Urea-Modified Electrophoresis Medium for Single-Stranded Nucleic Acid Staining
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Solution Overview
Problem
Conventional electrophoresis techniques face challenges in reliably staining a wide range of nucleic acid molecule sizes, particularly short single-stranded RNA and DNA oligonucleotides, which results in incomplete visualization and reduced analysis resolution.
Innovation Solution
A medium comprising a staining compound and a urea derivative is used in electrophoresis, allowing for improved staining of nucleic acids by modulating the staining agent, enhancing the visibility of even small-sized nucleic acids during electrophoretic separation, particularly utilizing intercalating fluorescent dyes like SYTO 61 and TOTO-3 with urea derivatives such as N-methylurea, N,N′-dimethylurea, and N-ethylurea.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional intercalating dyes are used for staining nucleic acids, then staining of long nucleic acids is achieved, but staining of short single-stranded nucleic acids is insufficient
Solution Approach 1:
The patent modifies the chemical parameters of the staining medium by adding urea derivatives that change the conformational state of single-stranded nucleic acids, making them more accessible to intercalating dyes. This parameter change enables the staining compound to effectively bind to short single-stranded nucleic acids while maintaining ability to stain double-stranded nucleic acids.
Solution Approach 2:
Urea derivatives serve as intermediary substances that mediate between the intercalating dye and single-stranded nucleic acids. The urea derivative temporarily alters the nucleic acid structure to facilitate dye binding, acting as a chemical mediator that enables staining of previously difficult-to-stain molecules.
2Manufacturing precision
If standard electrophoresis medium is used, then separation of nucleic acids is achieved, but resolution of short nucleic acid fragments is reduced
Solution Approach 1:
The patent merges the separation function and detection function into a single integrated medium. The electrophoresis gel contains both the sieving matrix for separation and the urea-activated staining compound for detection, allowing simultaneous separation and reliable visualization of short nucleic acid fragments in the same medium.
Solution Approach 2:
The staining compound is pre-loaded into the electrophoresis gel matrix before running the electrophoresis. This preliminary action ensures that as nucleic acids migrate through the gel, they are continuously exposed to the staining agent, allowing short fragments to be stained and detected with high reliability during the separation process.
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 enables reliable and enhanced staining of nucleic acids, improving resolution and reducing baseline noise in electropherograms, allowing for accurate analysis of small RNA and DNA species, including those as short as 5 to 50 nucleotides.
Implementation Method 1
a urea derivative, capable of modulating the staining compound such that advantageously even nucleic acids having a short length become stained
Implementation Method 2
electrophoresis is understood as being migration of charged molecules through a sieving material while an electrical field is applied to said material
Implementation Method 3
The staining agent may preferably be an intercalating fluorescent dye
Data Source
AI summary
A medium is provided, being adapted to be applied in electrophoretic separation of nucleic acids. The medium comprises a staining reagent adapted to stain nucleic acids. Said medium further comprises a urea derivative, adapted to interact with said staining reagent and thereby providing an enhanced staining of said nucleic acids. Further, an electrophoresis device is provided, adapted to perform electrophoretic separation of nucleic acids, comprising the before medium and comprising electrodes for applying an electrical field across the medium. A method to perform electrophoresis using the before electrophoresis device and medium is provided.