DNA Sizing via Fluorescent Distribution Analysis
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Solution Overview
Problem
Current methods for sizing large DNA molecules, such as gel electrophoresis and capillary electrophoresis, are time-consuming and limited in their ability to separate DNA fragments beyond 50 kilo base pairs, making it challenging to efficiently size DNA molecules up to mega base pairs.
Innovation Solution
A DNA sizing device with slit-like channels and a buffer solution is used to analyze the intensity and area distribution of DNA molecules, allowing for rapid separation and sizing of DNA molecules up to mega base pairs by using a buffer solution and fluorescently labeled DNA molecules, with reference DNA ladders for calibration.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If gel electrophoresis or capillary electrophoresis is used to size DNA molecules, then separation can be achieved, but the separation time becomes excessively long (14 hours for PFGE, 1 hour for CE)
Solution Approach 1:
The patent replaces traditional electrophoresis-based mechanical separation with an optical measurement system. DNA molecules are separated by size through free diffusion in a buffer solution, and their sizes are determined by fluorescent detection and image analysis rather than physical migration through gels or capillaries. This substitution of mechanical separation with optical measurement eliminates the time-consuming separation process while maintaining sizing accuracy.
Solution Approach 2:
The patent changes the measurement parameter from migration distance (in electrophoresis) to fluorescent intensity and area distribution (in the new method). By measuring the spatial distribution of fluorescently labeled DNA molecules in a buffer solution and analyzing intensity/area parameters, the system determines DNA size without requiring long migration times through electrophoretic fields.
2Productivity
If capillary electrophoresis with polymer solution is used, then separation time is reduced compared to gel electrophoresis, but the maximum detectable DNA size is limited to about 50 kilo base pairs
Solution Approach 1:
The patent creates a universal sizing system that can handle a broad range of DNA sizes (from small fragments to mega base pairs) using a single buffer solution-based approach. The system removes the polymer solution constraint that limited CE to 50 kbp, allowing the same apparatus and methodology to size DNA molecules across the entire range from kbp to Mbp by analyzing fluorescent distribution patterns.
3Measurement precision
If traditional electrophoresis methods are used, then DNA separation is achieved, but the process requires complex apparatus and lengthy procedures
Solution Approach 1:
The patent extracts and removes the complex electrophoresis separation step (gels, capillaries, polymer solutions, high voltage fields) from the DNA sizing process. Only the essential functions remain: DNA labeling with fluorescent dyes, loading into a simple channel, and optical detection. This extraction of unnecessary complexity simplifies the apparatus while preserving the core measurement capability.
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 significantly reduces separation time and enables the sizing of DNA molecules up to mega base pairs, offering a faster and more efficient alternative to existing techniques, with the ability to detect sizes in minutes rather than hours or days.
Implementation Method 1
detecting and recording an intensity and an area of a distribution of the DNA molecule
Data Source
AI summary
A method for sizing a DNA molecule is disclosed, which comprises the following steps of: providing a DNA sizing device, comprising: a cover substrate; a substrate disposed on the cover substrate and comprising a first hole and a second hole; and a first slit-like channel disposed between the cover substrate and the substrate, wherein two ends of the first slit-like channel respectively connects to the first hole and the second hole; loading a sample comprising a DNA molecule to the first slit-like channel through the first hole, wherein the DNA molecule moves in a direction from the first hole to the second hole; detecting and recording an intensity and an area of a distribution of the DNA molecule; and analyzing the intensity and the area to obtain the size of a DNA molecule.