Synthetic Nucleotides with Ionic Reporter Linkers for Sequencing
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Solution Overview
Problem
Current nucleotide polymer analysis methods are costly and require complex, expensive devices, limiting their widespread adoption, especially in developing countries, due to the need for skilled technicians and sensitive fluorescence measurements.
Innovation Solution
Development of synthetic nucleotides with a high charge mass reporter moiety attached via a linker molecule, which can be detected by biosensors without interfering with polymerization, allowing for cost-effective and user-friendly nucleotide polymer analysis devices.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If fluorescent reporters are used for nucleotide detection, then detection sensitivity is improved, but device complexity and cost increase
Solution Approach 1:
The patent replaces optical/fluorescent detection systems with electrochemical detection. Instead of using fluorescent reporters that require complex optical instrumentation, the invention uses ionic reporters that generate electrical signals through redox reactions, substituting a simpler electrochemical system for the complex optical system.
Solution Approach 2:
The patent employs inexpensive ionic reporter molecules (such as ferrocene derivatives or viologen compounds) that can be attached to nucleotides, replacing expensive fluorescent dyes. These ionic reporters provide sufficient detection capability at a fraction of the cost while enabling the use of simpler, more affordable sequencing devices.
2Productivity
If ionic reporters are attached via short linkers, then detection efficiency is improved, but polymerization is inhibited
Solution Approach 1:
The patent employs variable-length linker molecules (ranging from 1 to 20 carbon atoms) that provide dynamic flexibility. The linker acts as a flexible tether that allows the ionic reporter to be positioned at optimal distances from the nucleotide base, enabling both efficient detection and unhindered polymerization by accommodating different spatial requirements during the sequencing process.
Solution Approach 2:
The patent extends the detection moiety into a different spatial dimension by using linker molecules that project the ionic reporter away from the nucleotide stacking plane. This dimensional extension allows the reporter to be positioned in a region where it can be detected by the electrode while not interfering with the two-dimensional stacking and hydrogen bonding required for polymerization.
3Reliability
If long linker molecules are used, then polymerization is maintained, but detection sensitivity decreases
Solution Approach 1:
The patent optimizes the linker length parameter within a specific range (1-20 carbon atoms) to achieve the best balance between polymerization efficiency and detection sensitivity. By systematically varying this parameter, the invention identifies the optimal linker length that maintains sufficient proximity for detection while ensuring adequate polymerization activity.
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 efficient and affordable nucleotide polymer analysis by using biosensors to detect charge changes, reducing the need for expensive equipment and skilled technicians, and allowing for longer read lengths in sequencing by synthesis reactions.
Implementation Method 1
a high charge mass moiety... for triggering a detectable change in a sensitive biosensor when the reporter composition is operably coupled to the biosensor
Implementation Method 2
the linker attaches to the nucleotide at the phosphate linkage in the nucleotide, or the sugar group or the base group so as to allow for polymerisation by a polymerase
Implementation Method 3
a net charge mass of the high charge mass moiety is positive in turn in an acidic pH and/or a net charge mass of the high charge mass moiety is negative in turn in an alkaline pH
Data Source
AI summary
Embodiments of the present disclosure relate generally to reporter compositions which are synthetic nucleotides that comprise nucleotides with a high charge mass moiety attached thereto via a linker molecule. The linker molecules can vary in length in part to enable the high charge mass moiety to extend out from a DNA polymerase complex so that polymerization may not be influenced.