Periodic Field Nucleic Acid Enrichment System
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Solution Overview
Problem
Current nucleic acid separation techniques face challenges in resolving rare nucleic acids present at low concentrations due to stochastic amplification errors and inability to isolate low-abundance molecules without introducing sequence errors or requiring amplification steps, which limits their application in analyzing mutations and diseases.
Innovation Solution
The method employs periodic fields to enrich target nucleic acids by driving non-target nucleic acids into a waste well, creating a subsample where the target nucleic acid becomes dominant, allowing for high-fidelity detection and sequencing without amplification errors, using techniques like SCODA (Synchronous Coefficient of Drag Alteration) and zero-integrated-field electrophoresis (ZIFE) to concentrate and extract particles.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If PCR amplification is used to increase the abundance of low-abundance nucleic acids, then the quantity of detectable nucleic acid increases, but sequence errors are introduced and stochastic amplification biases occur
Solution Approach 1:
The patent extracts and removes non-target nucleic acids from the sample using affinity matrices and periodic field applications. By selectively binding and removing background nucleic acids, the target nucleic acid becomes enriched without requiring amplification, thus maintaining sequence fidelity while increasing detectable abundance.
Solution Approach 2:
The patent applies periodic fields (electrophoretic, acoustic, or magnetic) to dynamically manipulate the binding and release of nucleic acids to the affinity matrix. This periodic action enables selective enrichment of target sequences through repeated cycles of binding, washing, and release, achieving high purity without amplification-induced errors.
2Measurement precision
If conventional separation techniques are used to isolate low-abundance nucleic acids, then separation occurs, but resolution and fidelity are insufficient to pull enough low-abundance nucleic acids from background
Solution Approach 1:
The patent performs preliminary enrichment of target nucleic acids before separation by using affinity matrices to selectively capture target sequences from the complex background. This preliminary action concentrates the low-abundance targets, enabling subsequent separation techniques to achieve both high resolution and sufficient recovery of target molecules.
Solution Approach 2:
The patent introduces an affinity matrix as an intermediary between the sample and separation techniques. This intermediary selectively binds target nucleic acids through complementary base pairing, enabling precise separation and enrichment of low-abundance targets from background sequences with high fidelity.
3Measurement precision
If all nucleic acids are amplified prior to isolation and analysis, then detection sensitivity increases, but stochastic effects cause rare nucleic acids to be missed in early rounds
Solution Approach 1:
The patent extracts target nucleic acids from the background by using affinity matrices to selectively bind and concentrate rare sequences. By removing background interference and enriching targets before detection, the method achieves high detection sensitivity and consistency without relying on stochastic amplification processes.
4Quantity of substance
If PCR amplification is performed to detect rare sequence variants, then signal strength increases, but error rate increases significantly affecting sequence data
Solution Approach 1:
The patent replaces the biochemical amplification mechanism (PCR) with a physical enrichment mechanism using periodic fields and affinity matrices. This substitution maintains signal strength by concentrating target molecules through selective binding and field-driven manipulation, while avoiding the polymerase errors inherent in biochemical amplification.
Solution Approach 2:
The patent changes the fundamental parameter of enrichment from biochemical replication (PCR) to physical concentration (periodic field manipulation). By altering the mechanism from copying molecules to concentrating existing molecules, the method maintains sequence accuracy while achieving sufficient signal strength for detection.
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 enables the isolation and analysis of low-abundance nucleic acids with high specificity and sensitivity, reducing sample loss and error introduction, and allows for the detection of rare mutations in biological samples, such as cancer diagnostics, by enriching target nucleic acids up to 1,000,000-fold without generating new molecules.
Implementation Method 1
The method employs periodic fields to enrich target nucleic acids by driving non-target nucleic acids into a waste well
Implementation Method 2
using techniques like SCODA (Synchronous Coefficient of Drag Alteration) and zero-integrated-field electrophoresis (ZIFE) to concentrate and extract particles
Implementation Method 3
using techniques like SCODA (Synchronous Coefficient of Drag Alteration) and zero-integrated-field electrophoresis (ZIFE) to concentrate and extract particles
Data Source
AI summary
Methods and apparatus providing for the isolation of an unknown mutation from a sample comprising wild type nucleic acids and mutated nucleic acids through the application of time-varying driving fields and periodically varying mobility-altering fields to the sample within in an affinity matrix.