Electrokinetic identification of ribonucleotide monophosphates (rNMPs) using thermoplastic nanochannels

Authors

Charuni A. Amarasekara, Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine.
Chathurika Rathnayaka, Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine.
Uditha S. Athapattu, Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine.
Lulu Zhang, Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine.
Junseo Choi, Center of Biomodular Multiscale Systems for Precision Medicine; Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803.
Sunggook Park, Center of Biomodular Multiscale Systems for Precision Medicine; Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803.
Aaron C. Nagel, Sunflower Genomics, Inc. Lawrence, KS 66047.
Steven A. Soper, Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine; Sunflower Genomics, Inc. Lawrence, KS 66047; Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045; Bioengineering Program, The University of Kansas, Lawrence, KS 66045; KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160. Electronic address: ssoper@ku.edu.

Document Type

Article

Publication Date

2-8-2021

Abstract

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 rNMPs was not possible using PMMA- or COC-based microchip electrophoresis. We also found that COC/COC devices could be assembled and UV/O activated after device assembly with the dose of the UV/O affecting the magnitude of the electroosmotic flow, EOF. In addition, the bond strength between the substrate and cover plate of unmodified COC/COC devices was higher compared to PMMA/COC devices. The large differences in the electrophoretic mobilities of the rNMPs afforded by nanoscale electrophoresis will enable a new single-molecule sequencing platform we envision, which uses molecular-dependent electrophoretic mobilities to identify the constituent rNMPs generated from an intact RNA molecule using a processive exonuclease. With optimized nanoscale electrophoresis, the rNMPs could be identified via mobility matching at an accuracy >99% in both COC/COC and PMMA/COC devices.

Publication Source (Journal or Book title)

Journal of chromatography. A

First Page

461892

Recommended Citation

Amarasekara, C. A., Rathnayaka, C., Athapattu, U. S., Zhang, L., Choi, J., Park, S., Nagel, A. C., & Soper, S. A. (2021). Electrokinetic identification of ribonucleotide monophosphates (rNMPs) using thermoplastic nanochannels. Journal of chromatography. A, 1638, 461892. https://doi.org/10.1016/j.chroma.2021.461892