Cleavable Nucleotide Linkers for Accurate Polymerase Sequencing
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Solution Overview
Problem
Existing DNA sequencing methods, particularly sequencing by synthesis (SBS), lack modified nucleotides and nucleosides that are efficiently recognized by DNA polymerases and accurately incorporated into growing DNA chains, hindering the goal of achieving the $1,000 genome.
Innovation Solution
Development of compounds with specific moieties that are recognized by DNA polymerases, incorporated into DNA chains, and include detectable labels for sequencing, utilizing nucleic acid polymerase complexes and methods for sequencing nucleic acids by incorporating these compounds into primers within reaction vessels.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If existing DNA sequencing methods are used, then sequencing can be performed, but modified nucleotides and nucleosides are not efficiently recognized by DNA polymerases and accurately incorporated into growing DNA chains
Solution Approach 1:
The patent applies local quality by making specific modifications to the nucleotide structure at particular positions. The modified nucleotides contain specific chemical groups (such as fluorinated alkyl groups, aromatic groups, or heterocyclic groups) at defined positions in the sugar or base moiety, allowing the polymerase to recognize and incorporate them accurately while maintaining the desired sequencing functionality.
Solution Approach 2:
The patent employs parameter changes by systematically varying chemical parameters of the nucleotide structure, including substitution of hydrogen atoms with fluorinated groups, aromatic groups, or heterocyclic groups. These parameter changes optimize both polymerase recognition efficiency and incorporation accuracy, resolving the contradiction between reliability and adaptability.
2Measurement precision
If modified nucleotides are developed for sequencing, then sequencing accuracy improves, but the complexity of the sequencing system increases
Solution Approach 1:
The patent applies preliminary action by pre-modifying the nucleotides with specific chemical groups that enable both accurate polymerase incorporation and detectable signal generation. The modified nucleotides are prepared in advance with incorporated fluorophores or other detectable moieties, allowing accurate sequencing without requiring complex real-time modification systems during the sequencing reaction.
Solution Approach 2:
The patent uses intermediary elements by introducing modified nucleotides that serve as mediators between the polymerase enzyme and the detection system. These modified nucleotides contain specific chemical groups that facilitate polymerase recognition while also incorporating detectable labels, thereby simplifying the overall sequencing system by combining multiple functions in a single intermediate molecule.
3Productivity
If standard nucleotides are used in SBS, then the process is simple, but the goal of achieving the $1,000 genome cannot be realized
Solution Approach 1:
The patent applies universality by designing modified nucleotides that perform multiple functions simultaneously: they serve as substrates for polymerase incorporation, provide detectable signals through incorporated fluorophores or other moieties, and enable reversible termination for controlled sequencing. This multi-functionality increases sequencing productivity without proportionally increasing manufacturing complexity, as the same modified nucleotide structure achieves multiple objectives.
Solution Approach 2:
The patent employs composite materials by creating hybrid nucleotide structures that combine standard nucleotide components with modified sugar or base moieties. These composite nucleotides integrate familiar structural elements that polymerases can recognize with novel functional groups that provide enhanced detectability and controlled incorporation, thereby improving productivity while maintaining reasonable ease of manufacture through modular design.
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 accurate and efficient DNA sequencing by allowing for the identification of incorporated compounds in extension strands, thereby improving the sequencing process.
Implementation Method 1
DNA polymerases... are efficiently and accurately incorporated into growing DNA chains during SBS
Data Source
AI summary
Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof for sequencing a nucleic acid.