Nucleic Acid Extraction Using Segmented Buffer and Magnetic Beads
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Solution Overview
Problem
Current nucleic acid extraction methods face challenges in efficiently extracting both large and small nucleic acid fragments, particularly circulating free DNA (cfDNA), with existing technologies often resulting in low purity and poor operability across varying blood sample volumes due to magnetic bead aggregation and inadequate separation of digestion and binding solutions.
Innovation Solution
A nucleic acid extraction composition and method utilizing a magnetic bead solution with silicon hydroxyl groups and a buffer system comprising separated digestion and binding solutions, including chaotropic salts, chelating agents, surfactants, and resolvents like isopropanol, which allows for effective binding and separation of nucleic acids, preventing magnetic bead aggregation and improving fragment recovery across different sample volumes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional nucleic acid extraction methods are used, then extraction can be performed, but magnetic bead aggregation occurs and purity is low
Solution Approach 1:
The patent divides the buffer system into separate digestion solution and binding solution, preventing mixing of components that cause magnetic bead aggregation. The digestion solution contains chaotropic salts for protein denaturation, while the binding solution contains resolvent for nucleic acid binding, allowing controlled, sequential operations that maintain bead dispersion and improve extraction purity.
Solution Approach 2:
The patent introduces a resolvent (isopropanol or ethanol) as an intermediary substance in the binding solution. This resolvent exposes organic groups on nucleic acids to bind to silicon hydroxyl groups on magnetic beads, facilitating specific binding while preventing non-specific aggregation and maintaining bead dispersion throughout the extraction process.
2Productivity
If conventional extraction methods are used, then extraction can be performed, but fragment length selection bias occurs
Solution Approach 1:
The patent optimizes parameters including chaotropic salt concentration (1-6 M), resolvent concentration (20-50%), and silicon hydroxyl group density on magnetic beads. These parameter adjustments enable efficient binding of nucleic acids across different fragment lengths, reducing selection bias while maintaining high extraction rates for both long and short fragments.
Solution Approach 2:
The patent applies local quality by using silicon hydroxyl groups specifically modified on magnetic bead surfaces to bind to organic groups on nucleic acids. This localized modification creates specific binding sites that uniformly interact with nucleic acids of various lengths, preventing size-based selection bias while maintaining high extraction efficiency.
3Adaptability or versatility
If conventional methods are used, then extraction can be performed, but operability varies across blood sample volumes
Solution Approach 1:
The patent creates a universal extraction system where the separated buffer system can handle various blood sample volumes effectively. The digestion solution and binding solution can be adjusted in volume to match sample size, while the core mechanism of chaotropic salt digestion followed by resolvent-mediated binding remains consistent, ensuring reliable extraction across different volumes from 0.5 mL to 10 mL of blood.
4Device complexity
If digestion and binding solutions are mixed, then processing is simplified, but magnetic bead aggregation and low purity result
Solution Approach 1:
The patent segments the buffer system into two separate solutions: digestion solution containing chaotropic salts and binding solution containing resolvent. This segmentation prevents premature mixing of incompatible components, allowing magnetic beads to remain dispersed during digestion, then enabling controlled binding in the second step, thereby maintaining high extraction purity despite increased system complexity.
Solution Approach 2:
The patent maintains continuity of useful action by performing digestion first to denature proteins and release nucleic acids, then sequentially adding binding solution to capture nucleic acids on magnetic beads. This continuous, sequential process ensures that each step builds upon the previous one, maintaining bead dispersion and preventing aggregation while achieving high purity extraction.
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 solution achieves high nucleic acid extraction rates with improved purity and reduced bias in fragment length selection, enabling efficient extraction of both long and short nucleic acid fragments, particularly valuable for cfDNA detection, and maintains stability across varying blood sample volumes.
Implementation Method 1
The digestion solution is separated from the binding solution, and includes a chaotropic salt
Implementation Method 2
The binding solution includes a resolvent for exposing an organic group in a nucleic acid to allow the organic group to bind to the first group during nucleic acid extraction
Implementation Method 3
a magnetic bead solution, including magnetic beads and a first group linked to the magnetic beads... allow the organic group to bind to the first group during nucleic acid extraction
Data Source
AI summary
The invention provides a nucleic acid extraction composition, a nucleic acid extraction device and a nucleic acid extraction method. The nucleic acid extraction composition comprises: a magnetic bead liquid, wherein the magnetic bead liquid comprises magnetic beads and a first group connected with the magnetic beads; the buffer solution system comprises digestive juice, protease liquid and binding liquid; wherein the digestive juice and the binding liquid are separated from each other, and the digestive juice comprises chaotropic salt; the binding liquid comprises a decomposer for exposing an organic group in the nucleic acid, so that the organic group is bound with the first group in the nucleic acid extraction process.