Electrophoretic Nucleic Acid Extraction Device for FFPE Samples
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Solution Overview
Problem
Current nucleic acid extraction methods are inadequate for processing a wide range of biological samples, particularly challenging for FFPE tissue due to preservation-induced damage and fragmentation, and require more robust and rapid systems for clinical diagnostics.
Innovation Solution
An electrophoretic device with a top and bottom reservoir, a collection chamber, a sieving matrix, and a semi-permeable membrane, utilizing electrolyte buffers and applying voltage to extract and concentrate nucleic acids, capable of handling various sample types including FFPE tissue.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional nucleic acid extraction methods are used, then the extraction process is simple, but the system is not robust and rapid enough for processing wide range of biological samples including FFPE tissue
Solution Approach 1:
The extraction system is segmented into distinct functional chambers: a first chamber for sample loading and initial extraction, and a second chamber for concentration and final collection. This segmentation allows each chamber to be optimized for its specific function, improving overall extraction efficiency and robustness while managing complexity through modular design.
Solution Approach 2:
A semi-permeable membrane is introduced as an intermediary component between the first and second chambers. This membrane mediates the transfer of nucleic acids from the extraction chamber to the concentration chamber while blocking larger contaminants, enabling rapid and robust extraction without requiring complex mechanical manipulation.
2Reliability
If FFPE tissue samples are processed using conventional methods, then the preservation process maintains tissue structure, but the preservation process damages and fragments the nucleic acids
Solution Approach 1:
The extraction process is divided into two sequential stages occurring in separate chambers: initial extraction in the first chamber followed by concentration and purification in the second chamber. This segmentation allows gentle handling of fragmented nucleic acids from FFPE samples during extraction, then concentrated collection in the second chamber, improving recovery of damaged nucleic acids while maintaining the beneficial tissue preservation.
Solution Approach 2:
The system specifically extracts nucleic acids from the FFPE tissue sample by passing them through the semi-permeable membrane into the concentration chamber, separating them from the damaged tissue matrix and other contaminants. This selective extraction recovers nucleic acids that would otherwise be lost or degraded in conventional single-chamber systems.
3Quantity of substance
If large volume body fluids are analyzed, then the sample volume is sufficient, but the nucleic acid concentration is trace amounts
Solution Approach 1:
The system extracts nucleic acids from large volume body fluid samples by allowing them to pass through the semi-permeable membrane into the second chamber where they are concentrated. This extraction process separates the nucleic acids from the large volume of body fluid, achieving both sufficient sample processing and concentrated nucleic acid recovery.
Solution Approach 2:
The system changes the concentration parameter of nucleic acids by utilizing the semi-permeable membrane to retain nucleic acids in the second chamber while allowing smaller molecules to pass through. This parameter change from dilute to concentrated enables detection of trace nucleic acids from large volume samples.
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
The device effectively isolates and concentrates nucleic acids from diverse samples, including FFPE tissue, enhancing the sensitivity and specificity of downstream analytical steps like next-generation sequencing.
Implementation Method 1
Devices and methods for electrophoretic extraction of nucleic acids from biological samples
Implementation Method 2
a semipermeable membrane not capable of passing the biological polymers to be extracted
Data Source
AI summary
The invention relates to a device methods and an assembly for isolating biological polymers from a sample, the device comprising a top reservoir, a bottom reservoir, a collection chamber located between the top and the bottom reservoirs and operably connected to the top and bottom reservoirs, a sieving matrix capable of passing the biological polymers to be extracted, a semipermeable membrane not capable of passing the biological polymers to be extracted, and at least one set of a working electrode and a counter electrode.