Fragmented DNA Pre-treatment for Soil Nucleic Acid Extraction
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Solution Overview
Problem
Conventional methods for extracting DNA/RNA from low-biomass samples, such as clay-rich soil, face challenges due to DNA/RNA adsorption onto clay particles, leading to reduced yields and quality, with existing solutions like poly-dIdC being costly and contaminated.
Innovation Solution
A cost-efficient method involving pre-treatment with fragmented DNA of natural origin, which blocks DNA/RNA binding sites on adsorbing matrices, preventing adsorption and allowing for improved extraction efficiency without contaminating downstream PCR reactions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If poly-dIdC is used as a blocking agent to improve DNA extraction yield from low-biomass samples, then extraction yield is improved, but cost increases and contamination with rRNA sequences occurs requiring additional decontamination steps
Solution Approach 1:
The patent replaces expensive poly-dIdC with a cheap, readily available carrier molecule (such as salmon sperm DNA or other genomic DNA) that can be used in large amounts without concern for cost. This carrier DNA is used as a disposable blocking agent that competes for adsorption sites on clay particles, preventing loss of target DNA from low-biomass samples while avoiding the contamination and decontamination issues associated with poly-dIdC
Solution Approach 2:
The patent changes the chemical composition parameter from synthetic poly-dIdC to natural genomic DNA or salmon sperm DNA. This parameter change maintains the blocking function while eliminating contamination issues and reducing cost. The carrier DNA can be added in excess to ensure complete blocking of adsorption sites without requiring precise optimization
2Ease of operation
If conventional extraction methods are used on clay-rich soil samples, then procedure simplicity is maintained, but DNA/RNA adsorption onto clay particles reduces extraction yield and quality
Solution Approach 1:
The patent introduces a preliminary step before extraction where carrier DNA is added to the clay-rich soil sample to pre-block the adsorption sites on clay particles. This preliminary action prevents DNA loss during subsequent extraction steps, improving yield and quality without complicating the overall procedure. The carrier DNA simply needs to be added and incubated briefly before proceeding with standard extraction protocols
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 method significantly enhances DNA/RNA extraction yields and quality from adsorbing matrices by blocking binding sites with fragmented DNA, reducing contamination and operational costs, while ensuring the extracted DNA/RNA is suitable for PCR analysis.
Implementation Method 1
bringing the sample into contact with DNA of natural origin in a fragmented form ('fragmented DNA') so as to essentially block said DNA/RNA binding sites of said adsorbing matrix
Data Source
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AI summary
The present application discloses a method for pre-treating a sample of a DNA/RNA adsorbing matrix (e.g. soil) suitable for extracting cell-derived (deoxy) ribonucleic acid therefrom, comprising the steps of : isolating a sample of a DNA/RNA adsorbing matrix, said sample comprising DNA/RNA-containing cells; and bringing the sample into contact with DNA of natural origin in a fragmented form (e.g. salmon sperm DNA) so as to essentially block said DNA/RNA adsorbing binding sites of said adsorbing matrix, said fragmented DNA being "unrelated" to the target DNA/RNA of said DNA/RNA-containing cells. The fragmented DNA of natural origin can be depurinated and/or freeze-dried. The application further discloses a method for extracting DNA/RNA from a sample and a kit useful for pre-treating samples.