Splice-Junction Probe Linking for Precise Nucleic Acid Analysis
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing methods for analyzing splice junction sites in nucleic acid molecules, such as those found in mRNA isoforms, are inefficient and lack the ability to accurately identify and associate these sites with specific diseases or cell surface proteins.
Innovation Solution
A method involving the use of probes that hybridize to exon segments flanking a splice junction site, linking these probes together to form a probe-linked nucleic acid molecule, and identifying the sequence to locate the splice junction, optionally with barcode sequences for sample association.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional methods are used for analyzing splice junction sites, then the analysis can be performed, but the efficiency is low and accuracy is insufficient
Solution Approach 1:
The method divides the splice junction analysis into distinct segments: first exon segment targeting, second exon segment targeting, and junction site identification. Probes are designed to hybridize to specific exon segments flanking the splice junction, enabling systematic and efficient analysis of splice sites while maintaining high accuracy through structured multi-step processing.
Solution Approach 2:
The method performs preliminary hybridization of probes to exon segments before final junction identification. By pre-positioning probes on the first and second exon segments, the system prepares the nucleic acid molecule for accurate splice junction detection, improving both efficiency by avoiding repeated attempts and accuracy by ensuring proper probe alignment.
2Measurement precision
If probes are designed to hybridize to exon segments flanking the splice junction, then precise localization is achieved, but the complexity of the method increases
Solution Approach 1:
The probe set is designed with universal applicability across different splice junction sites. The same basic probe structure and hybridization protocol can be applied to various exon segments and splice junctions, reducing method complexity while maintaining high localization precision. The modular probe design allows reuse across multiple analysis scenarios.
Solution Approach 2:
The probes serve as intermediary molecules that bridge the gap between the detection system and the splice junction site. By hybridizing to exon segments flanking the junction, the probes mediate precise localization without requiring direct interaction with the junction itself, simplifying the overall detection mechanism while achieving high precision.
3Measurement precision
If barcode sequences are incorporated for sample association, then disease and isoform identification accuracy is enhanced, but the manufacturing complexity increases
Solution Approach 1:
The barcode sequence is merged directly into the probe structure, combining the detection function and the identification function into a single molecular entity. This integration allows the same probe that hybridizes to the exon segment also carries the barcode for sample association, reducing manufacturing steps while enhancing disease and isoform identification accuracy through linked data.
Solution Approach 2:
The barcode sequence acts as a copyable identifier that can be replicated across multiple probes targeting the same or different splice junctions. This copying mechanism allows standardized identification tags to be efficiently manufactured and distributed, reducing overall manufacturing complexity while enabling accurate sample association for disease identification.
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 precise localization of splice junction sites and association with diseases or mRNA isoforms, enhancing the accuracy of disease identification and protein expression analysis.
Implementation Method 1
a first probe, wherein the first probe hybridizes to a first target sequence of the first exon segment, and (ii) a second probe, wherein the second probe hybridizes to a second target sequence of the second exon segment
Data Source
AI summary
Provided herein are systems and methods for analyzing biomolecules (e.g., nucleic acid molecules, proteins). A method of nucleic acid analysis can comprise: (a) providing a sample comprising a cell comprising a target polynucleotide comprising a first exon segment and a second exon segment, wherein the first exon segment and the second exon segment flank opposite ends of a splice junction site of the target polynucleotide. The method can further comprise (b) contacting the cell with: (i) a first probe, wherein the first probe hybridizes to a first target sequence of the first exon segment, and (ii) a second probe, wherein the second probe hybridizes to a second target sequence of the second exon segment. The method can further comprise (c) linking the first probe and the second probe together, thereby generating a probe-linked nucleic acid molecule comprising the first probe and the second probe. The method can further comprise (d) identifying a sequence of the probe-linked nucleic acid molecule or derivative thereof, thereby locating the splice junction site of the target polynucleotide.