DNA extraction from complex matrices using magnetic ionic liquids prepared by green synthetic methods and their compatibility with nucleic acid amplification assays
Date
2025-09-08
Authors
Lee, Seong-Soo
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Elsevier B.V.
Abstract
Background: Amplification techniques for deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), including quantitative polymerase chain reaction (qPCR) and loop-mediated isothermal amplification (LAMP), enable accurate and precise nucleic acid (NA) assays. NAs must be isolated and purified from samples including biofluids, cell lysate, and food products prior to their amplification. However, general NA extraction methods can be expensive, time-consuming, and require toxic reagents. Magnetic ionic liquids (MILs) have emerged as effective solvents for the rapid extraction and purification of NAs for direct coupling with downstream analyses.
Results: Hydrophobic MILs composed of the bis[(trifluoromethyl)sulfonyl]imide ([NTf2−]) anion and N-alkylimidazole ligands with nickel or cobalt metal centers were systematically examined for their DNA extraction capabilities and compatibility with NA amplification techniques. All prepared MILs were found to selectively extract 227 base pair (bp) DNA and an 18-mer oligonucleotide. The MIL composed of [NTf2−] anions and 1-octylimidazole ligands with nickel(II) metal center ([Ni(OIm)62+][NTf2-]2) was found to be compatible with qPCR, achieving a qPCR efficiency of 92.0%. The highest DNA recovery after extraction using the [Ni(OIm)62+][NTf2-]2 MIL was observed by qPCR under optimized desorption conditions (25 minutes at 95 °C), and was approximately 40-fold greater recovery than non-optimized desorption conditions. The LAMP assay containing a MIL composed of [NTf2−] anions and 1-butylimidazole ligands with the cobalt(II) metal center ([Co(BIm)62+][NTf2-]2) detected as low as 2.63 × 102 copies of plasmid DNA (pDNA) in less than 15 minutes.
Significance: Transition metal chelated cation-based MILs featuring [NTf2-] anions and N-alkylimidazole ligands were synthesized via a solvent-free approach using cost-effective reagents. DNA analyses integrating the MIL extraction solvents were developed and optimized conditions identified. The LAMP assay using the [Co(BIm)62+][NTf2-]2 MIL detected pDNA from both deionized water and milk containing E. coli cell lysate of 5.2 colony-forming units per milliliter (CFU mL-1) within 33 minutes, suggesting that the assay holds significant potential for rapid pathogen diagnosis.
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Comments
This is a manuscript of an article published as Lee, Seong-Soo, and Jared L. Anderson. "DNA extraction from complex matrices using magnetic ionic liquids prepared by green synthetic methods and their compatibility with nucleic acid amplification assays." Analytica Chimica Acta (2025): 344631. doi: https://doi.org/10.1016/j.aca.2025.344631.
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This manuscript is licensed as CC BY-NC-ND.
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Funding
The work performed by the authors was supported by the Chemical Measurement and Imaging Program at the National Science Foundation (Grant No. CHE-2203891).