Nucleic Acid Probe Selection via Empirical Hybridization
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Solution Overview
Problem
Current nucleic acid probes face challenges in specificity due to hybridization with non-target sequences and splice isoforms, leading to non-specific detection and inefficient hybridization with target sequences.
Innovation Solution
The proposed solution involves empirical evidence-based probe selection techniques, including dimensional reduction of intensity pattern data to identify similar probes, hybridization to diverse biological isolates and orthogonal organisms, and evaluation of dynamic range and weighted parameter combinations to select or eliminate candidate probes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If probes are designed based on current sequence information, then probe selection can be performed, but the probes may hybridize to undocumented splice isoforms resulting in non-specific detection
Solution Approach 1:
The patent applies preliminary action by hybridizing candidate probes to nucleic acids from diverse biological isolates before final probe selection. This preliminary empirical testing identifies probes that maintain specificity across multiple isolates, filtering out probes that would hybridize to undocumented splice isoforms or non-target sequences. The process performs the selection criterion evaluation in advance using empirical data from multiple biological sources.
2Measurement precision
If bioinformatic techniques are used to simulate hybridization, then candidate probes can be evaluated, but the selected probes often do not perform as expected in actual hybridization
Solution Approach 1:
The patent implements feedback by comparing empirical hybridization results from diverse biological isolates with theoretical predictions. The actual hybridization behavior observed in empirical testing feeds back into the selection process, allowing refinement of probe selection criteria. This feedback loop ensures that selected probes demonstrate both theoretical selectivity and actual empirical performance, resolving the discrepancy between simulated and real-world hybridization behavior.
3Measurement precision
If probes are designed to detect target sequences, then detection capability is achieved, but hybridization to non-target sequences with sufficient similarity generates false signals
Solution Approach 1:
The patent applies segmentation by evaluating probe performance across multiple segmented biological isolates rather than a single target. Candidate probes are tested against a segmented panel of diverse biological isolates, and only probes that maintain consistent specificity across all segments are selected. This segmentation approach divides the validation process into multiple independent tests, ensuring robust discrimination against non-target sequences.
4Reliability
If empirical testing across diverse biological isolates is performed, then probe specificity is improved, but the complexity of the selection process increases
Solution Approach 1:
The patent applies universality by using the same empirical testing approach and selection criteria across multiple diverse biological isolates. The methodology is designed to be universally applicable to different probe targets and biological systems, using a consistent multi-isolate testing framework. This universal approach streamlines the process by applying a single robust methodology rather than requiring separate optimization for each probe type.
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 improves probe selection by enhancing specificity and efficiency of hybridization, reducing non-specific binding and identifying more effective probes for target sequence detection.
Implementation Method 1
A probe is typically a molecule that includes a nucleic acid sequence that is complementary to a nucleic acid sequence within a target molecule of interest, such as a gene or an RNA molecule
Data Source
AI summary
Probe selection techniques are based, at least in part, on empirical evidence concerning the hybridization of candidate probes across a panel of diverse biological isolates. Various principles concerning the behavior of the most preferable probes across a panel of diverse biological isolates are applied to select from among a set of candidate probes or to eliminate candidate probes from further consideration.