Electrokinetic transport properties of deoxynucleotide monophosphates (dNMPs) through thermoplastic nanochannels

Colleen O'Neil, Department of Chemistry, The University of North Carolina, Chapel Hill, NC, USA; NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA.
Charuni A. Amarasekara, Department of Chemistry, Department of Mechanical Engineering, The University of Kansas, USA; NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA.
Kumuditha M. Weerakoon-Ratnayake, Department of Chemistry, Department of Mechanical Engineering, The University of Kansas, USA; NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA.
Bethany Gross, Department of Chemistry, Department of Mechanical Engineering, The University of Kansas, USA; NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA.
Zheng Jia, NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA; Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA, USA.
Varshni Singh, Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC, USA; NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA.
Sunggook Park, NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA; Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA, USA.
Steven A. Soper, Department of Chemistry, Department of Mechanical Engineering, The University of Kansas, USA; Department of Cancer Biology, Kansas University Medical Center, USA; NIH Biotechnology Resource Center of BioModular Multiscale Systems for Precision Medicine, USA; Ulsan National Institute of Science and Technology, Ulsan, South Korea. Electronic address: ssoper@ku.edu.

Abstract

The electrokinetic behavior of molecules in nanochannels (<100 nm in>length) have generated interest due to the unique transport properties observed that are not seen in microscale channels. These nanoscale dependent transport properties include transverse electromigration arising from partial electrical double layer overlap, enhanced solute/wall interactions due to the small channel diameter, and field-dependent intermittent motion produced by surface roughness. In this study, the electrokinetic transport properties of deoxynucleotide monophosphates (dNMPs) were investigated, including the effects of electric field strength, surface effects, and composition of the carrier electrolyte (ionic concentration and pH). The dNMPs were labeled with a fluorescent reporter (ATTO 532) to allow tracking of the electrokinetic transport of the dNMPs through a thermoplastic nanochannel fabricated via nanoimprinting (110 nm × 110 nm, width × depth, and 100 μm in length). We discovered that the transport properties in plastic nanochannels of the dye-labeled dNMPs produced differences in their apparent mobilities that were not seen using microscale columns. We built histograms for each dNMP from their apparent mobilities under different operating conditions and fit the histograms to Gaussian functions from which the separation resolution could be deduced as a metric to gage the ability to identify the molecule based on their apparent mobility. We found that the resolution ranged from 0.73 to 2.13 at pH = 8.3. Changing the carrier electrolyte pH > 10 significantly improved separation resolution (0.80-4.84) and reduced the standard deviation in the Gaussian fit to the apparent mobilities. At low buffer concentrations, decreases in separation resolution and increased standard deviations in Gaussian fits to the apparent mobilities of dNMPs were observed due to the increased thickness of the electric double layer leading to a partial parabolic flow profile. The results secured for the dNMPs in thermoplastic nanochannels revealed a high identification efficiency (>99%) in most cases for the dNMPs due to differences in their apparent mobilities when using nanochannels, which could not be achieved using microscale columns.