Periodate-Ionic Liquid Composition for Polynucleotide Linearization
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing enzymatic methods for linearizing double-stranded polynucleotides in sequencing-by-synthesis reactions face challenges such as enzyme stability, cost, variability in activity, and interference with nucleotide detection, necessitating an alternative method that is stable under various conditions and compatible with downstream reactions.
Innovation Solution
A composition comprising a periodate salt and an ionic liquid additive, such as 1-benzyl-3-methylimidazolium chloride, is used to chemically cleave double-stranded polynucleotides, preventing precipitate formation and enhancing linearization efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If enzymatic methods are used for linearization, then cleavage efficiency is achieved, but enzyme stability, cost, and variability in activity become problematic
Solution Approach 1:
The patent replaces the enzymatic system with a chemical system using periodate salt and ionic liquid. This substitution eliminates the need for biological enzymes while achieving comparable or superior linearization efficiency. The chemical composition provides consistent activity without the stability and cost issues associated with enzymatic methods.
Solution Approach 2:
The patent changes the chemical parameters by introducing ionic liquid to the periodate salt solution. This parameter modification enhances the solubility and reactivity of periodate, preventing precipitate formation and improving linearization rates by up to 300% compared to traditional periodate compositions alone.
2Productivity
If traditional periodate compositions are used, then chemical cleavage is achieved, but precipitate formation reduces efficiency
Solution Approach 1:
The ionic liquid acts as an intermediary substance that mediates between periodate salt and aqueous solution. It prevents precipitate formation by improving the solubility and distribution of periodate ions in the solution, thereby maintaining high linearization efficiency throughout the reaction.
Solution Approach 2:
The patent creates a composite chemical system combining periodate salt and ionic liquid. This composite composition leverages the properties of both components: periodate provides the cleaving activity while ionic liquid ensures solubility and prevents precipitation, resulting in a stable and efficient linearization reagent.
3Productivity
If enzymes are used for linearization, then cleavage is achieved, but costs of enzyme production and handling increase
Solution Approach 1:
The patent employs a disposable chemical composition (periodate salt with ionic liquid) that can be synthesized inexpensively and used directly. This replaces expensive, delicate enzymes that require costly production, purification, and specialized handling. The chemical reagent can be prepared at scale with minimal infrastructure.
4Productivity
If enzymatic methods are used, then linearization is achieved, but high background intensity in sequencing reading occurs
Solution Approach 1:
The patent replaces enzymatic reactions with chemical oxidation using periodate. This substitution eliminates enzyme-related background signals that interfere with sequencing detection. The chemical method produces cleaner reactions with lower background intensity, improving signal-to-noise ratio in sequencing reads.
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 chemical method improves linearization rates by up to 300% compared to traditional periodate compositions, offering stability and compatibility with sequencing processes.
Implementation Method 1
EP 2 021 415 A2 discloses a cleaving method of products containing diol linkages wherein the method uses periodate.
Data Source
Figure 1
Figure 2~3
Figure 4A~4B
AI summary
Embodiments of the present disclosure relates to periodate salt compositions for use in the chemical linearization of double-stranded polynucleotides in preparation for sequencing application, for example, sequencing-by-synthesis (SBS). Kits containing the periodate salt composition and methods of sequencing polynucleotides are also described.