Oligonucleotide Candidate Design for Diverse Nucleic Acid Detection
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Solution Overview
Problem
Conventional oligonucleotide design methods struggle to efficiently detect target nucleic acid molecules with genetic diversity, particularly in multiplex detection scenarios, due to the computational complexity of handling large sequence information and sequence variability.
Innovation Solution
A computer-implemented method that designs a first oligonucleotide candidate group based on a selected nucleotide sequence of the target nucleic acid molecule, using complementary probes and/or primers, and incorporates degenerate or universal bases to enhance target coverage, while selecting oligonucleotides based on specific criteria such as non-complementarity levels and thermodynamic properties.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If conventional oligonucleotide design methods are used to detect target nucleic acid molecules with genetic diversity, then detection coverage is limited, but computational complexity increases significantly when handling large sequence information
Solution Approach 1:
The patent segments the target nucleic acid sequences into multiple groups based on genetic diversity characteristics. By dividing the large sequence information into manageable segments, the method reduces computational complexity while maintaining comprehensive detection coverage across diverse genetic variants
Solution Approach 2:
The patent designs universal oligonucleotides that can bind to multiple different target sequences with varying genetic diversity. These universal probes are engineered to accommodate sequence variations through degenerate bases and flexible binding regions, enabling a single oligonucleotide design to detect multiple genetic variants without requiring separate designs for each variant
2Measurement precision
If oligonucleotides are designed to cover all genetic variants, then detection accuracy improves, but the design process becomes increasingly difficult
Solution Approach 1:
The patent applies local quality by designing oligonucleotides with different functional regions having distinct properties. The 5' region uses degenerate bases to accommodate genetic diversity, the central region maintains high specificity for accurate binding, and the 3' region ensures proper elongation. This localized optimization allows the oligonucleotide to simultaneously achieve broad coverage and high detection accuracy without overwhelming design complexity
Solution Approach 2:
The patent systematically varies key parameters of oligonucleotide design including length, GC content, melting temperature, and degenerate base positioning to optimize detection accuracy across genetic variants. By establishing parameter ranges and selection criteria, the method transforms the complex design process into a systematic parameter optimization approach
3Adaptability or versatility
If conventional design methods are used for multiplex detection, then detection capability is limited, but the difficulty of designing suitable oligonucleotides becomes remarkable
Solution Approach 1:
The patent merges multiple detection capabilities into a single oligonucleotide design framework. By combining degenerate bases for genetic diversity accommodation, specific binding regions for target recognition, and optimized structural elements for multiplex compatibility, the method enables simultaneous detection of multiple genetic variants in a single reaction system
Solution Approach 2:
The patent introduces dynamic elements into oligonucleotide design through adjustable parameters such as degenerate base composition, length variations, and flexible binding regions. These dynamic design elements allow the oligonucleotides to adapt to different target sequences and detection conditions, enabling flexible multiplex detection configurations
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
Enables accurate detection of nucleic acid molecules with genetic diversity by providing optimized oligonucleotides that improve detection efficiency and adaptability to diverse sequences.
Implementation Method 1
designing oligonucleotides for detecting the target nucleic acid molecule... wherein the first oligonucleotide candidate group comprises a probe and/or a primer comprising a nucleotide sequence complementary to the first selected nucleotide sequence
Data Source
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AI summary
The present invention relates to technology for preparing oligonucleotides for detecting a target nucleic acid molecule in a sample. Unlike the conventional methods, the present invention provides a first oligonucleotide candidate group designed appropriately for the first selected nucleotide sequence of the target nucleic acid molecule as a standard instead of simultaneously referring to all of the sequences exhibiting the genetic diversity. Then, an optimal oligonucleotide capable of accurately detecting a target nucleic acid molecule exhibiting genetic diversity in a sample is provided by using the first oligonucleotide candidate group.