Spatially Inhomogeneous Nanoporous Media for Selective Nucleic Acid Purification
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Solution Overview
Problem
Conventional methods for purifying PCR amplicons are time-consuming and labor-intensive, often introducing undesirable components like organic solvents and chaotropic salts that interfere with subsequent reactions, and fail to efficiently remove excess primers and unincorporated dNTPs, leading to suboptimal sequencing results.
Innovation Solution
The use of spatially inhomogeneously functionalized nanoporous materials with differently functionalized pore and non-pore surfaces to selectively adsorb single-stranded nucleic acids and free nucleotides, allowing for efficient separation of double-stranded nucleic acids from mixtures, utilizing materials like porous silica or alumina with pore sizes between 2 to 300 nm.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If conventional immobilization methods using chaotropic salts and multiple solvent elutions are used, then PCR products can be separated from primers and dNTP, but the process becomes time-consuming, labor-intensive, and introduces undesirable components that interfere with subsequent reactions
Solution Approach 1:
The patent extracts and removes unwanted components (primers and dNTPs) from the PCR mixture by selectively adsorbing them onto the porous material surface, leaving the desired PCR products in the supernatant. This extraction approach eliminates the need for multiple solvent elution steps while achieving complete removal of contaminants.
Solution Approach 2:
The patent introduces a porous material as an intermediary substance that mediates the separation process. The porous material's surface groups selectively interact with and bind to primers and dNTPs, enabling their removal from the PCR mixture without requiring harsh chaotropic salts or multiple processing steps.
2Manufacturing precision
If conventional multiple step cleanup processes are used, then contaminants can be removed, but undesirable components like organic solvents and chaotropic salts are introduced that interfere with subsequent reactions
Solution Approach 1:
The patent employs a disposable porous material that can be simply discarded after use, eliminating the need for complex waste disposal procedures. The material absorbs contaminants and can be thrown away with the waste, avoiding the introduction of harmful solvents and salts into the final product.
Solution Approach 2:
The patent changes the surface chemistry parameters of the porous material by incorporating specific surface groups (such as hydroxyl, carboxyl, or amine groups) that provide selective affinity for contaminants. This parameter modification enables the material to remove impurities without introducing harmful substances, as the separation is based on chemical affinity rather than harsh chemical treatments.
3Productivity
If conventional purification methods are used, then some cleanup is achieved, but excess primers and unincorporated dNTPs remain that lead to suboptimal sequencing results
Solution Approach 1:
The patent designs a universal porous material that simultaneously binds to multiple types of contaminants (primers, dNTPs, and other reaction byproducts) through its selectively functionalized surface. This multi-functional approach ensures complete removal of all unwanted components in a single step, achieving superior sequencing quality without requiring multiple specialized cleanup procedures.
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 enables rapid and efficient removal of impurities while retaining double-stranded DNA, improving the usability of PCR amplicons for downstream applications by reducing contamination and enhancing sequencing quality.
Implementation Method 1
the single-stranded nucleic acids and/or free nucleotides are selectively adsorbed to the pore surface
Data Source
AI summary
Compositions and methods for separating double-stranded nucleic acids out of a mixture comprising single-stranded nucleic acids and/or dNTPs and/or enzymes. The method uses spatially inhomogeneously functionalized nanoporous materials. For example, the compositions and methods of the present invention can be used to purify DNA amplification reaction products.