Oligonucleotide Design for Maximum Nucleic Acid Sequence Coverage
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Solution Overview
Problem
Current methods for detecting nucleic acid sequences with genetic diversity, such as those from viral genomes, face challenges in achieving maximum target coverage due to genetic variability, leading to false negatives and inefficiencies, especially when dealing with a large number of sequences.
Innovation Solution
The development of an optimization logic for introducing degenerate and universal bases into oligonucleotides to maximize target coverage, involving the selection of probing sequences, a reference oligonucleotide, and strategic introduction of bases to ensure maximum matching with multiple sequences, utilizing linear programming for optimal base placement.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional sequential or random methods are used to introduce degenerate bases into oligonucleotides, then the design process is simple to implement, but the target coverage is insufficient and detection accuracy deteriorates
Solution Approach 1:
The patent transforms the oligonucleotide design problem from a sequential/random process into an optimization problem by changing the parameter selection strategy. Linear programming is used to optimize the introduction positions and numbers of degenerate bases, transforming subjective design into objective mathematical optimization that maximizes target coverage while maintaining design feasibility.
Solution Approach 2:
The patent replaces the mechanical/manual design process with computational optimization. Instead of sequentially or randomly introducing degenerate bases through manual design, the system uses linear programming algorithms to automatically determine optimal base introduction positions and quantities, substituting computational mathematics for traditional manual oligonucleotide design methods.
2Measurement precision
If multiple probes are designed to cover all nucleic acid sequences, then target coverage is improved, but the number of probes increases and operational complexity worsens
Solution Approach 1:
The patent creates universal oligonucleotides that can detect multiple different target sequences simultaneously through the strategic use of degenerate bases. A single optimized oligonucleotide with degenerate bases at specific positions can hybridize to multiple variant sequences, replacing the need for multiple separate probes and simplifying the detection system while maintaining comprehensive coverage.
3Adaptability or versatility
If degenerate bases are introduced to detect diverse sequences, then versatility is improved, but the number of possible sequences increases and manufacturing precision worsens
Solution Approach 1:
The patent applies local quality by introducing degenerate bases only at specific positions where sequence variation occurs, rather than throughout the entire oligonucleotide. The linear programming optimization identifies exactly which positions benefit from degeneracy, allowing the oligonucleotide to maintain high specificity at most positions while having controlled variability only where needed for detecting diverse sequences.
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 rapid and accurate detection of multiple nucleic acid sequences with improved speed and accuracy, enhancing the ability to cover diverse sequences effectively and efficiently.
Implementation Method 1
designing oligonucleotides with taking into account a certain sequence of a target nucleic acid molecule of this pathogen is very likely to lead to false negative results. Thus, in order to determine whether a certain pathogen is present in an unknown sample, probes or primers should be designed in consideration of all nucleic acid sequences or as many nucleic acid sequences as possible of known genetic diversity for one target nucleic acid molecule of this certain pathogen.
Data Source
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AI summary
The present invention relates to optimization logic for preparing an optimal introduction of degenerate bases and/or universal bases into an oligonucleotide used to detect a plurality of target nucleic acid sequences, in a completely different approach from conventional methods, i.e., empirical and manual methods. In addition, the optimization logic of the present invention may be used in (i) the preparation of an oligonucleotide into which a limited number of degenerate bases and/or universal bases are introduced for detecting a plurality of target nucleic acid sequences with a maximum target coverage, and (ii) the determination of a probing region in a plurality of target nucleic acid sequences.