Electrode-Free Concentration and Recovery of DNA at Physiologically Relevant Ionic Concentrations

• Published in: Analytical chemistry (Washington) 2020-04, Vol.92 (8), p.6150-6157
• Main Authors: Li, Sixuan, Li, Andrew, Hsieh, Kuangwen, Friedrich, Sarah M, Wang, Tza-Huei
• Format: Article
• Language: English
• Subjects: Biological properties; Biological samples; Biomarkers; Blood levels; Chemistry; Concentration gradient; Deoxyribonucleic acid; DNA; DNA - analysis; Electric fields; Electrokinetics; External pressure; Ion concentration; Ions - chemistry; Microfluidic Analytical Techniques; Microfluidics; Nucleic acids; Rheotaxis; Salts - chemistry; Signal to noise ratio; Size separation
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.0c00831

Advances in microanalytical and microfluidic technologies have enabled rapid and amplification-free detection of DNA with a high signal-to-noise ratio. The low sample volume, however, poses a limit in the DNA detection sensitivity, which can be challenging for analyzing rare DNA in physiological samples. One way to improve the sensitivity is to concentrate the DNA in the sample prior to the analysis. The most common DNA concentration techniques are based on electrokinetics, which require an external electric field and generally become ineffective in high ionic concentration conditions. In this work, we present a facile method termed high-salt molecular rheotaxis (HiSMRT) to concentrate and recover DNA from samples with physiologically relevant ionic concentrations without any external electric field. HiSMRT requires only pressure-driven flow and ion concentration gradient to induce a stable local electric field and achieve DNA concentration, making it impervious to high ionic concentrations. We demonstrate that HiSMRT performs robustly at ionic concentrations equivalent to 2%–20% of the ionic concentration in blood serum. HiSMRT can concentrate DNA by up to 960-fold and recover an average of 96.4% of the DNA fragments from 2.0 to 23 kbp uniformly. The concentration process using HiSMRT takes as little as 7.5 min. Moreover, we show that this technique can be easily integrated to perform DNA concentration, size separation, and single-molecule detection all in one platform. We anticipate that this technique will be applicable to a wide range of biological samples and will help to improve the sensitivity of nucleic acid detection for low-abundance DNA biomarkers.