Sedimentation-Based Nucleic Acid Purification for Serum Detection
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Solution Overview
Problem
Current methods for detecting and quantifying cell-free DNA in biological samples, such as serum, face challenges due to high background noise, reduced sensitivity, and labor-intensive processes, including autofluorescence from serum and the need for DNA extraction and purification.
Innovation Solution
The method employs sedimentation particles with specific surface properties to capture and concentrate nucleic acids, using gravitational or centrifugal forces to separate and purify DNA, reducing interference from serum components and enhancing detection sensitivity through the use of high-affinity labeling agents like SYBR Gold.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If fluorescent dyes like PicoGreen are used to measure DNA directly in serum, then DNA detection capability is achieved, but background noise and autofluorescence from serum components increase, reducing sensitivity
Solution Approach 1:
The patent extracts DNA from serum using silica-based magnetic particles that selectively bind DNA through silica-DNA interactions in the presence of chaotropic salts. This extraction step separates DNA from interfering serum components, eliminating autofluorescence background noise while preserving DNA for sensitive detection
Solution Approach 2:
The patent introduces silica-based magnetic particles as an intermediary substance that mediates between serum and detection reagents. These particles selectively capture DNA from serum through silica-DNA binding, allowing subsequent detection without direct interference from serum autofluorescence
2Measurement precision
If UV absorbance spectroscopy is used to determine DNA concentration, then direct measurement is achieved, but serum components also absorb at relevant wavelengths, complicating analysis
Solution Approach 1:
The patent extracts DNA from serum using silica-based magnetic particles before measurement. This extraction removes DNA from the complex serum matrix, eliminating interfering absorption from serum components and enabling accurate UV absorbance measurement of pure DNA
3Measurement precision
If high sensitivity methods like qPCR are used to measure CFD, then detection sensitivity is improved, but labor-intensive steps including DNA extraction, purification, and gel electrophoresis are required
Solution Approach 1:
The patent combines DNA extraction, purification, and concentration steps into a single magnetic bead-based operation. Silica-based magnetic particles simultaneously perform extraction from serum, purification from contaminants, and concentration of DNA, eliminating the need for separate gel electrophoresis and reducing overall procedure complexity
Solution Approach 2:
The silica-based magnetic particles serve multiple functions: they act as extraction agents to capture DNA from serum, as purification media to remove contaminants, and as concentration devices to accumulate DNA in a small volume, replacing multiple separate操作步骤
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 rapid and sensitive detection and quantification of cell-free DNA, reducing the need for amplification and improving signal clarity, with detection limits within clinically significant ranges, and achieving high capture efficiency.
Implementation Method 1
Devices, systems, and methods for detecting nucleic acids using sedimentation
Implementation Method 2
using gravitational or centrifugal forces to separate and purify DNA
Implementation Method 3
enhancing detection sensitivity through the use of high-affinity labeling agents like SYBR Gold
Data Source
AI summary
Embodiments of the present invention are directed toward devices, systems, and method for conducting nucleic acid purification and quantification using sedimentation. In one example, a method includes generating complexes which bind to a plurality of beads in a fluid sample, individual ones of the complexes comprising a nucleic acid molecule such as DNA or RNA and a labeling agent. The plurality of beads including the complexes may be transported through a density media, wherein the density media has a density lower than a density of the beads and higher than a density of the fluid sample, and wherein the transporting occurs, at least in part, by sedimentation. Signal may be detected from the labeling agents of the complexes.