaction spaces, allowing oligonucleotide sequences to react with target nucleic acid sequences, and separating to obtain reaction products with barcode sequences for sequencing and amplification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional oligo synthesis and ligation methods are used for DNA barcoding, then DNA barcodes can be attached to target DNAs, but construction costs and time consumption increase significantly
Solution Approach 1:
Barcode sequences are pre-synthesized and immobilized on solid support beads before the actual barcoding process. This preliminary preparation allows multiple barcodes to be ready simultaneously, eliminating the need for sequential ligation operations and significantly reducing time consumption while maintaining barcoding accuracy
Solution Approach 2:
The invention uses solid support beads as reusable templates that can be copied and distributed across multiple reaction vessels. Each bead carrying a barcode sequence serves as a template that can be replicated and used in parallel reactions, reducing the need for synthesizing large quantities of individual oligos and decreasing both time and material costs
2Reliability
If traditional oligo synthesis methods are used for DNA barcoding, then DNA barcodes can be attached to target DNAs, but construction costs increase considerably
Solution Approach 1:
The invention uses solid support beads as reusable templates that can be copied and distributed across multiple reaction vessels. Each bead carrying a barcode sequence serves as a template that can be replicated and used in parallel reactions, reducing the need for synthesizing large quantities of individual oligos and decreasing both time and material costs
Solution Approach 2:
The solid support beads serve multiple functions: they act as immobilization matrices for barcode sequences, as reaction templates, and as separation carriers. This multi-functionality eliminates the need for separate components for each function, reducing overall construction costs while maintaining barcoding reliability
3Reliability
If sequential ligation operations are performed for DNA barcoding, then DNA barcodes can be attached to target DNAs, but labor requirements and time consumption increase
Solution Approach 1:
Barcode sequences are pre-synthesized and immobilized on solid support beads before the actual barcoding process. This preliminary preparation allows multiple barcodes to be ready simultaneously, eliminating the need for sequential ligation operations and significantly reducing time consumption while maintaining barcoding accuracy
Solution Approach 2:
The invention combines multiple ligation operations into a single parallel reaction step by distributing pre-prepared barcode-bearing beads across multiple reaction vessels. This merging of sequential operations into parallel processing dramatically increases analysis throughput while maintaining the reliability of accurate barcode attachment
4Reliability
If large amounts of materials are used for DNA barcoding reactions, then DNA barcodes can be attached to target DNAs, but costs increase considerably
Solution Approach 1:
The invention uses solid support beads as reusable templates that can be copied and distributed across multiple reaction vessels. Each bead carrying a barcode sequence serves as a template that can be replicated and used in parallel reactions, reducing the need for synthesizing large quantities of individual oligos and decreasing both time and material costs
Solution Approach 2:
The invention employs solid support beads that can be easily discarded after a single use, eliminating the need for expensive purification and regeneration processes. These disposable beads reduce material consumption and costs while ensuring high barcoding accuracy through consistent, pre-manufactured barcode sequences
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 reduces costs and time by enabling efficient parallel analysis of large gene samples, allowing for simultaneous and spatially separated reactions, and facilitates the acquisition of desired samples through selective amplification using barcode information.
Implementation Method 1
allowing the oligonucleotide sequences of the DNA spots to react with the target nucleic acid sequences of the samples in the micro reaction spaces to combine the sequence information of the DNA spots with the sequence information of the samples
Data Source
AI summary
A heterologous DNA barcoding method is provided. The method includes (a) providing a DNA microarray having DNA oligonucleotide spots, which are distinguished from each other by their barcode sequences, (b) providing a microwell array having microwells whose spatial arrangement corresponds to that of the DNA spots on the DNA microarray, (c) loading a solution of samples containing target nucleic acid sequences into the microwells, (d) assembling the DNA microarray to the microwell array to form micro reaction spaces in which the DNA spots are spatially separated by the microwells, (e) allowing the oligonucleotide sequences of the DNA spots to react with the target nucleic acid sequences of the samples in the micro reaction spaces to combine the sequence information of the DNA spots with the sequence information of the samples, and (f) separating the DNA microarray and the microwell array from each other to obtain reaction products including the barcode sequences.