Attenuator Oligonucleotides for High-Abundance Sequence Suppression
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Solution Overview
Problem
Existing nucleic acid detection methods struggle to accurately quantify less abundant target sequences when highly abundant sequences (HATs) dominate the sample, leading to diminished detection sensitivity and dynamic range.
Innovation Solution
The use of attenuator oligonucleotides that compete with or replace detector oligonucleotides for highly abundant target sequences, reducing the overall number of HAT-related ligation or amplification products through hybridization, ligation blocking, and amplification inhibition.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If detector oligonucleotides are used to detect highly abundant target sequences, then detection sensitivity for HATs is improved, but the overall dynamic range and ability to detect less abundant sequences deteriorates
Solution Approach 1:
The patent segments the detection system into two functional components: detector oligonucleotides for detecting target sequences and attenuator oligonucleotides for suppressing highly abundant sequences. This segmentation allows independent optimization of each component's function, enabling sensitive detection of HATs while simultaneously attenuating their overwhelming signal to preserve dynamic range for less abundant sequences.
Solution Approach 2:
The attenuator oligonucleotides serve as intermediary elements that mediate between the detector oligonucleotides and the highly abundant target sequences. The attenuators bind to HATs and prevent detector oligonucleotides from binding to these abundant sequences, thereby reducing their signal contribution and preserving the dynamic range for detecting less abundant targets.
2Adaptability or versatility
If attenuator oligonucleotides are introduced to reduce HAT signal, then dynamic range for less abundant sequences is improved, but assay complexity increases
Solution Approach 1:
The patent employs parameter changes by designing attenuators with specific sequence characteristics (complementarity to HATs, appropriate binding affinity) and controlling their concentration relative to detector oligonucleotides. By adjusting these parameters, the system achieves effective attenuation of HATs while maintaining simplicity in the overall assay design and execution.
3Measurement precision
If detector oligonucleotides bind strongly to target sequences, then detection accuracy is improved, but non-specific binding and background noise increase
Solution Approach 1:
The patent extracts the problematic binding interaction by introducing attenuators that specifically target and sequester highly abundant sequences. This removes the source of non-specific binding and background noise generated by excessive HAT signals, thereby improving detection accuracy for genuine targets while reducing false positives.
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
Enhances the detection of less abundant target sequences by attenuating the signal from highly abundant sequences, optimizing the dynamic range and sensitivity of nucleic acid detection assays.
Implementation Method 1
Some attenuators are provided that can replace one or both detectors for a HAT. Other attenuators can be contacted with the sample in competition with the detectors.
Implementation Method 2
reducing the overall number of HAT-related ligation or amplification products through hybridization, ligation blocking, and amplification inhibition.
Implementation Method 3
reducing the overall number of HAT-related ligation or amplification products through hybridization, ligation blocking, and amplification inhibition.
Data Source
AI summary
Methods for detecting nucleic acid sequences, where attenuator oligonucleotides are provided to reduce the number of detection products resulting from highly abundant sequences.