Electrokinetic identification of ribonucleotide monophosphates (rNMPs) using thermoplastic nanochannels

• Published in: Journal of Chromatography A 2021-02, Vol.1638, p.461892-461892, Article 461892
• Main Authors: Amarasekara, Charuni A., Rathnayaka, Chathurika, Athapattu, Uditha S., Zhang, Lulu, Choi, Junseo, Park, Sunggook, Nagel, Aaron C., Soper, Steven A.
• Format: Article
• Language: English
• Subjects: electrophoresis; Nanofluidics; ribonucleotides; thermoplastics
• ISSN: 0021-9673; 1873-3778
• DOI: 10.1016/j.chroma.2021.461892

•Greater than 99% identification efficiency of the ribonucleotide monophosphates (rNMPs) through mobility matching using a 110 × 110 nm (width x depth) plastic channels that are 100 µm in length using free solution nanoscale electrophoresis.•The nanochannels can be made in a thermoplastic using Nanoimprint Lithography (NIL) to produce nanofluidic devices in plastics at a much higher rate and lower cost compared to glass-based nanofluidic devices. We are currently working on fabricating the nanofluidic devices using nano-injection molding to further reduce cost and increase production rate.•The high identification efficiency afforded by nanoscale electrophoresis will support a new single-molecule RNA sequencing strategy being developed by our group. With advances in the design and fabrication of nanofluidic devices during the last decade, there have been a few reports on nucleic acid analysis using nanoscale electrophoresis. The attractive nature of nanofluidics is the unique phenomena associated with this length scale that are not observed using microchip electrophoresis. Many of these effects are surface-related and include electrostatics, surface roughness, van der Waals interactions, hydrogen bonding, and the electric double layer. The majority of reports related to nanoscale electrophoresis have utilized glass-based devices, which are not suitable for broad dissemination into the separation community because of the sophisticated, time consuming, and high-cost fabrication methods required to produce the relevant devices. In this study, we report the use of thermoplastic nanochannels (110 nm x 110 nm, depth x width) for the free solution electrokinetic analysis of ribonucleotide monophosphates (rNMPs). Thermoplastic devices with micro- and nanofluidic networks were fabricated using nanoimprint lithography (NIL) with the structures enclosed via thermal fusion bonding of a cover plate to the fluidic substrate. Unique to this report is that we fabricated devices in cyclic olefin copolymer (COC) that was thermally fusion bonded to a COC cover plate. Results using COC/COC devices were compared to poly(methyl methacrylate), PMMA, devices with a COC cover plate. Our results indicated that at pH = 7.9, the electrophoresis in free solution resulted in an average resolution of the rNMPs >4 (COC/COC device range = 1.94 – 8.88; PMMA/COC device range = 1.4 – 7.8) with some of the rNMPs showing field-dependent electrophoretic mobilities. Baseline separation of the rNM