Barcode Probe Sequencing for Enzyme-Free Nucleotide Detection
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Solution Overview
Problem
Current nucleic acid sequencing methods require enzymatic amplification and polymerization steps, which are costly and time-consuming, and there is a need for a rapid, amplification- and enzyme-free sequencing method with long-read-lengths and low error rates.
Innovation Solution
The use of sequencing probes with barcode domains where each position corresponds to at least two nucleotides in the target binding domain, combined with a synthetic backbone and cleavable linkers, allows for enzyme-free, amplification-free nucleic acid sequencing with rapid sample-to-answer capability.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If enzymatic amplification and polymerization steps are used for nucleic acid sequencing, then detectable signal can be produced, but the process becomes costly and time-consuming
Solution Approach 1:
The patent extracts and eliminates the enzymatic amplification and polymerization steps from the sequencing process. By using probes with barcode domains that directly hybridize to target nucleic acids, the method removes the need for costly and time-consuming enzymatic reactions while maintaining detectable signal through optical detection of barcode positions.
Solution Approach 2:
The patent replaces the biochemical enzymatic system with a physical hybridization-based system. Instead of using enzymes for amplification and polymerization, the method uses nucleic acid hybridization to attach probes to target sequences, followed by optical detection of fluorescent barcodes, thereby substituting mechanical/physical processes for biochemical ones.
2Reliability
If enzymatic amplification and polymerization steps are used for nucleic acid sequencing, then detectable signal can be produced, but the cost increases
Solution Approach 1:
The patent extracts and eliminates the enzymatic amplification and polymerization steps from the sequencing process. By using probes with barcode domains that directly hybridize to target nucleic acids, the method removes the need for costly and time-consuming enzymatic reactions while maintaining detectable signal through optical detection of barcode positions.
Solution Approach 2:
The patent employs disposable probes with barcode domains that can be synthesized inexpensively and used in large numbers. Each probe is a short-lived, single-use element that hybridizes to the target and is then detected and discarded, replacing the need for expensive reusable enzymatic systems and amplification reagents.
3Reliability
If conventional sequencing methods are used, then nucleic acid can be sequenced, but amplification and enzyme steps are required
Solution Approach 1:
The patent segments the sequencing process into distinct functional domains within the probe structure: a target-binding domain for specific hybridization and a barcode domain for detection. This segmentation allows the probe to perform multiple functions (binding and encoding) in a single element, eliminating the need for separate amplification and enzyme steps.
Solution Approach 2:
The patent creates a universal probe structure that combines target recognition and information encoding in a single molecule. The barcode domain serves multiple functions by encoding positional information about the target sequence, eliminating the need for separate amplification and detection reagents, thereby reducing process complexity while maintaining accuracy.
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 enables rapid, cost-effective nucleic acid sequencing with long read lengths and low error rates, particularly suitable for clinical applications.
Implementation Method 1
the target binding domain hybridizes to a target nucleic acid
Implementation Method 2
a first complementary nucleic acid molecule hybridized to a first attachment position of the at least three attachment positions
Data Source
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AI summary
The present disclosure relates to chemical compositions, kits, and apparatuses and methods for using these compositions, kits and apparatuses in various assays.