Label-Free Nucleic Acid Isolation via DMA Binding and SPR Detection
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Solution Overview
Problem
Current methods for isolating and analyzing methylated DNA from genomic DNA are labor-intensive, technically challenging, and lack sufficient sensitivity to detect low concentrations of native DNA biomarkers in bodily fluids, making them inadequate for in vitro diagnostic use without DNA amplification.
Innovation Solution
A method involving Dimethyl adipimidate (DMA) that directly binds to nucleic acids, allowing for their isolation and analysis on a solid phase device, such as a silicon microring resonator, without the need for label-based techniques, enabling real-time detection and amplification of methylated DNA.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional methods are used for isolating and analyzing methylated DNA, then the analysis can be performed, but the process is labor-intensive and technically challenging
Solution Approach 1:
The patent replaces conventional mechanical and chemical isolation methods with a label-free optical detection system using surface plasmon resonance (SPR). The SPR biosensor directly detects methylated DNA in genomic DNA samples without requiring labor-intensive isolation, purification, or labeling steps, thereby improving productivity while reducing technical complexity
Solution Approach 2:
The patent introduces an MBD (methyl-CpG binding domain) protein as an intermediary that specifically binds to methylated DNA sequences. This MBD protein is immobilized on the SPR sensor surface, enabling selective capture and detection of methylated DNA from complex genomic samples, simplifying the overall process while maintaining high specificity
2Measurement precision
If label-based techniques are used for DNA detection, then detection sensitivity can be improved, but the method becomes more complex and costly
Solution Approach 1:
The patent extracts and utilizes the specific binding property of MBD proteins for methylated DNA, separating this functional capability from complex labeling procedures. By immobilizing MBD on the SPR surface, the system achieves sensitive detection of methylated DNA through direct binding events, eliminating the need for labels while maintaining measurement precision
Solution Approach 2:
The patent employs surface plasmon resonance, an optical phenomenon that detects changes in refractive index at the sensor surface. When methylated DNA binds to MBD on the SPR surface, it causes a measurable shift in resonance angle or wavelength, providing label-free detection with high sensitivity without requiring fluorescent or radioactive labels
3Measurement precision
If conventional DNA isolation methods are used, then DNA can be extracted, but the sensitivity to detect low concentrations of native DNA biomarkers is insufficient
Solution Approach 1:
The patent performs preliminary enrichment of methylated DNA by immobilizing MBD proteins on the SPR sensor surface before sample introduction. This pre-positioning of specific binding sites allows the system to capture and concentrate low-abundance methylated DNA sequences from genomic DNA samples, enhancing detection sensitivity for trace biomarkers
Solution Approach 2:
The MBD protein acts as a mediator that specifically recognizes and binds to methylated cytosine-guanosine dinucleotides (CpG sites). This intermediary binding mechanism enables selective detection of methylated DNA sequences even at very low concentrations within complex genomic backgrounds, overcoming the sensitivity limitations of conventional isolation methods
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 provides a simple, cost-effective, and highly sensitive means for capturing and measuring nucleic acids, including methylated DNA, enhancing DNA detection in clinical applications like cancer research by improving the sensitivity and efficiency of DNA methylation analysis.
Implementation Method 1
Dimethyl adipimidate (DMA) that directly binds to nucleic acids
Implementation Method 2
silicon microring resonator
Data Source
AI summary
Methods and system for the isolation and/or analysis of nucleic acids on a solid phase device comprising (i) incubating a nucleic acid sample with Dimethyl adipimidate (DMA) on said solid phase under conditions that allow formation of a complex of the nucleic acid with the DMA; contacting the complex of (i) with said surface; and isolating and/or analyzing the nucleic acid of the complex.