Nanopore Detection of Coded Molecules for Multiplexed SNP Analysis
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Solution Overview
Problem
Existing nucleic acid detection methods, such as microarrays and microbeads, are susceptible to variability in amplification efficiency and limited by the need for signal summation from probe-target interactions, which affects sensitivity and consistency in detecting nucleic acids, especially in multiplexing reactions for single nucleotide polymorphisms (SNPs).
Innovation Solution
The use of coded molecules with block polymer regions and target probes that undergo modification upon hybridization with target polynucleotides, followed by translocation through a nanopore to detect signal patterns indicative of the presence and identity of specific nucleic acids, allowing for sensitive and specific detection of multiple targets in a single reaction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If microarray and microbead based detection methods are used, then high-throughput capacity and sensitivity are achieved, but variability in amplification efficiency adversely affects determination of target presence
Solution Approach 1:
The patent extracts the amplification step from the detection workflow by using nanopore sequencing to directly detect target nucleic acids without requiring prior amplification. This eliminates the source of variability while maintaining high-throughput capability through parallel nanopore measurements
Solution Approach 2:
The patent replaces the optical signal detection system (microarray/microbead fluorescence) with an electrical measurement system (nanopore current blockade). This substitution enables direct detection of individual molecules without signal summation, improving both reliability and sensitivity
2Measurement precision
If signal summation from population of probe-target interactions is used, then detection capability is achieved, but sensitivity is limited
Solution Approach 1:
The patent uses nanopore sequencing to create digital copies of the detection signal through sequential reading of individual nucleic acid molecules. Each molecule translocation through the nanopore generates a discrete electrical signal that can be independently analyzed, enabling detection of rare targets without signal dilution
Solution Approach 2:
The patent changes the detection parameter from optical signal intensity (analog, summated) to electrical current blockade duration and magnitude (digital, molecule-specific). This parameter change enables discrimination of individual target molecules based on their unique translocation signatures, dramatically improving sensitivity
3Use of energy by moving object
If amplification of target nucleic acid is performed, then detection signal is enhanced, but variability in amplification efficiency adversely affects result determination
Solution Approach 1:
The patent segments the detection process into independent nanopore measurement events, where each target molecule is detected individually as it translocates through the nanopore. This segmentation eliminates the need for bulk amplification while maintaining sufficient signal through direct electrical detection of each molecule's unique translocation signature
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 enhances sensitivity and adaptability for multiplexed SNP detection, reducing variability and improving consistency by isolating modified coded molecules based on signal pattern changes, enabling the detection of various nucleic acids, including those associated with diseases and genetic markers.
Implementation Method 1
The coded molecule is then translocated through a nanopore and interrogated to detect a signal that is reflective of the polymer characteristics of the block polymer region
Implementation Method 2
the coded molecule comprises one or more block polymer regions and a target probe capable of hybridizing to the target polynucleotide
Data Source
AI summary
The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.