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High-Speed Atomic Force Microscopy Revealing Contamination in DNA Purification Systems
Andrey Mikheikin1, Anita Olsen1, Loren Picco2
1Department of Physics, Virginia Commonwealth University , Richmond, Virginia 23284, United States.
Analytical Chemistry
|February 16, 2016
Summary
High-speed atomic force microscopy (HS-AFM) detected DNA-like contamination in several commercial DNA purification kits. Beckman Coulter AMPure XP showed no contaminants, making it ideal for stringent analyses.
Area of Science:
- Molecular Biology
- Nanotechnology
- Analytical Chemistry
Background:
- Reports of low-level DNA contamination in commercial DNA purification kits prompted an investigation.
- Novel high-speed atomic force microscopy (HS-AFM) was employed to detect and characterize contaminants.
- HS-AFM offers label-free, near-single-molecule sensitivity, avoiding amplification artifacts.
Discussion:
- HS-AFM revealed filamentous contamination, resembling dsDNA, in Qiagen, Zymo, and Invitrogen kits.
- Beckman Coulter AMPure XP demonstrated no detectable contaminants.
- Fluorescent dye and whole genome amplification (WGA) assays corroborated HS-AFM findings to varying degrees.
Key Insights:
- Zymo kits showed DNA contamination via HS-AFM, fluorescence, and WGA assays.
- Qiagen kits exhibited contamination via HS-AFM and fluorescence, but not WGA.
- ChargeSwitch and AMPure XP tested negative in fluorescence assays, with ambiguous WGA results.
Outlook:
- AMPure XP is recommended for applications demanding high analytical stringency.
- HS-AFM is a valuable tool for characterizing trace contaminants in molecular biology reagents.
- Further research could combine HS-AFM with chemical specificity techniques for comprehensive contaminant analysis.
