Polypeptide-Coated Container for Methylated DNA Detection
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Solution Overview
Problem
Current methods for detecting methylated DNA are limited in their ability to reliably detect CpG methylation throughout the genome, especially when dealing with low DNA amounts, and often require bisulfate treatment or methylation-sensitive restriction enzymes, which have limitations in throughput and accuracy.
Innovation Solution
A single-tube assay method involving a polypeptide capable of binding methylated DNA, coated on a container, which allows for direct detection and analysis of methylated DNA without the need for bisulfate treatment or methylation-sensitive restriction enzymes, enabling fast and sensitive detection of methylated DNA and estimation of methylation degree.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If bisulfate treatment or methylation-sensitive restriction enzymes are used for detecting methylated DNA, then detection capability is achieved, but the process complexity and time consumption increase
Solution Approach 1:
The patent extracts and eliminates the need for bisulfate treatment and methylation-sensitive restriction enzymes from the detection process. By using a polypeptide that specifically binds to methylated DNA sequences, the method removes these complex preprocessing steps while maintaining reliable detection capability through direct immunological recognition of methylated cytosine residues.
Solution Approach 2:
The patent introduces a polypeptide as an intermediary substance that specifically recognizes and binds to methylated DNA. This polypeptide acts as a mediator between the methylated DNA target and the detection system, enabling direct detection without requiring chemical modification or enzymatic digestion steps.
2Reliability
If bisulfate treatment or methylation-sensitive restriction enzymes are used for detecting methylated DNA, then detection capability is achieved, but the detection time increases
Solution Approach 1:
The patent removes the time-consuming bisulfate treatment and restriction enzyme digestion steps from the detection workflow. By using a polypeptide-based direct binding approach, the method achieves reliable methylation detection in a significantly reduced time frame, eliminating multiple incubation and processing steps.
Solution Approach 2:
The patent skips the intermediate chemical treatment and enzymatic digestion steps that traditionally slow down methylation detection. The polypeptide directly binds to methylated DNA in a single step, rushing through the detection process while maintaining accuracy through specific molecular recognition.
3Measurement precision
If traditional methods are used for detecting methylated DNA, then detection of known loci is possible, but analysis of low DNA amounts and genome-wide detection are limited
Solution Approach 1:
The patent creates a universal detection system using polypeptides that can recognize methylated DNA sequences across the entire genome. This multi-functional approach allows the same basic methodology to detect methylation at any locus, whether known or unknown, and works with limited DNA amounts, thereby expanding detection scope while maintaining precision.
Solution Approach 2:
The patent changes the detection parameters by using polypeptide binding affinity instead of chemical modification or enzymatic cleavage. This parameter change enables the system to work with low DNA amounts and provides genome-wide coverage, as the polypeptide can bind to any methylated sequence regardless of its location or context.
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 method provides a rapid, reliable, and sensitive detection of methylated DNA, capable of analyzing target DNA fragments based on methylation degree, even with limited DNA samples, and generates methylation profiles of single or multiple gene loci, suitable for tumorous tissue analysis.
Implementation Method 1
a polypeptide capable of binding methylated DNA
Data Source
AI summary
The present invention relates to an in vitro method for detecting methylated DNA comprising (a) coating a container with a polypeptide capable of binding methylated DNA; (b) contacting said polypeptide with a sample comprising methylated and/or unmethylated DNA; and (c) detecting the binding of said polypeptide to methylated DNA. In a preferred embodiment, said method further comprises step (d) analyzing the detected methylated DNA by sequencing. Another aspect of the present invention is a kit for detecting methylated DNA according to the methods of the invention comprising (a) a polypeptide capable of binding methylated DNA; (b) a container which can be coated with said polypeptide; (c) means for coating said container; and (d) means for detecting methylated DNA.