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

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.

Open‐tubular nanoelectrochromatography (OT‐NEC): gel‐free separation of single stranded DNAs (ssDNAs) in thermoplastic nanochannels

“…The imaging system for monitoring the transport of ssDNAs through the thermoplastic nanochannel used a fluorescence imaging system we have reported [28]. More information can be found in Supporting Information Fig.…”

“…There have been a limited number of studies on nanoscale separations using thermoplastic devices [27,28], Weerakoon‐Ratnayake et al. [27] showed the electrokinetic transport of silver nanoparticles (AgNPs) using PMMA nanoslits.…”

“…Most recently, O'Neil et al. [28–30] showed the separation of deoxynucleotide monophosphates (dNMPs) in free solution using thermoplastic nanochannel devices fabricated in PMMA substrates with COC cover plates. High electric field strengths provided better separations.…”

Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing

“…As noted, we are developing a single-molecule exosequencing approach, which uses a chip-based sequencer consisting of a solid-phase enzymatic bioreactor coupled to a column that measures in real time the electrophoretic mobility of free nucleotides with nanoscale electrophoresis following clipping using an exonuclease ( 19 , 21 , 22 ). While we have previously reported the use of λ-exonuclease solid-phase reactions for producing deoxynucleotide monophosphates, dNMPs ( 20 ), the work reported herein demonstrates the potential for repurposing the sequencer for RNAs.…”

“…Once a single DMD RNA molecule was located that was complexed to the immobilized XRN1, enzyme buffer containing Mg 2+ cofactor was introduced into the device to initiate digestion and the fluorescence intensity (532 nm excitation, 0.01 W) of the DMD RNA–XRN1 complex was monitored continuously. For these experiments, an epifluorescence microscope was used, which consisted of a NIKON TE 2000 microscope fitted with a 100X/1.4 NA oil-immersion objective and an Andor iXon3 EMCCD camera ( 21 ). All images were acquired using Metamorph advanced v7.5.6.0 software (10 fps acquisition rate).…”