Biosensing with Polymerase Chain Reaction-Stable DNA-Functionalized Magnetically Susceptible Carbon–Iron Microparticles

• Published in: Analytical chemistry (Washington) Vol. 95; no. 45; pp. 16631 - 16638
• Main Authors: Koirala, Dipak, Dalbec, Forrest, May, Jeremy, Hamal, Kailash, Allen, Peter B., Cheng, I. Francis
• Format: Journal Article
• Language: English
• Published: Washington American Chemical Society 14-11-2023
• Subjects: Biosensors; Carbon; Carbon sources; Coated particles; DNA probes; Electrophoresis; Ethidium bromide; Fluorescence; Gene sequencing; High temperature; Hybridization; Iron; Microparticles; Nucleic acids; Nucleotide sequence; Nucleotides; Polymerase chain reaction; Polystyrene; Polystyrene resins; Primers (coatings); Substrates
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.3c02978

We demonstrate a rapid and sensitive method for DNA detection without the need for fluorescence. This is based on carbon-coated magnetic iron (Fe) microparticles with a covalent surface attachment of DNA. We show that these magnetic microparticles can capture complementary DNA. Significantly, the DNA covalent surface bonds are robust to high temperatures and can be included in a sample during polymerase chain reaction (PCR). This method is employed for the detection of targeted DNA sequences (40–50 bp). Hybridization probes on the surface of the magnetically susceptible Fe microparticle recognize the target DNA sequence-specifically. The double-stranded DNA (dsDNA) microparticles are then quickly captured with a magnet from the sample matrix. This foregoes postpurification processes, such as electrophoresis, which make our technique time- and cost-effective. Captured dsDNA can be detected with intercalating dyes such as ethidium bromide through a loss in the UV absorption signal with a limit of detection (LOD) of 24 nM within 15 min. Likewise, surface-bound DNA can act as a primer in PCR to decrease the LOD to 5 pM within 2 h. This is the first instance of a nucleotide-modified magnetically susceptible carbon substrate that is PCR-compatible. Besides DNA capture, this strategy can eventually be applied to sequence-specific nucleic acid purification and enrichment, PCR cleanup, and single-strand generation. The DNA-coated particles are stable under PCR conditions (unlike commonly used polystyrene or gold particles).