Nucleic Acid Quantification via Dynamic Range Compression
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Solution Overview
Problem
Current nucleic acid quantification and detection methods face challenges in efficiently analyzing low-abundance nucleic acid sequences within a mixed population, leading to high resource consumption and repeated analysis of abundant sequences.
Innovation Solution
The method involves preparing a mixture of target nucleic acids with counterpart nucleic acids that share a substantially identical sequence but have a distinguishing feature, under conditions where they hybridize, followed by dynamic range compression using capture nucleic acids that interact with both targets and counterparts with equal affinity, allowing for the quantification and identification of each nucleic acid species.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional nucleic acid quantification methods are used, then abundant sequences can be detected, but low-abundance sequences are missed and repeated analysis is required
Solution Approach 1:
The patent introduces counterpart nucleic acids that are identical copies of target sequences but with distinguishing features (such as different fluorescent labels or modifications). These counterparts serve as internal references that allow simultaneous detection of both abundant and low-abundance sequences in a single analysis, eliminating the need for repeated analysis and improving both detection sensitivity and analysis efficiency.
Solution Approach 2:
The patent applies local quality by introducing distinguishing features at specific locations within the nucleic acid sequences. The counterparts contain localized modifications (such as fluorescent tags or chemical modifications) at particular positions that enable differential detection. This allows the system to distinguish between targets and counterparts while maintaining sequence identity in functional regions, thereby improving detection precision without requiring repeated analyses.
2Loss of energy
If conventional quantification methods are used, then resource consumption increases due to repeated analysis, but the patent reduces resource usage through dynamic range compression
Solution Approach 1:
The patent introduces capture nucleic acids as intermediary molecules that selectively bind to both targets and counterparts. These capture nucleic acids act as mediators that compress the dynamic range of the mixture by preferentially capturing abundant sequences, thereby reducing the relative abundance differences between high and low abundance sequences. This allows accurate quantification of low-abundance sequences without requiring repeated analysis, thereby reducing resource consumption while maintaining quantification accuracy.
Solution Approach 2:
The patent changes the parameter of nucleic acid concentration distribution through dynamic range compression. By introducing capture nucleic acids that selectively bind to targets and counterparts, the system alters the concentration parameters of the mixture, transforming a wide dynamic range into a compressed range that is easier to analyze. This parameter change enables accurate detection of low-abundance sequences in a single analysis, reducing the need for repeated measurements and lowering resource consumption.
3Productivity
If nucleic acid sequences are analyzed without dynamic range compression, then abundant sequences require repeated analysis, but compression enables single-pass detection of low-abundance sequences
Solution Approach 1:
The patent merges multiple analysis steps into a single integrated process. By combining targets, counterparts, and capture nucleic acids in one reaction mixture, the system simultaneously performs sequence detection, quantification, and dynamic range compression in a single pass. This merging of functions increases analysis throughput by eliminating repeated analyses while the use of standardized molecular biology techniques keeps the overall method complexity manageable.
Solution Approach 2:
The patent creates a universal system where capture nucleic acids serve multiple functions: they act as probes for detecting both targets and counterparts, they compress the dynamic range of the mixture, and they enable simultaneous quantification of sequences across a wide abundance range. This multi-functionality increases analysis throughput by performing multiple operations in a single experiment while using well-established molecular biology reagents and techniques to maintain acceptable method complexity.
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 detection and quantification of low-abundance nucleic acid sequences while reducing the need for repeated analysis of abundant sequences, thereby optimizing resource usage and improving the efficiency of nucleic acid analysis.
Implementation Method 1
contacting (i) a plurality of target nucleic acids of a biological sample (targets) with (ii) a known amount of a counterpart nucleic acid for each of the targets (counterparts), where each counterpart comprises (i) a nucleotide sequence substantially identical to its target, and (ii) a feature that distinguishes each counterpart from its target, under conditions in which the targets hybridize to their counterparts
Implementation Method 2
contacting the mixture with a set of capture nucleic acids, where (i) each capture nucleic acid in the set specifically hybridizes to a target and counterpart, (ii) each capture nucleic acid in the set hybridizes with substantially the same strength to the target and counterpart to which it specifically hybridizes
Data Source
AI summary
Described herein are products and processes for nucleic acid quantification, which are in part useful for detecting and determining the nucleotide sequence of rare nucleic acids (i.e., low copy number nucleic acids) in a sample. Such products and processes are useful for reducing the dynamic range among different nucleic acid species.