Hairpin Chimeric Primers for Low-Background Multiplex Amplification
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing nucleic acid amplification and detection techniques require optimization of primer concentrations, are slow, have high non-specific background, low sensitivity, and limited multiplexing capabilities.
Innovation Solution
The use of chimeric primers with hairpin conformations, comprising target-specific sequences, anti-tag sequences, and blockers, which form stable hairpins until amplification, allowing for efficient amplification and detection with reduced non-specific signals and higher multiplexing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional primers are used for nucleic acid amplification, then amplification can be achieved, but primer concentration optimization is required and results are slow
Solution Approach 1:
The patent modifies the physical-chemical parameters of primers by adding hairpin-forming sequences with specific thermodynamic properties. The hairpin structures have controlled melting temperatures and stability constants that enable automatic primer concentration optimization, eliminating the need for manual optimization while accelerating amplification kinetics.
Solution Approach 2:
The hairpin sequences are pre-designed and incorporated into primers before the amplification reaction. The hairpin structures form preliminary stable conformations that control primer availability and binding kinetics, enabling faster amplification without requiring optimization during the assay setup.
2Measurement precision
If conventional detection methods are used, then nucleic acid detection is achieved, but non-specific background is high and sensitivity is low
Solution Approach 1:
The patent introduces localized hairpin structures at specific positions within primers, creating regions of enhanced stability and specificity. These localized modifications improve binding discrimination at the molecular level, reducing non-specific background while enhancing detection sensitivity without affecting overall primer function.
3Adaptability or versatility
If standard primer sets are used, then amplification works, but multiplexing capability is limited
Solution Approach 1:
The patent designs universal hairpin sequences that can be incorporated into multiple primer sets simultaneously. These universal elements provide consistent performance characteristics across different primer pairs, enabling reliable multiplexing of multiple targets in a single reaction while maintaining assay consistency through the standardized hairpin structures.
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
These primers provide faster results, lower background noise, higher sensitivity, and improved representation of product concentration, enabling higher multiplexing and reducing the need for optimization.
Implementation Method 1
chimeric primers with hairpin conformations, comprising target-specific sequences, anti-tag sequences, and blockers, which form stable hairpins until amplification
Implementation Method 2
the anti-tag sequence and the tag sequence of the primer hybridize to form a hairpin structure
Data Source
AI summary
Methods and compositions for nucleic acid amplification, detection, and genotyping techniques are disclosed. In one embodiment, a nucleic acid molecule having a target-specific primer sequence; an anti-tag sequence 5′ of the target-specific primer sequence; a tag sequence 5′ of the anti-tag sequence; and a blocker between the anti-tag sequence and the tag sequence is disclosed. Compositions containing such a nucleic acid molecule and methods of using such a nucleic acid molecule are also disclosed.