Small RNA Detection via Barcoded Sensor DNA and Nanopore Sequencing
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Solution Overview
Problem
Existing methods struggle to detect and quantify small RNA with high sensitivity and accuracy, particularly in early stages of diseases such as cancer and infectious diseases, and are limited by nanopore sequencing's inability to analyze short base sequences.
Innovation Solution
A method involving sensor DNA hybridization, polymerization, amplification, and nanopore sequencing, using a unique barcode region to identify and count target small RNAs, allowing for high sensitivity and accuracy detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If nanopore sequencing is used for detection, then the detection method is simple, but it cannot analyze short base sequences of small RNA
Solution Approach 1:
The patent embeds the small RNA target within a larger structure by hybridizing it to sensor DNA, creating a hybrid molecule that combines the short RNA with longer DNA sequences. This nested structure allows the short RNA to be analyzed by nanopore sequencing, which can detect the electrical signal changes caused by the RNA portion while the DNA provides sufficient length for reliable sequencing.
Solution Approach 2:
The sensor DNA acts as an intermediary that bridges the gap between the short small RNA target and the nanopore sequencing system. The sensor DNA hybridizes with the target RNA to form a stable complex that can be effectively detected, while the unique barcode region of the sensor DNA enables identification and counting of target molecules.
2Ease of operation
If existing detection methods are used, then the detection process is straightforward, but sensitivity and accuracy are insufficient for early stage disease diagnosis
Solution Approach 1:
The patent performs preliminary enrichment and specific binding of target small RNA to sensor DNA before sequencing. This preliminary action concentrates the target molecules and removes background noise, thereby improving detection sensitivity and accuracy without significantly complicating the overall process.
Solution Approach 2:
The sensor DNA contains a unique barcode region that provides local quality differentiation. This barcode region enables precise identification and counting of individual target molecules, improving measurement precision while maintaining ease of operation through standardized protocols.
3Reliability
If quantitative detection of small RNA is achieved, then early disease diagnosis is enabled, but detection limits must reach femtomolar and attomolar levels
Solution Approach 1:
The patent uses the unique barcode region in the sensor DNA to create identifiable copies of the target RNA. Each barcode serves as a unique identifier that can be amplified and detected, allowing quantitative measurement at extremely low concentrations through signal amplification while maintaining reliability for clinical diagnosis.
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
The method achieves detection limits at femtomolar and attomolar levels, enabling early and latent stage disease diagnosis with high sensitivity and accuracy, overcoming limitations of existing technologies.
Implementation Method 1
hybridizing sensor DNA comprising a complementary sequence of target small RNA to be detected with the target small RNA
Implementation Method 2
performing polymerization with a polymerase using a module region of the sensor DNA as a template and the target small RNA as a primer
Implementation Method 3
analyzing a sequence of the amplicon
Data Source
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AI summary
The present invention relates to a method of analyzing and detecting small RNA. In particular, the present invention can also analyze even RNA having a short base sequence, and quantitatively detect the RNA with high sensitivity and accuracy, and thus can be widely used for diagnosis of various diseases such as infectious diseases and cancer.