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Identifying DNA Mismatches at Single-Nucleotide Resolution by Probing Individual Surface Potentials of DNA-Capped Nanoparticles

Abstract

Here, we demonstrate a powerful method to discriminate DNA mismatches at single-nucleotide resolution from 0 to 5 mis-matches (χ0 to χ5) using Kelvin probe force microscopy (KPFM). Using our previously developed method, we quantified the surface potentials (SPs) of individual DNA-capped nanoparticles (DCNPs, ~100 nm). On each DCNP, DNA hybridization occurs between ~2,200 immobilized probe DNA (pDNA) and target DNA with mismatches (tDNA, ~80 nM). Thus, each DCNP used in the bioassay (each pDNA-tDNA interaction) corresponds to a single ensemble in which a large number of pDNA-tDNA interactions take place. Moreover, one KPFM image can scan at least dozens of ensembles, which allows statistical analysis (i.e., an ensemble average) of many bioassay cases (ensembles) under the same conditions. We found that as the χn increased from χ0 to χ5 in the tDNA, the average SP of dozens of ensembles (DCNPs) was attenuated owing to fewer hybridization events between the pDNA and the tDNA. Remarkably, the SP attenuation vs. the χn showed an inverse-linear correlation, albeit the equilibrium constant for DNA hybridization exponentially decreased asymptotically as the χn increased. In addition, we observed a cascade reaction at a 100-fold lower concentration of tDNA (~0.8 nM); the average SP of DCNPs exhibited no significant decrease but rather split into two separate states (no-hybridization vs. full-hybridization). Compared to complementary tDNA (i.e., χ0), the ratio of no-hybridization/full-hybridization within a given set of DCNPs became ~1.6 times higher in the presence of tDNA with single mismatches (i.e., χ1). The results imply that our method opens new avenues not only in the research on DNA hybridization mechanism in the presence of DNA mismatches but also in development of a robust technology for DNA mismatch detection.

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Publication details

The article was received on 19 Jul 2017, accepted on 05 Nov 2017 and first published on 06 Nov 2017


Article type: Paper
DOI: 10.1039/C7NR05250B
Citation: Nanoscale, 2017, Accepted Manuscript
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    Identifying DNA Mismatches at Single-Nucleotide Resolution by Probing Individual Surface Potentials of DNA-Capped Nanoparticles

    H. Lee, S. W. Lee, G. Lee, W. Lee, K. Nam, J. H. Lee, K. S. Hwang, J. Yang, H. Lee, S. Kim, S. W. Lee and D. S. Yoon, Nanoscale, 2017, Accepted Manuscript , DOI: 10.1039/C7NR05250B

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