Binding-Induced Hairpin Detection System for Low Background Noise
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Solution Overview
Problem
Current detection systems face challenges in minimizing background noise and achieving high sensitivity for detecting target molecules, as they often result in high background levels due to non-specific binding of probes, which limits the detection of trace amounts of target molecules.
Innovation Solution
A detection system that forms a binding-induced hairpin structure only when bound to a target molecule, using a first probe with a targeting molecule and an oligonucleotide with a free end, and a second probe with a complementary oligonucleotide that hybridizes to form a stable hairpin structure, reducing background noise and enhancing sensitivity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If the concentration of probes is increased to improve sensitivity for detecting target molecules, then the detection sensitivity is improved, but the background noise increases
Solution Approach 1:
The probe is pre-configured with a blocking oligonucleotide that prevents premature hybridization. This preliminary blocking action allows the probe to be used at higher concentrations for improved sensitivity while the blocking mechanism prevents background noise by inhibiting non-specific binding until the target is present
Solution Approach 2:
The blocking oligonucleotide acts as an intermediary element that mediates between the probe and non-specific binding sites. It temporarily blocks the probe's binding capability and only allows hybridization when the target molecule is present, thus enabling high probe concentrations without background noise
2Object-generated harmful factors
If the concentration of probes is decreased to reduce background noise, then the background is minimized, but the detection sensitivity decreases
Solution Approach 1:
The probe is pre-configured with a blocking oligonucleotide that prevents premature hybridization. This preliminary blocking action allows the probe to be used at higher concentrations for improved sensitivity while the blocking mechanism prevents background noise by inhibiting non-specific binding until the target is present
Solution Approach 2:
The blocking oligonucleotide changes the binding parameters of the probe by introducing a conditional blocking mechanism. This allows the probe to maintain high affinity for the target while exhibiting low affinity for non-specific binding sites, effectively changing the probe's interaction parameters based on the presence of the target
3Stability of the object's composition
If a stable hybridization structure is formed without target binding to improve detection signal, then the signal stability is improved, but the specificity decreases due to non-target specific binding
Solution Approach 1:
The probe is pre-configured with a blocking oligonucleotide that prevents premature hybridization. This preliminary blocking action allows the probe to be used at higher concentrations for improved sensitivity while the blocking mechanism prevents background noise by inhibiting non-specific binding until the target is present
Solution Approach 2:
The blocking oligonucleotide introduces dynamic behavior to the probe's binding characteristics. The probe transitions from a blocked state (low stability with non-targets) to an unblocked state (high stability with target) based on the presence of the target molecule, making the hybridization stability dynamic rather than static
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 minimizes background noise and increases sensitivity by forming a stable, amplifiable hairpin structure specifically when the probes are bound to a target molecule, allowing for effective detection of trace amounts of target molecules.
Implementation Method 1
the free end of the oligonucleotide of the second probe hybridizes at or near the free end of the oligonucleotide of the first probe forming a hairpin stem
Data Source
AI summary
This application relates to a binding-induced hairpin detection system comprising: a. a first probe comprising a targeting molecule and an oligonucleotide that has a free end and an end attached to the targeting molecule; and b. a second probe comprising a targeting molecule and an oligonucleotide that has an end attached to the targeting molecule and a free end comprising a nucleotide sequence that is complementary to a nucleotide sequence at or near the free end of the oligonucleotide of the first probe; wherein upon binding of the targeting molecule to a target molecule, the free end of the oligonucleotide of the second probe hybridizes at or near the free end of the oligonucleotide of the first probe forming a hairpin stem, the non-hybridized portions of the first and second probes together with the target molecule bound thereto forming a hairpin loop, thereby providing a binding-induced hairpin.