Rigid Linker Arms for Nucleic Acid Labeling Reagents
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Solution Overview
Problem
Current labeling methods for nucleic acids face challenges such as reduced yield and efficiency due to interactions between label moieties and polymerases, and the need for longer linker arms to minimize interference, which can still result in incomplete compensation and solubility issues.
Innovation Solution
Development of labeling reagents with a marker moiety and reactive group capable of forming a carbon-carbon linkage, using cyanine dyes and porphyrins with novel linker arms that provide increased separation and accessibility, and non-metallic porphyrins with reactive groups on non-pyrrole positions for efficient labeling.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If longer linker arms are used to minimize interference between label moieties and polymerases, then labeling efficiency is improved, but solubility issues arise and the linker arms may still result in incomplete compensation of interference
Solution Approach 1:
The patent changes the chemical parameters of the linker arm by incorporating rigid polar units (such as peptide bonds and aromatic rings) instead of traditional flexible aliphatic chains. This parameter change maintains appropriate length for minimizing polymerase interference while improving solubility through the polar characteristics of the rigid units.
Solution Approach 2:
The linker arm is constructed as a composite structure combining rigid polar units (peptide bonds, aromatic rings) with appropriate spacing. This composite approach creates a linker that simultaneously provides the rigidity needed to minimize interference and the polarity needed for solubility, resolving the contradiction between length and solubility.
2Quantity of substance
If traditional flexible linker arms are used, then solubility is maintained, but interference with polymerases is not sufficiently minimized
Solution Approach 1:
The patent transforms the linker arm from a flexible aliphatic chain to a rigid polar structure containing peptide bonds and aromatic rings. This parameter change maintains solubility through polarity while the rigidity provides better spatial separation to minimize polymerase interference, thereby improving labeling efficiency.
Solution Approach 2:
The patent replaces the mechanical flexibility of traditional linker arms with a rigid polar structure. This substitution maintains the necessary spacing function while the polar units provide solubility, achieving both goals simultaneously rather than trading one for the other.
3Quantity of substance
If label moieties are attached close to the target, then labeling density is increased, but interference with polymerases occurs reducing yield
Solution Approach 1:
The patent applies local quality by creating a rigid polar linker arm with specific structural characteristics (peptide bonds, aromatic rings) that provides localized spatial separation. This localized rigidity at the linker region maintains labeling density while creating sufficient distance to minimize polymerase interference, resolving the contradiction between density and yield.
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
Enhances labeling efficiency and accessibility, reducing interference with polymerases and improving solubility, allowing for more effective attachment of labels to nucleic acids and proteins while maintaining spectral characteristics.
Implementation Method 1
labeling reagents with a marker moiety and reactive group capable of forming a carbon-carbon linkage, using cyanine dyes and porphyrins with novel linker arms that provide increased separation and accessibility
Implementation Method 2
Among the various compounds used as non-radioactive labels, aromatic dyes that produce fluorescent or luminescent signal are especially useful. Notable examples of such compounds include fluorescein, rhodamine, coumarin and cyanine dyes such as Cy3 and Cy5.
Implementation Method 3
aromatic dyes that produce fluorescent or luminescent signal are especially useful
Implementation Method 4
the reactive group R being capable of forming a carbon-carbon linkage with the target
Data Source
AI summary
This invention provides for labeling reagents, labeled targets and processes for preparing labeling reagents. The labeling reagents can take the form of cyanine dyes, xanthene dyes, porphyrin dyes, coumarin dyes or composite dyes. These labeling reagents are useful for labeling probes or targets, including nucleic acids and proteins. These reagents can be usefully applied to protein and nucleic acid probe based assays. They are also applicable to real-time detection processes.