DNA Strand Sequencing Using Redox-Modified Nucleotides
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Solution Overview
Problem
Existing nucleic acid sequencing methods are limited in efficiency and precision, particularly in determining the sequence of DNA strands, and there is a need for alternative approaches that enhance sequencing accuracy and reduce computational requirements.
Innovation Solution
The method involves forming a ligated product from a double-stranded DNA fragment using hairpin oligonucleotides, followed by rolling circle amplification and primer extension with redox-modified nucleotides, and electrochemical sequencing to determine the DNA sequence.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional sequencing methods are used, then sequencing can be performed, but sequencing precision and efficiency are limited
Solution Approach 1:
The patent changes the chemical parameters of nucleotides by introducing redox modifications with different oxidation/reduction potentials. This allows nucleotides to be distinguished by their electrochemical properties rather than just optical or structural characteristics, thereby improving sequencing precision while maintaining efficiency through parallel processing of multiple nucleotide types
Solution Approach 2:
The patent introduces redox-modified nucleotides as intermediaries that carry both genetic information and detectable electrochemical signals. These modified nucleotides act as mediators between the DNA sequence and the detection system, enabling simultaneous measurement of multiple parameters (sequence identity and redox potential) to improve both precision and efficiency
2Measurement precision
If redox-modified nucleotides are used, then sequencing precision is improved, but computational demands increase
Solution Approach 1:
The patent segments the sequencing problem into distinct electrochemical measurements for different redox-modified nucleotide types. By dividing the nucleotide set into groups with different redox potentials (first group: dATP, dTTP, dUTP; second group: dCTP, dGTP), the system can identify nucleotides through sequential electrochemical readings, reducing the computational complexity compared to analyzing all nucleotides simultaneously with a single detection method
Solution Approach 2:
The patent employs periodic electrochemical measurements with varying oxidation and reduction potentials to sequentially identify different nucleotide types. This periodic application of different electrochemical conditions allows the system to extract information about multiple nucleotide types through repeated cycles of oxidation and reduction, thereby reducing the computational burden by spreading measurements over time rather than requiring simultaneous complex analysis
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 increases sequencing precision and reduces computational demands by using redox-modified nucleotides to generate distinct electrochemical signals for accurate sequence determination, enhancing the efficiency of DNA sequencing.
Implementation Method 1
each redox-modified nucleotide in the first group having a first redox species with a first oxidation or reduction potential and each redox-modified nucleotide in the second group having a second redox species with a second oxidation or reduction potential
Data Source
AI summary
The disclosure relates to a method for sequencing of a DNA strand, the method includes (S200) providing a double-stranded DNA fragment with a first strand and a second strand, the DNA strand to be sequenced corresponding to the first strand or the second strand, (S300A) connecting the first and second strands with a first hairpin oligonucleotide and a second hairpin oligonucleotide, (S500A) amplifying the ligated product obtained in step (S300A) using rolling circle amplification (RCA), (S600A) amplifying the ligated product obtained in step (S300A) using RCA or the amplicons obtained in step (S500A) using primer extension using a first group of redox-modified nucleotides and a second group of redox-modified nucleotides, and (S800A) determining the sequence of the DNA strand by sequencing the amplicons (80) obtained in step (S600A) using an electrochemical sequencing method.