1
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Rathnayaka C, Chandrosoma IA, Choi J, Childers K, Chibuike M, Akabirov K, Shiri F, Hall AR, Lee M, McKinney C, Verber M, Park S, Soper SA. Detection and identification of single ribonucleotide monophosphates using a dual in-plane nanopore sensor made in a thermoplastic via replication. LAB ON A CHIP 2024; 24:2721-2735. [PMID: 38656267 PMCID: PMC11091956 DOI: 10.1039/d3lc01062g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
We report the generation of ∼8 nm dual in-plane pores fabricated in a thermoplastic via nanoimprint lithography (NIL). These pores were connected in series with nanochannels, one of which served as a flight tube to allow the identification of single molecules based on their molecular-dependent apparent mobilities (i.e., dual in-plane nanopore sensor). Two different thermoplastics were investigated including poly(methyl methacrylate), PMMA, and cyclic olefin polymer, COP, as the substrate for the sensor both of which were sealed using a low glass transition cover plate (cyclic olefin co-polymer, COC) that could be thermally fusion bonded to the PMMA or COP substrate at a temperature minimizing nanostructure deformation. Unique to these dual in-plane nanopore sensors was two pores flanking each side of the nanometer flight tube (50 × 50 nm, width × depth) that was 10 μm in length. The utility of this dual in-plane nanopore sensor was evaluated to not only detect, but also identify single ribonucleotide monophosphates (rNMPs) by using the travel time (time-of-flight, ToF), the resistive pulse event amplitude, and the dwell time. In spite of the relatively large size of these in-plane pores (∼8 nm effective diameter), we could detect via resistive pulse sensing (RPS) single rNMP molecules at a mass load of 3.9 fg, which was ascribed to the unique structural features of the nanofluidic network and the use of a thermoplastic with low relative dielectric constants, which resulted in a low RMS noise level in the open pore current. Our data indicated that the identification accuracy of individual rNMPs was high, which was ascribed to an improved chromatographic contribution to the nano-electrophoresis apparent mobility. With the ToF data only, the identification accuracy was 98.3%. However, when incorporating the resistive pulse sensing event amplitude and dwell time in conjunction with the ToF and analyzed via principal component analysis (PCA), the identification accuracy reached 100%. These findings pave the way for the realization of a novel chip-based single-molecule RNA sequencing technology.
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Affiliation(s)
- Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Indu A Chandrosoma
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Maximillian Chibuike
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Khurshed Akabirov
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Adam R Hall
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
- Atrium Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston Salem, NC 27157, USA.
| | - Maxwell Lee
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
| | - Collin McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Verber
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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2
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Shiri F, Choi J, Vietz C, Rathnayaka C, Manoharan A, Shivanka S, Li G, Yu C, Murphy MC, Soper SA, Park S. Nano-injection molding with resin mold inserts for prototyping of nanofluidic devices for single molecular detection. LAB ON A CHIP 2023; 23:4876-4887. [PMID: 37870483 PMCID: PMC10995647 DOI: 10.1039/d3lc00543g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
While injection molding is becoming the fabrication modality of choice for high-scale production of microfluidic devices, especially those used for in vitro diagnostics, its translation into the growing area of nanofluidics (structures with at least one dimension <100 nm) has not been well established. Another prevailing issue with injection molding is the high startup costs and the relatively long time between device iterations making it in many cases impractical for device prototyping. We report, for the first time, functional nanofluidic devices with dimensions of critical structures below 30 nm fabricated by injection molding for the manipulation, identification, and detection of single molecules. UV-resin molds replicated from Si masters served as mold inserts, negating the need for generating Ni-mold inserts via electroplating. Using assembled devices with a cover plate via hybrid thermal fusion bonding, we demonstrated two functional thermoplastic nanofluidic devices. The first device consisted of dual in-plane nanopores placed at either end of a nanochannel and was used to detect and identify single ribonucleotide monophosphate molecules via resistive pulse sensing and obtain the effective mobility of the molecule through nanoscale electrophoresis to allow its identification. The second device demonstrated selective binding of a single RNA molecule to a solid phase bioreactor decorated with a processive exoribonuclease, XRN1. Our results provide a simple path towards the use of injection molding for device prototyping in the development stage of any nanofluidic or even microfluidic application, through which rapid scale-up is made possible by transitioning from prototyping to high throughput production using conventional Ni mold inserts.
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Affiliation(s)
- Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Chad Vietz
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Anishkumar Manoharan
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Suresh Shivanka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Guoqiang Li
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Chengbin Yu
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Michael C Murphy
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
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3
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Zhao Z, Vaidyanathan S, Bhanja P, Gamage S, Saha S, McKinney C, Choi J, Park S, Pahattuge T, Wijerathne H, Jackson JM, Huppert ML, Witek MA, Soper SA. In-plane Extended Nano-coulter Counter (XnCC) for the Label-free Electrical Detection of Biological Particles. ELECTROANAL 2022; 34:1961-1975. [PMID: 37539083 PMCID: PMC10399599 DOI: 10.1002/elan.202200091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022]
Abstract
We report an in-plane extended nanopore Coulter counter (XnCC) chip fabricated in a thermoplastic via imprinting. The fabrication of the sensor utilized both photolithography and focused ion beam milling to make the microfluidic network and the in-plane pore sensor, respectively, in Si from which UV resin stamps were generated followed by thermal imprinting to produce the final device in the appropriate plastic (cyclic olefin polymer, COP). As an example of the utility of this in-plane extended nanopore sensor, we enumerated SARS-CoV-2 viral particles (VPs) affinity-selected from saliva and extracellular vesicles (EVs) affinity-selected from plasma samples secured from mouse models exposed to different ionizing radiation doses.
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Affiliation(s)
- Zheng Zhao
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
| | - Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
| | - Payel Bhanja
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160
| | - Sachindra Gamage
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Subhrajit Saha
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160
| | - Collin McKinney
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- CRITCL, The University of North Carolina, Chapel Hill, NC
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- CRITCL, The University of North Carolina, Chapel Hill, NC
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- CRITCL, The University of North Carolina, Chapel Hill, NC
| | - Thilanga Pahattuge
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Harshani Wijerathne
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Joshua M Jackson
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Mateusz L Huppert
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803
| | - Małgorzata A Witek
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Steven A Soper
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
- BioFluidica, Inc., San Diego, CA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045
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4
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Rathnayaka C, Amarasekara CA, Akabirov K, Murphy MC, Park S, Witek MA, Soper SA. Nanofluidic devices for the separation of biomolecules. J Chromatogr A 2022; 1683:463539. [PMID: 36223665 PMCID: PMC9795076 DOI: 10.1016/j.chroma.2022.463539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/30/2022]
Abstract
Over the last 30-years, microchip electrophoresis and its applications have expanded due to the benefits it offers. Nanochip electrophoresis, on the other hand, is viewed as an evolving area of electrophoresis because it offers some unique advantages not associated with microchip electrophoresis. These advantages arise from unique phenomena that occur in the nanometer domain not readily apparent in the microscale domain due to scale-dependent effects. Scale-dependent effects associated with nanochip electrophoresis includes high surface area-to-volume ratio, electrical double layer overlap generating parabolic flow even for electrokinetic pumping, concentration polarization, transverse electromigration, surface charge dominating flow, and surface roughness. Nanochip electrophoresis devices consist of channels with dimensions ranging from 1 to 1000 nm including classical (1-100 nm) and extended (100 nm - 1000 nm) nanoscale devices. In this review, we highlight scale-dependent phenomena associated with nanochip electrophoresis and the utilization of those phenomena to provide unique biomolecular separations that are not possible with microchip electrophoresis. We will also review the range of materials used for nanoscale separations and the implication of material choice for the top-down fabrication and operation of these devices. We will also provide application examples of nanochip electrophoresis for biomolecule separations with an emphasis on nano-electrophoresis (nEP) and nano-electrochromatography (nEC).
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Affiliation(s)
- Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA,Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Charuni A. Amarasekara
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA,Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Khurshed Akabirov
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA,Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Michael C. Murphy
- Center of BioModular Multiscale Systems for Precision Medicine, USA,Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70810, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, USA,Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70810, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA,Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA,Center of BioModular Multiscale Systems for Precision Medicine, USA,Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA,Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA,KU Cancer Center and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA, Corresponding author at: Integrated Science Building, University of Kansas, 1567 Irving Hill Road, Lawrence, KS 66044, USA. (S.A. Soper)
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5
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Bhattacharjee S, Mondal S, De S. Electro‐kinetically enhanced mass transport of charged macro‐solutes through a microchannel with porous walls. AIChE J 2022. [DOI: 10.1002/aic.17899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Saikat Bhattacharjee
- Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur India
- Civil and Environmental Engineering Technion Institute of Technology Haifa Israel
| | - Sourav Mondal
- Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur India
| | - Sirshendu De
- Department of Chemical Engineering Indian Institute of Technology Kharagpur Kharagpur India
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6
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Choi J, Jia Z, Riahipour R, McKinney CJ, Amarasekara CA, Weerakoon-Ratnayake KM, Soper SA, Park S. Label-Free Identification of Single Mononucleotides by Nanoscale Electrophoresis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102567. [PMID: 34558175 PMCID: PMC8542607 DOI: 10.1002/smll.202102567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Nanoscale electrophoresis allows for unique separations of single molecules, such as DNA/RNA nucleobases, and thus has the potential to be used as single molecular sensors for exonuclease sequencing. For this to be envisioned, label-free detection of the nucleotides to determine their electrophoretic mobility (i.e., time-of-flight, TOF) for highly accurate identification must be realized. Here, for the first time a novel nanosensor is shown that allows discriminating four 2-deoxyribonucleoside 5'-monophosphates, dNMPs, molecules in a label-free manner by nanoscale electrophoresis. This is made possible by positioning two sub-10 nm in-plane pores at both ends of a nanochannel column used for nanoscale electrophoresis and measuring the longitudinal transient current during translocation of the molecules. The dual nanopore TOF sensor with 0.5, 1, and 5 µm long nanochannel column lengths discriminates different dNMPs with a mean accuracy of 55, 66, and 94%, respectively. This nanosensor format can broadly be applicable to label-free detection and discrimination of other single molecules, vesicles, and particles by changing the dimensions of the nanochannel column and in-plane nanopores and integrating different pre- and postprocessing units to the nanosensor. This is simple to accomplish because the nanosensor is contained within a fluidic network made in plastic via replication.
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Affiliation(s)
- Junseo Choi
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Zheng Jia
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Ramin Riahipour
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Collin J. McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Charuni A. Amarasekara
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Kumuditha M. Weerakoon-Ratnayake
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Steven A. Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, University of Kansas, Lawrence, KS 66047, USA
- Department of Kansas Biology and KUCC, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sunggook Park
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
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7
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Athapattu US, Rathnayaka C, Vaidyanathan S, Gamage SST, Choi J, Riahipour R, Manoharan A, Hall AR, Park S, Soper SA. Tailoring Thermoplastic In-Plane Nanopore Size by Thermal Fusion Bonding for the Analysis of Single Molecules. ACS Sens 2021; 6:3133-3143. [PMID: 34406743 PMCID: PMC8482307 DOI: 10.1021/acssensors.1c01359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report a simple method for tailoring the size of in-plane nanopores fabricated in thermoplastics for single-molecule sensing. The in-plane pores were fabricated via nanoimprint lithography (NIL) from resin stamps, which were generated from Si masters. We could reduce the size of the in-plane nanopores from 30 to ∼10 nm during the thermal fusion bonding (TFB) step, which places a cover plate over the imprinted polymer substrate under a controlled pressure and temperature to form the relevant nanofluidic devices. Increased pressures during TFB caused the cross-sectional area of the in-plane pore to be reduced. The in-plane nanopores prepared with different TFB pressures were utilized to detect single-λ-DNA molecules via resistive pulse sensing, which showed a higher current amplitude in devices bonded at higher pressures. Using this method, we also show the ability to tune the pore size to detect single-stranded (ss) RNA molecules and single ribonucleotide adenosine monophosphate (rAMP). However, due to the small size of the pores required for detection of the ssRNA and rAMPs, the surface charge arising from carboxylate groups generated during O2 plasma oxidation of the surfaces of the nanopores to make them wettable had to be reduced to allow translocation of coions. This was accomplished using EDC/NHS coupling chemistry and ethanolamine. This simple modification chemistry increased the event frequency from ∼1 s-1 to >136 s-1 for an ssRNA concentration of 100 nM.
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Affiliation(s)
- Uditha S Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Sachindra S T Gamage
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Ramin Riahipour
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Anishkumar Manoharan
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Adam R Hall
- Wake Forest School of Medicine, Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and Comprehensive Cancer Center, Winston-Salem, North Carolina 27101, United States
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66045, United States
- KU Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
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8
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DNA translocation through pH-dependent soft nanopores. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:905-914. [PMID: 34120216 DOI: 10.1007/s00249-021-01552-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/19/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Controlling the translocation velocity of DNA is the main challenge in the process of sequencing by means of nanopores. One of the main methods to overcome this challenge is covering the inner walls of the nanopore with a layer of polyelectrolytes, i.e., using soft nanopores. In this paper the translocation of DNA through soft nanopores, whose inner polyelectrolyte layer (PEL) charge is pH-dependent, is theoretically studied. We considered the polyelectrolyte to be made up of either acidic or basic functional groups. It was observed that the electroosmotic flow (EOF) induced by the PEL charge is in the opposite/same direction of DNA electrophoresis (EPH) when the PEL is made up of acidic/basic groups. It was found that, not only the DNA charge and consequently the EPH, but also the EOF are influenced by the electrolyte acidity. The synergy between the changes in the retardation, EOF and EPH, determines how the intensity and direction of DNA translocation alter with pH. In fact, for both cases, at mild values of pH (as long as [Formula: see text] for the case that PEL is of acidic nature), the more the pH, the less the translocation velocity. However, for PELs of acidic nature, higher values of pH increase the intensity of the EOF so much that DNA may experience a change in the translocation direction. Ultimately, conducting the process at a particular range of pH values, and at higher pH values, in the cases of using PELs of acidic nature, and basic nature, respectively, was recommended.
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9
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Vaidyanathan S, Weerakoon-Ratnayake KM, Uba FI, Hu B, Kaufman D, Choi J, Park S, Soper SA. Thermoplastic nanofluidic devices for identifying abasic sites in single DNA molecules. LAB ON A CHIP 2021; 21:1579-1589. [PMID: 33651049 PMCID: PMC8293902 DOI: 10.1039/d0lc01038c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy of many drugs, such as doxorubicin. While there are different assays to search for DNA damage, they are fraught with limitations, such as the need for large amounts of DNA secured from millions of cells. This is challenging due to the growing importance of using liquid biopsies as a source of biomarkers for many in vitro diagnostic assays. To accommodate the mass limits imposed by the use of liquid biopsies, we report a single-molecule DNA damage assay that uses plastic nanofluidic chips to stretch DNA to near its full contour length when the channel dimensions (width and depth) are near the persistence length (∼50 nm) of double-stranded (ds) DNA. The nanofluidic chip consisted of input funnels for high loading efficiency of single DNA molecules, entropic traps to store the DNA and simultaneously load a series of nanochannels for high throughput processing, and an array of stretching nanochannels to read the AP sites. Single dsDNA molecules, which were labeled with an intercalating dye and a biotinylated aldehyde reactive probe (bARP), could be parked in the stretching nanochannels, where the AP sites were read directly using a dual-color fluorescence microscope equipped with an EMCCD camera. One color of the microscope was used to read the DNA length and the second color detected the AP sites. The nanofluidic chip was made from thermoplastics via nanoimprint lithography, which obviated the need for direct writing the devices in glass or quartz using focused ion beam milling. We show that we can read the frequency of AP sites in single dsDNA molecules with the frequency of AP sites determined by associating fluorescently-labeled streptavidin with bARP through a biotin/streptavidin complex.
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Affiliation(s)
- Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA and Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Kumuditha M Weerakoon-Ratnayake
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Franklin I Uba
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Bo Hu
- Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David Kaufman
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Mechanical & Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Mechanical & Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Steven A Soper
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA and Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA and Department of Cancer Biology and KU Cancer Center, The University of Kansas Medical Center, Kansas City, KS 66106, USA. and Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
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10
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Athapattu US, Amarasekara CA, Immel JR, Bloom S, Barany F, Nagel AC, Soper SA. Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing. Nucleic Acids Res 2021; 49:e41. [PMID: 33511416 PMCID: PMC8053086 DOI: 10.1093/nar/gkab001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 01/29/2023] Open
Abstract
Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s-1 and a processivity of >10.5 kb at 25°C.
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Affiliation(s)
| | | | - Jacob R Immel
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | | | | | - Steven A Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Sunflower Genomics, Inc., Lawrence, KS 66047, USA
- Department of Mechanical Engineering and Bioengineering, University of Kansas, Lawrence, KS 66045, USA
- Department of Cancer Biology and KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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11
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Amarasekara CA, Rathnayaka C, Athapattu US, Zhang L, Choi J, Park S, Nagel AC, Soper SA. Electrokinetic identification of ribonucleotide monophosphates (rNMPs) using thermoplastic nanochannels. J Chromatogr A 2021; 1638:461892. [PMID: 33477027 PMCID: PMC8107831 DOI: 10.1016/j.chroma.2021.461892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
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/O3 activated after device assembly with the dose of the UV/O3 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.
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Affiliation(s)
- 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
| | | | - 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.
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12
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Tong X, Novak BR, Kavousi S, Moldovan D. Single Nucleotides Moving through Nanoslits Composed of Self-Assembled Monolayers via Equilibrium and Nonequilibrium Molecular Dynamics. J Phys Chem B 2021; 125:1259-1270. [PMID: 33481603 DOI: 10.1021/acs.jpcb.0c07797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonequilibrium molecular dynamics (MD) simulations were used to study the effect of three chemical surface groups on the separation of DNA mononucleotide velocity (or time-of-flight) distributions as they pass through nanoslits. We used nanoslits functionalize with self-assembled monolayers (SAMs) since they have relatively smooth surfaces. The SAM molecules were terminated with either a methyl, methylformyl, or phenoxy group, and the nucleotides were driven electrophoretically with an electric field intensity of 0.1 V/nm in slits about 3 nm wide. Although these large driving forces are physically difficult to achieve experimentally, the simulations are still of great value as they provide molecular level insight into nucleotide translocation events and allow comparison of different surfaces. Nucleotides adsorbed and desorbed from the slit surface multiple times during the simulations. The required slit length for 99% accuracy in identifying the deoxynucleotide monophosphates (dNMPs), based on the separation of the distributions of time of flight, was used to compare the surfaces with shorter lengths indicating more efficient separation. The lengths were 6.5 μm for phenoxy-terminated SAMs, 270 μm for methylformyl-terminated SAMs, and 2400 μm for methyl-terminated SAMs. Our study showed that a slit with a section with methyl termination and the second section with methylformyl termination lead to a required length of 120 μm, which was significantly lower than for only a methylformyl- or methyl-terminated surface.
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Affiliation(s)
- Xinjie Tong
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Brian R Novak
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sepideh Kavousi
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Dorel Moldovan
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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13
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Amarasekara CA, Athapattu US, Rathnayaka C, Choi J, Park S, Soper SA. Open-tubular nanoelectrochromatography (OT-NEC): gel-free separation of single stranded DNAs (ssDNAs) in thermoplastic nanochannels. Electrophoresis 2020; 41:1627-1640. [PMID: 33460211 DOI: 10.1002/elps.202000109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022]
Abstract
Electrophoresis or electrochromatography carried out in nanometer columns (width and depth) offers some attractive benefits compared to microscale columns. These advantages include unique separation mechanisms that are scale dependent, fast separation times, and simpler workflow due to the lack of a need for column packing and/or wall coatings to create a stationary phase. We report the use of thermoplastics, in this case PMMA, as the substrate for separating single-stranded DNAs (ssDNAs). Electrophoresis nanochannels were created in PMMA using nanoimprint lithography (NIL), which can produce devices at lower cost and in a higher production mode compared to the fabrication techniques required for glass devices. The nanochannel column in PMMA was successful in separating ssDNAs in free solution that was not possible using microchip electrophoresis in PMMA. The separation could be performed in <1 s with resolution >1.5 when carried out using at an electric field strength of 280 V/cm and an effective column length of 60 μm (100 nm × 100 nm, depth and width). The ssDNAs transport through the PMMA column was driven electrokinetically under the influence of an EOF. The results indicated that the separation was dominated by chromatographic effects using an open tubular nano-electrochromatography (OT-NEC) mode of separation. Interesting to these separations was that no column packing was required nor a wall coating to create the stationary phase; the separation was affected using the native polymer that was UV/O3 activated and an aqueous buffer mobile phase.
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Affiliation(s)
- Charuni A Amarasekara
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA
| | - Uditha S Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA
| | - Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA
| | - Junseo Choi
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA.,Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Sunggook Park
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA.,Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA.,Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA.,Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas, USA.,Bioengineering Program, The University of Kansas, Lawrence, Kansas, USA.,KU Cancer Center, University of Kansas Medical Center, Kansas City, Kansas, USA
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14
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Affiliation(s)
- Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66044, United States
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66044, United States
- Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ian M. Freed
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66044, United States
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66044, United States
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66044, United States
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66044, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66044, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66044, United States
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15
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Siwy Z, Ensinger W, Laube B, Baldwin R. Preface. Anal Chim Acta 2019; 1086:14-15. [DOI: 10.1016/j.aca.2019.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Ganjizade A, Ashrafizadeh SN, Sadeghi A. Significant alteration in DNA electrophoretic translocation velocity through soft nanopores by ion partitioning. Anal Chim Acta 2019; 1080:66-74. [DOI: 10.1016/j.aca.2019.06.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 12/24/2022]
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