Nucleic Acid Sequencing Ternary Complex Imputation
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Solution Overview
Problem
Current nucleic acid sequencing methods are inadequate for rapid, accurate, and cost-effective clinical applications, particularly in diagnosing diseases where timely results are critical, as they often require complex detection hardware and consume significant time and reagents.
Innovation Solution
The method involves forming ternary complexes with a primed template nucleic acid, polymerase, and nucleotide cognates under stabilizing conditions, allowing for the identification of the next correct nucleotide by detecting ternary complex formation and imputing the presence of absent nucleotide types, reducing the need for multiple reagent deliveries and detection channels.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If multiple separate mixtures and detection channels are used to identify all nucleotide types, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The patent extracts only three nucleotide types from the complete set of four nucleotide types for detection. By detecting ternary complexes formed with three specific nucleotide cognates and imputing the fourth type based on its absence, the method reduces the number of detection channels and reagent mixtures required, thereby simplifying device complexity while maintaining measurement precision
Solution Approach 2:
The patent uses imputation to create a virtual representation of the undetected nucleotide type. By detecting the presence or absence of ternary complexes for three nucleotide types and logically inferring the fourth type, the method creates an accurate copy of the complete nucleotide information without requiring direct detection of all four types, thus reducing hardware complexity
2Measurement precision
If multiple separate mixtures are delivered sequentially to identify all nucleotide types, then measurement precision is improved, but loss of time increases
Solution Approach 1:
The patent extracts detection of only three nucleotide types per sequencing cycle instead of delivering and detecting all four nucleotide types. This reduction in the number of reagent deliveries and detection steps directly decreases the time required for each sequencing cycle while maintaining accurate nucleotide identification through imputation of the fourth type
Solution Approach 2:
The patent performs preliminary detection with a reduced set of three nucleotide types, and the imputation of the fourth nucleotide type is performed as a computational step rather than requiring additional experimental time. This preliminary action with fewer reagents reduces the experimental cycle time while achieving complete nucleotide identification
3Measurement precision
If multiple separate mixtures with different nucleotide types are used, then measurement precision is improved, but quantity of substance increases
Solution Approach 1:
The patent extracts and detects only three nucleotide types per sequencing cycle instead of using all four nucleotide types in separate mixtures. This reduction in the number of nucleotide cognates required per cycle directly decreases reagent consumption while maintaining measurement precision through the imputation of the fourth nucleotide type based on the absence of its ternary complex signal
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 enhances the speed, accuracy, and cost-effectiveness of nucleic acid sequencing by minimizing hardware complexity and reagent consumption, enabling more efficient nucleotide identification and sequencing.
Implementation Method 1
forming a mixture under ternary complex stabilizing conditions, wherein the mixture includes a primed template nucleic acid, a polymerase and nucleotide cognates of first, second and third base types in the template
Data Source
AI summary
A method of nucleic acid detection including (a) contacting a primed template with a polymerase, nucleotide cognate of a first base type and nucleotide cognate of a second base type under ternary complex stabilizing conditions; (b) contacting the primed template nucleic acid with a polymerase, nucleotide cognate of the first base type and nucleotide cognate of a third base type under ternary complex stabilizing conditions; (c) examining products of (a) and (b) for signals produced by a ternary complex that includes the primed template nucleic acid, polymerase and next correct nucleotide, wherein signals for the product of (a) are ambiguous for the first and second base type, and signals for the product of (b) are ambiguous for the first and third base type; (d) disambiguating signals acquired in (c) to identify the next correct nucleotide.