Chemical Sequencing Probe Compositions for Enzyme-Free Long-Read Sequencing
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Solution Overview
Problem
Current nucleic acid sequencing methods are costly and time-consuming due to the need for enzymatic amplification and polymerization steps.
Innovation Solution
The development of sequencing probes with a target binding domain and a barcode domain that allow for enzyme-free, amplification-free, and library-free nucleic acid sequencing, featuring long-read-lengths and low error rates, utilizing modified nucleotides and a synthetic backbone with attachment positions for 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 detection sensitivity and signal strength are improved, but cost and time consumption increase
Solution Approach 1:
The patent extracts and eliminates the enzymatic amplification and polymerization steps from the sequencing process. By using direct hybridization of probes to target nucleic acids followed by imaging, the method removes the time-consuming enzymatic reactions while maintaining detection capability through fluorescently labeled probes that bind directly to the target sequence
Solution Approach 2:
The patent uses fluorescently labeled probes that act as detectable copies or signals for the target nucleic acid sequence. Instead of requiring enzymatic amplification to generate detectable signals, the fluorescent labels on the hybridized probes provide direct optical detection, enabling rapid imaging and sequence determination
2Reliability
If enzymatic amplification and polymerization steps are used for nucleic acid sequencing, then detection sensitivity is improved, but cost increases
Solution Approach 1:
The patent removes expensive enzymatic reagents and amplification materials from the sequencing workflow. By using direct probe hybridization with fluorescent labels, the method eliminates the need for costly polymerases, dNTPs, and other enzymatic components while maintaining adequate detection sensitivity through the fluorescent signal from bound probes
Solution Approach 2:
The patent employs disposable fluorescently labeled probes that can be synthesized economically and used in a single sequencing run. These probes replace expensive and complex enzymatic systems, providing a cost-effective alternative that achieves detection through direct hybridization and fluorescent imaging without requiring expensive enzymatic amplification reagents
3Reliability
If modified nucleotides are used in the target binding domain, then binding affinity and specificity are improved, but manufacturing complexity increases
Solution Approach 1:
The patent modifies the chemical parameters of the nucleotides in the probe's target binding domain by incorporating modified nucleotides such as locked nucleic acids (LNAs) or other analogs. These parameter changes in nucleotide structure enhance the probe's binding affinity and specificity for the target sequence, while the modifications are integrated into standard oligonucleotide synthesis protocols to manage manufacturing complexity
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
Enables rapid, cost-effective nucleic acid sequencing with high accuracy and long read lengths, suitable for clinical applications.
Implementation Method 1
the target binding domain comprises at least eight nucleotides and is capable of binding a target nucleic acid
Data Source
AI summary
The present disclosure relates to chemical compositions, kits, and apparatuses and methods for using these compositions, kits and apparatuses in various assays.