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ARS Home » Plains Area » Lincoln, Nebraska » Agroecosystem Management Research » Research » Publications at this Location » Publication #424467
Research Project: Managing Manure as a Soil Resource for Improved Biosecurity, Nutrient Availability, and Soil Sustainability

Location: Agroecosystem Management Research

Title: DNA isolation & quantification SOP

Author
item Condon, Justine
item Durso, Lisa

Submitted to: Protocols.io
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2025
Publication Date: 4/11/2025
Citation: Condon, J.C., Durso, L.M. 2025. DNA isolation & quantification SOP. Protocols.io. https://doi.org/10.17504/protocols.io.5jyl8dz8dg2w/v1.
DOI: https://doi.org/10.17504/protocols.io.5jyl8dz8dg2w/v1

Interpretive Summary: One way to study, track, and characterize bacteria is by looking at information contained in their DNA. Before that is possible, the DNA must be extracted from the sample. The quality of extracted DNA impacts the success of subsequent experiments, making precise protocols important. This protocol describes the process starting with careful collection of samples, though to final DNA isolation and proper short and long term storage.

Technical Abstract: Purpose To describe the correct procedures on how isolate and quantify DNA from manure and environmental samples for further polymerase chain reaction (PCR) processing. Scope DNA extraction is an essential process in molecular biology, allowing scientists to isolate DNA from various biological samples for applications like genetic research, forensic analysis, and medical diagnostics. The quality of extracted DNA impacts the success of subsequent experiments, making precise protocols important (Biology Insights, 2025). The process starts with careful collection of samples. Sterile techniques prevent contamination, and the timing of collection influences the DNA quality, with fresh samples generating better results. Many environmental samples also require careful handling to prevent degradation, such as immediate freezing or preservation efforts. The isolation procedure first involves cell lysis, which breaks open the cellular structures to release the genetic material. This is often completed via bead beating or sonication, which physically breaks the cell walls. The physical technique is frequently combined with a chemical technique for maximum yield and purity. Purification is essential to eliminate any remaining contaminates that may interfere with analyses. Quality control measures, such as spectrophotometry (Nanodrop System), are a common technique to measure the concentration and purity of the extracted DNA. Spectrophotometry uses the A260/A280 and A260/A230 ratios to serve as standards for contamination. This protocol describes the Microlab procedures for DNA isolation when using the DNeasy PowerSoil Pro kit (47016, Qiagen, Germantown, MD), followed by quantification using the Nanodrop (NanoDrop One System, Nano Drop Technologies, Wilmington, DE).