Epigenetic Binder Bacterial DNA Segregation
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Solution Overview
Problem
Current methods for detecting and isolating bacterial DNA from mixed samples, such as blood or environmental samples, are hindered by the overwhelming presence of eukaryotic DNA, making it difficult to identify and analyze bacterial threats like sepsis or anthrax, as existing techniques require lengthy culture-based methods or expensive PCR assays that do not allow for purification or analysis of bacterial genomes.
Innovation Solution
The use of epigenetic modifications specific to prokaryotic DNA, like N4-methylcytosine and N6-Methyladenine, to selectively isolate and purify bacterial DNA using epigenetic binders, such as antibodies or mutated restriction enzymes, allowing for rapid diagnosis and genomic characterization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If culture-based methods are used to detect bacterial DNA, then sensitivity is improved, but detection time increases significantly (1-5 days)
Solution Approach 1:
The patent applies preliminary action by performing selective enrichment of bacterial DNA using epigenetic markers (methylated DNA immunoprecipitation) before detection. This pre-concentration step allows rapid PCR detection without requiring lengthy culture growth, achieving both high sensitivity and rapid results within hours rather than days.
2Loss of time
If PCR-based assays are used for rapid detection, then detection time is reduced, but cost increases and purification capability is lost
Solution Approach 1:
The patent extracts and isolates bacterial DNA from eukaryotic DNA using epigenetic marker-based immunoprecipitation. This purification step removes the need for expensive inhibitory controls in PCR and enables cost-effective detection while providing purified bacterial DNA for downstream applications.
Solution Approach 2:
The patent introduces an intermediary step (methylated DNA immunoprecipitation) that uses antibodies against epigenetic markers as mediators to selectively capture bacterial DNA. This intermediary purification step reduces PCR inhibition and enables more cost-effective and reliable detection compared to direct PCR from crude extracts.
3Loss of time
If standard PCR is used on mixed samples, then detection speed is improved, but measurement precision deteriorates due to eukaryotic DNA background
Solution Approach 1:
The patent applies local quality by targeting specific epigenetic markers (methylation patterns) that are locally unique to bacterial DNA. By using antibodies that recognize these localized epigenetic modifications, the method selectively enriches bacterial DNA sequences while excluding eukaryotic DNA, thereby improving detection precision without sacrificing speed.
4Reliability
If culture methods are used for pathogen identification, then purification of bacterial DNA is achieved, but time consumption increases to 1-5 days
Solution Approach 1:
The patent replaces the mechanical/biological culture system with an epigenetic-based immunoprecipitation system. Instead of relying on bacterial growth (mechanical replication), the method uses antibody-antigen interactions to selectively capture and purify bacterial DNA within hours, maintaining purification capability while dramatically reducing time.
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 efficient segregation and analysis of bacterial DNA from mixed samples, reducing the need for expensive assays and enabling rapid detection and characterization of bacterial threats, even in complex samples like blood, by exploiting unique epigenetic markers.
Implementation Method 1
The method involves the steps of: (1) applying an epigenetic binder to a sample under conditions sufficient to permit the epigenetic binder to form a complex with nucleic acid carrying the epigenetic modification
Implementation Method 2
（2）isolating the epigenetic binder/nucleic acid complex
Data Source
AI summary
The invention provides methods, compositions and kits for segregating a target nucleic acid from a mixed nucleic acid sample. The methods, compositions and kits comprise a non-processive endonuclease (e.g., a restriction enzyme) or an antibody that binds the target nucleic acid (e.g., has methylation specificity). The mixed nucleic acid sample can comprise prokaryotic and eukaryotic nucleic acid and/or nucleic acid from more than one prokaryotic or eukaryotic organisms.