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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Simon L, Lapinte V, Morille M. Exploring the role of polymers to overcome ongoing challenges in the field of extracellular vesicles. J Extracell Vesicles 2023; 12:e12386. [PMID: 38050832 PMCID: PMC10696644 DOI: 10.1002/jev2.12386] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
Extracellular vesicles (EVs) are naturally occurring nanoparticles released from all eucaryotic and procaryotic cells. While their role was formerly largely underestimated, EVs are now clearly established as key mediators of intercellular communication. Therefore, these vesicles constitute an attractive topic of study for both basic and applied research with great potential, for example, as a new class of biomarkers, as cell-free therapeutics or as drug delivery systems. However, the complexity and biological origin of EVs sometimes complicate their identification and therapeutic use. Thus, this rapidly expanding research field requires new methods and tools for the production, enrichment, detection, and therapeutic application of EVs. In this review, we have sought to explain how polymer materials actively contributed to overcome some of the limitations associated to EVs. Indeed, thanks to their infinite diversity of composition and properties, polymers can act through a variety of strategies and at different stages of EVs development. Overall, we would like to emphasize the importance of multidisciplinary research involving polymers to address persistent limitations in the field of EVs.
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Affiliation(s)
| | | | - Marie Morille
- ICGM, Univ Montpellier, CNRS, ENSCMMontpellierFrance
- Institut universitaire de France (IUF)ParisFrance
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3
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Hu M, Brown V, Jackson JM, Wijerathne H, Pathak H, Koestler DC, Nissen E, Hupert ML, Muller R, Godwin AK, Witek MA, Soper SA. Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles' mRNA. Anal Chem 2023; 95:7665-7675. [PMID: 37071799 PMCID: PMC10243595 DOI: 10.1021/acs.analchem.3c00624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Extracellular vesicles (EVs) carry RNA cargo that is believed to be associated with the cell-of-origin and thus have the potential to serve as a minimally invasive liquid biopsy marker for supplying molecular information to guide treatment decisions (i.e., precision medicine). We report the affinity isolation of EV subpopulations with monoclonal antibodies attached to the surface of a microfluidic chip that is made from a plastic to allow for high-scale production. The EV microfluidic affinity purification (EV-MAP) chip was used for the isolation of EVs sourced from two-orthogonal cell types and was demonstrated for its utility in a proof-of-concept application to provide molecular subtyping information for breast cancer patients. The orthogonal selection process better recapitulated the epithelial tumor microenvironment by isolating two subpopulations of EVs: EVEpCAM (epithelial cell adhesion molecule, epithelial origin) and EVFAPα (fibroblast activation protein α, mesenchymal origin). The EV-MAP provided recovery >80% with a specificity of 99 ± 1% based on exosomal mRNA (exo-mRNA) and real time-droplet digital polymerase chain reaction results. When selected from the plasma of healthy donors and breast cancer patients, EVs did not differ in size or total RNA mass for both markers. On average, 0.5 mL of plasma from breast cancer patients yielded ∼2.25 ng of total RNA for both EVEpCAM and EVFAPα, while in the case of cancer-free individuals, it yielded 0.8 and 1.25 ng of total RNA from EVEpCAM and EVFAPα, respectively. To assess the potential of these two EV subpopulations to provide molecular information for prognostication, we performed the PAM50 test (Prosigna) on exo-mRNA harvested from each EV subpopulation. Results suggested that EVEpCAM and EVFAPα exo-mRNA profiling using subsets of the PAM50 genes and a novel algorithm (i.e., exo-PAM50) generated 100% concordance with the tumor tissue.
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Affiliation(s)
- Mengjia Hu
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, Kansas 66160, United States
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Virginia Brown
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Joshua M Jackson
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harshani Wijerathne
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Devin C Koestler
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Department of Biostatistics & Data Science, The University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Emily Nissen
- Department of Biostatistics & Data Science, The University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | | | - Rolf Muller
- BioFluidica, Inc., San Diego, California 92121, United States
| | - Andrew K Godwin
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Malgorzata A Witek
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Steven A Soper
- Department of Cancer Biology, The University of Kansas Medical Center, Cancer Center, Kansas City, Kansas 66160, United States
- Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- BioFluidica, Inc., San Diego, California 92121, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66045, United States
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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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Unksov IN, Korosec CS, Surendiran P, Verardo D, Lyttleton R, Forde NR, Linke H. Through the Eyes of Creators: Observing Artificial Molecular Motors. ACS NANOSCIENCE AU 2022; 2:140-159. [PMID: 35726277 PMCID: PMC9204826 DOI: 10.1021/acsnanoscienceau.1c00041] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
![]()
Inspired by molecular
motors in biology, there has been significant
progress in building artificial molecular motors, using a number of
quite distinct approaches. As the constructs become more sophisticated,
there is also an increasing need to directly observe the motion of
artificial motors at the nanoscale and to characterize their performance.
Here, we review the most used methods that tackle those tasks. We
aim to help experimentalists with an overview of the available tools
used for different types of synthetic motors and to choose the method
most suited for the size of a motor and the desired measurements,
such as the generated force or distances in the moving system. Furthermore,
for many envisioned applications of synthetic motors, it will be a
requirement to guide and control directed motions. We therefore also
provide a perspective on how motors can be observed on structures
that allow for directional guidance, such as nanowires and microchannels.
Thus, this Review facilitates the future research on synthetic molecular
motors, where observations at a single-motor level and a detailed
characterization of motion will promote applications.
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Affiliation(s)
- Ivan N. Unksov
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Chapin S. Korosec
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | | | - Damiano Verardo
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
- AlignedBio AB, Medicon Village, Scheeletorget 1, 223 63 Lund, Sweden
| | - Roman Lyttleton
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Nancy R. Forde
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | - Heiner Linke
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
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6
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Zhao Z, Wijerathne H, Godwin AK, Soper SA. Isolation and analysis methods of extracellular vesicles (EVs). EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2021; 2:80-103. [PMID: 34414401 PMCID: PMC8372011 DOI: 10.20517/evcna.2021.07] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) have been recognized as an evolving biomarker within the liquid biopsy family. While carrying both host cell proteins and different types of RNAs, EVs are also present in sufficient quantities in biological samples to be tested using many molecular analysis platforms to interrogate their content. However, because EVs in biological samples are comprised of both disease and non-disease related EVs, enrichment is often required to remove potential interferences from the downstream molecular assay. Most benchtop isolation/enrichment methods require > milliliter levels of sample and can cause varying degrees of damage to the EVs. In addition, some of the common EV benchtop isolation methods do not sort the diseased from the non-diseased related EVs. Simultaneously, the detection of the overall concentration and size distribution of the EVs is highly dependent on techniques such as electron microscopy and Nanoparticle Tracking Analysis, which can include unexpected variations and biases as well as complexity in the analysis. This review discusses the importance of EVs as a biomarker secured from a liquid biopsy and covers some of the traditional and non-traditional, including microfluidics and resistive pulse sensing, technologies for EV isolation and detection, respectively.
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Affiliation(s)
- Zheng Zhao
- Bioengineering Program, University of Kansas, Lawrence, KS 66045, USA.,Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA
| | - Harshani Wijerathne
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA
| | - Andrew K Godwin
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Steven A Soper
- Bioengineering Program, University of Kansas, Lawrence, KS 66045, USA.,Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA.,Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.,Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045, USA.,KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA.,Ulsan National Institute of Science & Technology, Ulju-gun, Ulsan, 44919, South Korea
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7
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Campos CDM, Childers K, Gamage SST, Wijerathne H, Zhao Z, Soper SA. Analytical Technologies for Liquid Biopsy of Subcellular Materials. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:207-229. [PMID: 33974805 PMCID: PMC8601690 DOI: 10.1146/annurev-anchem-091520-093931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Liquid biopsy markers, which can be secured from a simple blood draw or other biological samples, are used to manage a variety of diseases and even monitor for bacterial or viral infections. Although there are several different types of liquid biopsy markers, the subcellular ones, including cell-free DNA, microRNA, extracellular vesicles, and viral particles, are evolving in terms of their utility. A challenge with liquid biopsy markers is that they must be enriched from the biological sample prior to analysis because they are a vast minority in a mixed population, and potential interferences may be present in the sample matrix that can inhibit profiling the molecular cargo from the subcellular marker. In this article, we discuss existing and developing analytical enrichment platforms used to isolate subcellular liquid biopsy markers, and discuss their figures of merit such as recovery, throughput, and purity.
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Affiliation(s)
- Camila D M Campos
- Life Science Department, Imec, 3001 Leuven, Belgium
- Department of Electrical Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Katie Childers
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
| | - Sachindra S T Gamage
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Harshani Wijerathne
- Department of Mechanical Engineering, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Zheng Zhao
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
| | - Steven A Soper
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, Kansas 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
- Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
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8
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Park J, Woo S, Kim J, Lee H, Yoo YE, Hong S. Rapid and simple single-chamber nucleic acid detection system prepared through nature-inspired surface engineering. Am J Cancer Res 2021; 11:6735-6745. [PMID: 34093850 PMCID: PMC8171086 DOI: 10.7150/thno.57153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Nucleic acid (NA)-based diagnostics enable a rapid response to various diseases, but current techniques often require multiple labor-intensive steps, which is a major obstacle to successful translation to a clinical setting. Methods: We report on a surface-engineered single-chamber device for NA extraction and in situ amplification without sample transfer. Our system has two reaction sites: a NA extraction chamber whose surface is patterned with micropillars and a reaction chamber filled with reagents for in situ polymerase-based NA amplification. These two sites are integrated in a single microfluidic device; we applied plastic injection molding for cost-effective, mass-production of the designed device. The micropillars were chemically activated via a nature-inspired silica coating to possess a specific affinity to NA. Results: As a proof-of-concept, a colorimetric pH indicator was coupled to the on-chip analysis of NA for the rapid and convenient detection of pathogens. The NA enrichment efficiency was dependent on the lysate incubation time, as diffusion controls the NA contact with the engineered surface. We could detect down to 1×103 CFU by the naked eye within one hour of the total assay time. Conclusion: We anticipate that the surface engineering technique for NA enrichment could be easily integrated as a part of various types of microfluidic chips for rapid and convenient nucleic acid-based diagnostics.
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Taskin MB, Ahmad T, Wistlich L, Meinel L, Schmitz M, Rossi A, Groll J. Bioactive Electrospun Fibers: Fabrication Strategies and a Critical Review of Surface-Sensitive Characterization and Quantification. Chem Rev 2021; 121:11194-11237. [DOI: 10.1021/acs.chemrev.0c00816] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mehmet Berat Taskin
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Taufiq Ahmad
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Laura Wistlich
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry and Helmholtz Institute for RNA Based Infection Research, 97074 Würzburg, Germany
| | - Michael Schmitz
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Angela Rossi
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Jürgen Groll
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
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10
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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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11
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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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12
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Dutta C, Bishop LDC, Zepeda O J, Chatterjee S, Flatebo C, Landes CF. Imaging Switchable Protein Interactions with an Active Porous Polymer Support. J Phys Chem B 2020; 124:4412-4420. [PMID: 32441098 DOI: 10.1021/acs.jpcb.0c01807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mechanistic details about how local physicochemistry of porous interfaces drives protein transport mechanisms are necessary to optimize biomaterial applications. Cross-linked hydrogels made of stimuli-responsive polymers have potential for active protein capture and release through tunable steric and chemical transformations. Simultaneous monitoring of dynamic changes in both protein transport and interfacial polymer structure is an experimental challenge. We use single-particle tracking (SPT) and fluorescence correlation spectroscopy Super-resolution Optical Fluctuation Imaging (fcsSOFI) to relate the switchable changes in size and structure of a pH-responsive hydrogel to the interfacial transport properties of a model protein, lysozyme. SPT analysis reveals the reversible switching of protein transport dynamics in and at the hydrogel polymer in response to pH changes. fcsSOFI allows us to relate tunable heterogeneity of the hydrogels and pores to reversible changes in the distribution of confined diffusion and adsorption/desorption. We find that physicochemical heterogeneity of the hydrogels dictates protein confinement and desorption dynamics, particularly at pH conditions in which the hydrogels are swollen.
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Affiliation(s)
- Chayan Dutta
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Logan D. C. Bishop
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Jorge Zepeda O
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Sudeshna Chatterjee
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Charlotte Flatebo
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Applied Physics Program, Rice University, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, HoustonTexas 77005, United States
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13
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Dutta C, Bishop LDC, Zepeda O J, Chatterjee S, Flatebo C, Landes CF. Imaging Switchable Protein Interactions With an Active Porous Polymer Support. J Phys Chem A 2020. [DOI: 10.1021/acs.jpca.0c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Liu H, Ye Z, Wang X, Wei L, Xiao L. Molecular and living cell dynamic assays with optical microscopy imaging techniques. Analyst 2019; 144:859-871. [PMID: 30444498 DOI: 10.1039/c8an01420e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Generally, the message elucidated by the conventional analytical methods overlooks the heterogeneity of single objects, where the behavior of individual molecules is shielded. With the advent of optical microscopy imaging techniques, it is possible to identify, visualize and track individual molecules or nanoparticles under a biological environment with high temporal and spatial resolution. In this work, we summarize the commonly adopted optical microscopy techniques for bio-analytical assays in living cells, including total internal reflection fluorescence microscopy (TIRFM), super-resolution optical microscopy (SRM), and dark-field optical microscopy (DFM). The basic principles of these methods and some recent interesting applications in molecular detection and single-particle tracking are introduced. Moreover, the development in high-dimensional optical microscopy to achieve three-dimensional (3-D) as well as sub-diffraction localization and tracking of biomolecules is also highlighted.
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Affiliation(s)
- Hua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China.
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15
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Niu Q, Wang D. Probing the polymer anomalous dynamics at solid/liquid interfaces at the single-molecule level. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2019.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Pujals S, Feiner-Gracia N, Delcanale P, Voets I, Albertazzi L. Super-resolution microscopy as a powerful tool to study complex synthetic materials. Nat Rev Chem 2019. [DOI: 10.1038/s41570-018-0070-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Jia Z, Choi J, Park S. Surface Charge Density-Dependent DNA Capture through Polymer Planar Nanopores. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40927-40937. [PMID: 30371050 DOI: 10.1021/acsami.8b14423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Surface charge density of nanopore walls plays a critical role in DNA capture in nanopore-based sensing platforms. This paper studied the effect of surface charge density on the capture of double-stranded (ds) DNA molecules into a polymer planar nanopore numerically and experimentally. First, we simulated the effective driving force ( Feff) for the translocation of a dsDNA through a planar nanopore with different sizes and surface charge densities. Focus was given on the capture stage from the nanopore mouth into the nanopore by placing a rodlike DNA at the nanopore mouth rather than inside the nanopore. For negatively charged DNA and nanopore walls, electrophoretic driving force ( FEP) under an electric field is opposed by the viscous drag force by electroosmotic flow ( FEOF). As the surface charge density of the nanopore wall becomes more negative, FEOF exceeds FEP beyond a threshold surface charge density, σthreshold, where DNA molecules cannot be driven through the nanopore via electrophoretic motion. For a 10 nm diameter nanopore filled with 1× TE buffer, σthreshold was determined to be -50 mC/m2. The simulation results were verified by performing dsDNA translocation experiments using a planar nanopore with 10 nm equivalent diameter imprinted on three polymer substrates with different surface charge densities. Both fluorescence observation and ionic current measurement confirmed that only nanopore devices with the surface charge density less negative than σthreshold allowed DNA translocation, indicating that the simulated σthreshold value can be used as a parameter to estimate the translocation of biopolymers in the design of nanopore devices.
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Affiliation(s)
- Zheng Jia
- Mechanical & Industrial Engineering Department and Center for BioModular Multiscale Systems for Precision Medicine , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Junseo Choi
- Mechanical & Industrial Engineering Department and Center for BioModular Multiscale Systems for Precision Medicine , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Sunggook Park
- Mechanical & Industrial Engineering Department and Center for BioModular Multiscale Systems for Precision Medicine , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
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18
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Campos CDM, Gamage SST, Jackson JM, Witek MA, Park DS, Murphy MC, Godwin AK, Soper SA. Microfluidic-based solid phase extraction of cell free DNA. LAB ON A CHIP 2018; 18:3459-3470. [PMID: 30339164 PMCID: PMC6391159 DOI: 10.1039/c8lc00716k] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cell-free DNA (cfDNA) is a liquid biopsy marker that can carry signatures (i.e., mutations) associated with certain pathological conditions. Therefore, the extraction of cfDNA from a variety of clinical samples can be an effective and minimally invasive source of markers for disease detection and subsequent management. In the oncological diseases, circulating tumor DNA (ctDNA), a cfDNA sub-class, can carry clinically actionable mutations and coupled with next generation sequencing or other mutation detection methods provide a venue for effective in vitro diagnostics. However, cfDNA mutational analyses require high quality inputs. This necessitates extraction platforms that provide high recovery over the entire ctDNA size range (50 → 150 bp) with minimal interferences (i.e., co-extraction of genomic DNA), and high reproducibility with a simple workflow. Herein, we present a novel microfluidic solid-phase extraction device (μSPE) consisting of a plastic chip that is activated with UV/O3 to generate surface-confined carboxylic acid functionalities for the μSPE of cfDNA. The μSPE uses an immobilization buffer (IB) consisting of polyethylene glycol and salts that induce cfDNA condensation onto the activated plastic microfluidic surface. The μSPE consists of an array of micropillars to increase extraction bed load (scalable to loads >700 ng of cfDNA) and can be produced at low-cost using replication-based techniques. The entire μSPE can be fabricated in a single molding step negating the need for adding additional extraction supports to the device simplifying production and keeping device and assay cost low. The μSPE allowed for recoveries >90% of model cfDNA fragments across a range of sizes (100-700 bp) and even the ability to extract efficiently short cfDNA fragments (50 bp, >70%). In addition, the composition of the IB allowed for reducing the interference of co-extracted genomic DNA. We demonstrated the clinical utility of the μSPE by quantifying the levels of cfDNA in healthy donors and patients with non-small-cell lung and colorectal cancers. μSPE extracted cfDNA from plasma samples was also subjected to a ligase detection reaction (LDR) for determining the presence of mutations in the KRAS gene for colorectal and non-small cell lung cancer patients.
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Affiliation(s)
- Camila D. M. Campos
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
| | - Sachindra S. T. Gamage
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
| | - Joshua M. Jackson
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
| | - Malgorzata A. Witek
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel S. Park
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Michael C. Murphy
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Andrew K. Godwin
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Steven A. Soper
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
- BioEngineering Program, The University of Kansas, Lawrence, KS 66047, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66047, USA
- Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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19
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Coceancigh H, Higgins DA, Ito T. Optical Microscopic Techniques for Synthetic Polymer Characterization. Anal Chem 2018; 91:405-424. [PMID: 30350610 DOI: 10.1021/acs.analchem.8b04694] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Herman Coceancigh
- Department of Chemistry , Kansas State University , 213 CBC Building , Manhattan , Kansas 66506-0401 , United States
| | - Daniel A Higgins
- Department of Chemistry , Kansas State University , 213 CBC Building , Manhattan , Kansas 66506-0401 , United States
| | - Takashi Ito
- Department of Chemistry , Kansas State University , 213 CBC Building , Manhattan , Kansas 66506-0401 , United States
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20
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O'Neil C, Amarasekara CA, Weerakoon-Ratnayake KM, Gross B, Jia Z, Singh V, Park S, Soper SA. Electrokinetic transport properties of deoxynucleotide monophosphates (dNMPs) through thermoplastic nanochannels. Anal Chim Acta 2018; 1027:67-75. [PMID: 29866271 PMCID: PMC6408931 DOI: 10.1016/j.aca.2018.04.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/06/2018] [Accepted: 04/16/2018] [Indexed: 01/19/2023]
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.
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Affiliation(s)
- 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.
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21
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Thompson S, Pappas D. A fluorescence toolbox: A review of investigation of electrophoretic separations, process, and interfaces. Electrophoresis 2018; 40:606-615. [DOI: 10.1002/elps.201800310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 01/23/2023]
Affiliation(s)
- S. Thompson
- Department of Chemistry and Biochemistry; Texas Tech University; Lubbock TX USA
| | - Dimitri Pappas
- Department of Chemistry and Biochemistry; Texas Tech University; Lubbock TX USA
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22
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Nevskyi O, Sysoiev D, Dreier J, Stein SC, Oppermann A, Lemken F, Janke T, Enderlein J, Testa I, Huhn T, Wöll D. Fluorescent Diarylethene Photoswitches-A Universal Tool for Super-Resolution Microscopy in Nanostructured Materials. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:1703333. [PMID: 29325203 DOI: 10.1002/smll.201703333] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Super-resolution fluorescence microscopy allows for unprecedented in situ visualization of biological structures, but its application to materials science has so far been comparatively limited. One of the main reasons is the lack of powerful dyes that allow for labeling and photoswitching in materials science systems. In this study it is shown that appropriate substitution of diarylethenes bearing a fluorescent closed and dark open form paves the way for imaging nanostructured materials with three of the most popular super-resolution fluorescence microscopy methods that are based on different concepts to achieve imaging beyond the diffraction limit of light. The key to obtain optimal resolution lies in a proper control over the photochemistry of the photoswitches and its adaption to the system to be imaged. It is hoped that the present work will provide researchers with a guide to choose the best photoswitch derivative for super-resolution microscopy in materials science, just like the correct choice of a Swiss Army Knife's tool is essential to fulfill a given task.
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Affiliation(s)
- Oleksii Nevskyi
- Institute for Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Dmytro Sysoiev
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78464, Konstanz, Germany
| | - Jes Dreier
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17121, Solna, Sweden
| | - Simon Christoph Stein
- III. Institute of Physics - Biophysics, Georg-August University, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Alex Oppermann
- Institute for Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Florian Lemken
- Institute for Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Tobias Janke
- Institute for Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg-August University, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Ilaria Testa
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17121, Solna, Sweden
| | - Thomas Huhn
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78464, Konstanz, Germany
| | - Dominik Wöll
- Institute for Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
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23
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Jackson JM, Witek MA, Kamande JW, Soper SA. Materials and microfluidics: enabling the efficient isolation and analysis of circulating tumour cells. Chem Soc Rev 2017; 46:4245-4280. [PMID: 28632258 PMCID: PMC5576189 DOI: 10.1039/c7cs00016b] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a critical review of microfluidic technologies and material effects on the analyses of circulating tumour cells (CTCs) selected from the peripheral blood of cancer patients. CTCs are a minimally invasive source of clinical information that can be used to prognose patient outcome, monitor minimal residual disease, assess tumour resistance to therapeutic agents, and potentially screen individuals for the early diagnosis of cancer. The performance of CTC isolation technologies depends on microfluidic architectures, the underlying principles of isolation, and the choice of materials. We present a critical review of the fundamental principles used in these technologies and discuss their performance. We also give context to how CTC isolation technologies enable downstream analysis of selected CTCs in terms of detecting genetic mutations and gene expression that could be used to gain information that may affect patient outcome.
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24
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Chen T, Dong B, Chen K, Zhao F, Cheng X, Ma C, Lee S, Zhang P, Kang SH, Ha JW, Xu W, Fang N. Optical Super-Resolution Imaging of Surface Reactions. Chem Rev 2017; 117:7510-7537. [DOI: 10.1021/acs.chemrev.6b00673] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Tao Chen
- State
Key Laboratory of Electroanalytical Chemistry and Jilin Province Key
Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, P.R. China
- University of Chinese Academy of Science, Beijing, 100049, P. R. China
| | - Bin Dong
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kuangcai Chen
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Fei Zhao
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Xiaodong Cheng
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Changbei Ma
- State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha 410013, China
| | - Seungah Lee
- Department
of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Peng Zhang
- Department
of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Seong Ho Kang
- Department
of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Ji Won Ha
- Department
of Chemistry, University of Ulsan, 93 Dahak-Ro, Nam-Gu, Ulsan 44610, Republic of Korea
| | - Weilin Xu
- State
Key Laboratory of Electroanalytical Chemistry and Jilin Province Key
Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, P.R. China
| | - Ning Fang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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25
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Weerakoon-Ratnayake KM, O'Neil CE, Uba FI, Soper SA. Thermoplastic nanofluidic devices for biomedical applications. LAB ON A CHIP 2017; 17:362-381. [PMID: 28009883 PMCID: PMC5285477 DOI: 10.1039/c6lc01173j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Microfluidics is now moving into a developmental stage where basic discoveries are being transitioned into the commercial sector so that these discoveries can affect, for example, healthcare. Thus, high production rate microfabrication technologies, such as thermal embossing and/or injection molding, are being used to produce low-cost consumables appropriate for commercial applications. Based on recent reports, it is clear that nanofluidics offers some attractive process capabilities that may provide unique venues for biomolecular analyses that cannot be realized at the microscale. Thus, it would be attractive to consider early in the developmental cycle of nanofluidics production pipelines that can generate devices possessing sub-150 nm dimensions in a high production mode and at low-cost to accommodate the commercialization of this exciting technology. Recently, functional sub-150 nm thermoplastic nanofluidic devices have been reported that can provide high process yield rates, which can enable commercial translation of nanofluidics. This review presents an overview of recent advancements in the fabrication, assembly, surface modification and the characterization of thermoplastic nanofluidic devices. Also, several examples in which nanoscale phenomena have been exploited for the analysis of biomolecules are highlighted. Lastly, some general conclusions and future outlooks are presented.
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Affiliation(s)
- Kumuditha M Weerakoon-Ratnayake
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA and NIH Biotechnology Resource Center of Biomodular Multiscale Systems for Precision Medicine, USA
| | - Colleen E O'Neil
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA and NIH Biotechnology Resource Center of Biomodular Multiscale Systems for Precision Medicine, USA
| | - Franklin I Uba
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Steven A Soper
- Department of Chemistry and Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66047, USA. and Kansas University Medical Center NIH Cancer Center, Kansas City, KS 66106, USA and NIH Biotechnology Resource Center of Biomodular Multiscale Systems for Precision Medicine, USA and Ulsan National Institute of Science and Technology, Ulsan, South Korea
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O'Neil CE, Taylor S, Ratnayake K, Pullagurla S, Singh V, Soper SA. Characterization of activated cyclic olefin copolymer: effects of ethylene/norbornene content on the physiochemical properties. Analyst 2016; 141:6521-6532. [PMID: 27827488 PMCID: PMC5354357 DOI: 10.1039/c6an01448h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ethylene/norbornene content within cyclic olefin copolymer (COC) is well known to affect the chemical and physical properties of the copolymer, such as the glass transition temperature (Tg) and transparency. However, no work has been reported evaluating the effects of the ethylene/norbornene content on the surface properties of COC following UV/O3 or O2 plasma activation. Activation with either O2 plasma or UV/O3 is often used to assist in thermal assembly of fluidic devices, increasing the wettability of the surfaces, or generating functional scaffolds for the attachment of biological elements. Thus, we investigated differences in the physiochemical surface properties of various ethylene/norbornene compositions of COC following activation using analytical techniques such as water contact angle (WCA), ATR-FTIR, XPS, TOF-SIMS, UV-VIS, AFM and a colorimetric assay utilizing Toluidine Blue O (TBO). Results showed that increased norbornene content led to the generation of more oxygen containing functionalities such as alcohols, ketones, aldehydes and carboxyl groups when activated with either UV/O3 or O2 plasma. Specifically, COC with ∼60% norbornene content showed a significantly higher -COOH functional group density when compared to COC with a 50% norbornene content and COC with a 35% norbornene content following UV/O3 or O2 plasma activation. Furthermore, COC with large norbornene contents showed a smaller average RMS roughness (0.65 nm) when compared to COC containing low norbornene contents (0.95 nm) following activation making this substrate especially suited for nanofluidic applications, which require smooth surfaces to minimize effects arising from dielectrophoretic trapping or non-specific adsorption. Although all COC substrates showed >90% transparency at wavelengths >475 nm, COC possessing high norbornene contents showed significantly less transparency at wavelengths below 475 nm following activation, making optical detection in this region difficult. Our data showed distinct physiochemical differences in activated COC that was dependent upon the ethylene/norbornene content of the thermoplastic and thus, careful selection of the particular COC grade must be considered for micro- and nanofluidics.
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Affiliation(s)
- Colleen E O'Neil
- Department of Chemistry, the University of North Carolina at Chapel Hill, NC, USA
| | - Scott Taylor
- Department of Chemistry, the University of North Carolina at Chapel Hill, NC, USA
| | | | - Swathi Pullagurla
- Department of Chemistry, the University of Kansas, Lawrence, KS, USA. and Center for Biomodular Multiscale Systems for Precision Medicine, USA
| | - Varshni Singh
- Department of Biomedical Engineering, UNC, Chapel Hill, NC, USA
| | - Steven A Soper
- Department of Chemistry, the University of Kansas, Lawrence, KS, USA. and Center for Biomodular Multiscale Systems for Precision Medicine, USA and Department of Mechanical Engineering, the University of Kansas, Lawrence, KS, USA and Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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Burrows ND, Lin W, Hinman JG, Dennison JM, Vartanian AM, Abadeer NS, Grzincic EM, Jacob LM, Li J, Murphy CJ. Surface Chemistry of Gold Nanorods. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9905-9921. [PMID: 27568788 DOI: 10.1021/acs.langmuir.6b02706] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Gold nanorods have garnered a great deal of scientific interest because of their unique optical properties, and they have the potential to greatly impact many areas of science and technology. Understanding the structure and chemical makeup of their surfaces as well as how to tailor them is of paramount importance in the development of their successful applications. This Feature Article reviews the current understanding of the surface chemistry of as-synthesized gold nanorods, methods of tailoring the surface chemistry of gold nanorods with various inorganic and organic coatings/ligands, and the techniques employed to characterize ligands on the surface of gold nanorods as well as the associated measurement challenges. Specifically, we address the challenges of determining how thick the ligand shell is, how many ligands per nanorod are present on the surface, and where the ligands are located in regiospecific and mixed-ligand systems. We conclude with an outlook on the development of the surface chemistry of gold nanorods leading to the development of a synthetic nanoparticle surface chemistry toolbox analogous to that of synthetic organic chemistry and natural product synthesis.
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Affiliation(s)
- Nathan D Burrows
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Wayne Lin
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Joshua G Hinman
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jordan M Dennison
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ariane M Vartanian
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Nardine S Abadeer
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Elissa M Grzincic
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Lisa M Jacob
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ji Li
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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