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Sensale S, Wang C, Chang HC. Resistive amplitude fingerprints during translocation of linear molecules through charged solid-state nanopores. J Chem Phys 2020; 153:035102. [PMID: 32716192 PMCID: PMC7367690 DOI: 10.1063/5.0013195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We report the first analytical theory on the amplitude of resistive signals during molecular translocation through charged solid-state nanopores with variable cross-sectional area and piecewise-constant surface charge densities. By providing closed-form explicit algebraic expressions for the concentration profiles inside charged nanopores, this theory allows the prediction of baseline and translocation resistive signals without the need for numerical simulation of the electrokinetic phenomena. A transversely homogenized theory and an asymptotic expansion for weakly charged pores capture DC or quasi-static rectification due to field-induced intrapore concentration polarization (as a result of pore charge inhomogeneity or a translocating molecule). This theory, validated by simulations and experiments, is then used to explain why the amplitude of a single stranded DNA molecule can be twice as high as the amplitude of its double stranded counterpart. It also suggests designs for intrapore concentration polarization and volume exclusion effects that can produce biphasic and other amplitude fingerprints for high-throughput and yet discriminating molecular identification.
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Affiliation(s)
- Sebastian Sensale
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
| | - Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
| | - Hsueh-Chia Chang
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556-5637, USA
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2
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Yeung ES. Autobiography of an Analytical Chemist. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:1-16. [PMID: 31904991 DOI: 10.1146/annurev-anchem-090519-111018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Most of my research directions were opportunistic. Having worked with lasers in the early stages of laser applications in analytical chemistry, attending conferences, workshops, and administrative meetings that were not exactly aligned with our own research, locating to a building or in a department that housed scientists with different backgrounds, having certain specialized equipment at the right time, and having funding agencies that were broad-minded clearly contributed to my ventures into diverse fields. Most of all, it had to be the many eager minds that I have had the fortune to work with. I have always tried to suggest research topics that might be interesting to the individual coworker rather than something straight out of my own research proposals. Only then did each person actually own the project rather than consider it a chore. After all, we work in the field of analytical chemistry, in which almost anything we do can fit in.
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Affiliation(s)
- Edward S Yeung
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA;
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3
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Li Z, Ashraf KM, Collinson MM, Higgins DA. Single Molecule Catch and Release: Potential-Dependent Plasmid DNA Adsorption along Chemically Graded Electrode Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8651-8662. [PMID: 28383916 DOI: 10.1021/acs.langmuir.7b00044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single molecule detection methods were employed to study the potential dependent adsorption and desorption of dye labeled plasmid DNA along chemical gradients prepared on indium tin oxide (ITO) electrodes. Gradients were formed over silica-base-layer-coated ITO surfaces by exposing them in a directional fashion to aminopropyltrimethoxysilane from the vapor phase. Sessile drop water contact angle measurements, spectroscopic ellipsometry, and X-ray photoelectron spectroscopy were used to verify that a gradient was formed and to characterize its wettability, thickness, and composition as a function of position. The gradient-coated ITO electrode served as both the working electrode and a window into the electrochemical cell used to manipulate DNA adsorption. For single molecule studies, the electrochemical cell was filled with buffer solution containing YOYO-1-labeled plasmid DNA. Fluorescence videos acquired along the gradients depicted clear position-, potential-, and pH-dependent variations in DNA adsorption and desorption. The results demonstrate that DNA adsorption was largely independent of applied potential and irreversible at high amine coverage (i.e., multilayers), under pH ∼ 6 buffer. DNA adsorption became more reversible as the amine coverage decreased and the solution pH increased. Potential dependent control over DNA adsorption and desorption was best achieved at monolayer-to-submonolayer aminosilane coverage under pH ∼ 8 buffer. The knowledge gained in these studies will aid in the development of electrochemical methods for the capture and release of DNA and other polyelectrolytes at electrode surfaces.
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Affiliation(s)
- Zi Li
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Kayesh M Ashraf
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Maryanne M Collinson
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Daniel A Higgins
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
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4
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Shi B, Shin YK, Hassanali AA, Singer SJ. Biomolecules at the amorphous silica/water interface: Binding and fluorescence anisotropy of peptides. Colloids Surf B Biointerfaces 2017; 157:83-92. [DOI: 10.1016/j.colsurfb.2017.05.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/19/2023]
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5
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Giri D, Li Z, Ashraf KM, Collinson MM, Higgins DA. Molecular Combing of λ-DNA using Self-Propelled Water Droplets on Wettability Gradient Surfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:24265-24272. [PMID: 27541167 DOI: 10.1021/acsami.6b08607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Surface wettability gradients were used to elongate and align double stranded λ-DNA. Gradients were prepared by vapor phase deposition of octyltrichlorosilane (C8-silane) and fluorinated octyltrichlorosilane (F-silane) precursors. Gradient formation was confirmed by water contact angle and ellipsometric film thickness measurements. Placement of a droplet of aqueous DNA solution on the hydrophobic end of each gradient led to spontaneous motion of the droplet toward the hydrophilic end and deposition of the DNA. Fluorescence imaging of surface-adsorbed YOYO-1 labeled DNA molecules revealed that they are elongated and aligned perpendicular to the droplet-surface contact line at all positions along the gradient, consistent with a dominant role played by surface tension forces in elongating the DNA. The density of adsorbed DNA was found to be greatest on the C8-silane gradient at its hydrophobic end. DNA density decreased toward the hydrophilic end, while the length of the elongated DNA was less dependent on position. The elongation of DNA molecules by spontaneous droplet motion on chemical gradient surfaces has possible applications in DNA barcoding and studies of DNA-protein interactions.
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Affiliation(s)
- Dipak Giri
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Zi Li
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Kayesh M Ashraf
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Maryanne M Collinson
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Daniel A Higgins
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
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6
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Affiliation(s)
- Bobo Shi
- Department of Chemistry and Biochemistry and ‡Biophysics Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yun Kyung Shin
- Department of Chemistry and Biochemistry and ‡Biophysics Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ali A. Hassanali
- Department of Chemistry and Biochemistry and ‡Biophysics Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sherwin J. Singer
- Department of Chemistry and Biochemistry and ‡Biophysics Program, The Ohio State University, Columbus, Ohio 43210, United States
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7
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Smerkova K, Dostalova S, Vaculovicova M, Kynicky J, Trnkova L, Kralik M, Adam V, Hubalek J, Provaznik I, Kizek R. Investigation of interaction between magnetic silica particles and lambda phage DNA fragment. J Pharm Biomed Anal 2013; 86:65-72. [DOI: 10.1016/j.jpba.2013.07.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 07/29/2013] [Indexed: 11/25/2022]
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Peterson EM, Harris JM. Single-molecule fluorescence imaging of DNA at a potential-controlled interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8292-8301. [PMID: 23741971 DOI: 10.1021/la400884t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Many interfacial chemical phenomena are governed in part by electrostatic interactions between polyelectrolytes and charged surfaces; these phenomena can influence the performance of biosensors, adsorption of natural polyelectrolytes (humic substances) on soils, and production of polyelectrolyte multilayer films. In order to understand electrostatic interactions that govern these phenomena, we have investigated the behavior of a model polyelectrolyte, 15 kbp fluorescently labeled plasmid DNA, near a polarized indium tin oxide (ITO) electrode surface. The interfacial population of DNA was monitored in situ by imaging individual molecules through the transparent electrode using total-internal-reflection fluorescence microscopy. At applied potentials of +0.8 V versus Ag/AgCl, the DNA interfacial population near the ITO surface can be increased by 2 orders of magnitude relative to bulk solution. The DNA molecules attracted to the interface do not adsorb to ITO, but rather they remain mobile with a diffusion coefficient comparable to free solution. Ionic strength strongly influences the sensitivity of the interfacial population to applied potential, where the increase in the interfacial population over a +300 mV change in potential varies from 20% in 30 mM ionic strength to over 25-fold in 300 μM electrolyte. The DNA accumulation with applied potential was interpreted using a simple Boltzmann model to predict average ion concentrations in the electrical double layer and the fraction of interfacial detection volume that is influenced by applied potential. A Gouy-Chapman model was also applied to the data to account for the dependence of the ion population on distance from the electrode surface, which indicates that the net charge on DNA responsible for interactions with the polarized surface is low, on the order of one excess electron. The results are consistent with a small fraction of the DNA plasmid being resident in the double-layer and with counterions screening much of the DNA excess charge.
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Affiliation(s)
- Eric M Peterson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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10
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Chan HM, Chan LS, Wong RNS, Li HW. Direct quantification of single-molecules of microRNA by total internal reflection fluorescence microscopy. Anal Chem 2010; 82:6911-8. [PMID: 20704380 DOI: 10.1021/ac101133x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) express differently in normal and cancerous tissues and thus are regarded as potent cancer biomarkers for early diagnosis. However, the short length and low abundance of miRNAs have brought challenges to the established detection assay in terms of sensitivity and selectivity. In this work, we present a novel miRNA detection assay in single-molecule level with total internal reflection fluorescence microscopy (TIRFM). It is a solution-based hybridization detection system that does not require pretreatment steps such as sample enrichment or signal amplification. The hsa-miR-21 (miR-21) is chosen as target miRNA for its significant elevated content in a variety of cancers as reported previously. Herein, probes of complementary single-stranded oligonucleotide were hybridized in solution to miR-21 and labeled with fluorescent dye YOYO-1. The fluorescent hybrids were imaged by an electron-multiplying charge-coupled device (EMCCD) coupled TIRFM system and quantified by single-molecule counting. This single molecule detection (SMD) assay shows a good correlation between the number of molecules detected and the factual concentration of miRNA. The detection assay is applied to quantify the miR-21 in extracted total RNA samples of cancerous MCF-7 cells, HepG2 cells, and normal HUVEC cells, respectively. The results agreed very well with those from the prevalent real-time polymerase chain reaction (qRT-PCR) analysis. This assay is of high potential for applications in miRNA expression profiling and early cancer diagnosis.
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Affiliation(s)
- Ho-Man Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, P.R. China
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Hassanali AA, Zhang H, Knight C, Shin YK, Singer SJ. The Dissociated Amorphous Silica Surface: Model Development and Evaluation. J Chem Theory Comput 2010; 6:3456-71. [DOI: 10.1021/ct100260z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ali A. Hassanali
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Hui Zhang
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Chris Knight
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Yun Kyung Shin
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Sherwin J. Singer
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
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12
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Ma C, Yeung ES. Entrapment of Individual DNA Molecules and Nanoparticles in Porous Alumina Membranes. Anal Chem 2009; 82:654-7. [DOI: 10.1021/ac902109g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Changbei Ma
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Edward S. Yeung
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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13
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Affiliation(s)
- Changbei Ma
- Ames Laboratory-U.S. DOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Edward S. Yeung
- Ames Laboratory-U.S. DOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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Geng T, Bao N, Gall OZ, Lu C. Modulating DNA adsorption on silica beads using an electrical switch. Chem Commun (Camb) 2008:800-2. [PMID: 19322446 DOI: 10.1039/b817034g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate active tuning of DNA adsorption on silica beads using an electrical switch in a microfluidic device; we use electrolysis of water to alter pH in a packed bed of silica beads and switch the silica bead surface between being adsorptive and desorptive for DNA molecules.
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Affiliation(s)
- Tao Geng
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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15
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Liu X, Wu Z, Nie H, Liu Z, He Y, Yeung E. Single DNA molecules as probes for interrogating silica surfaces after various chemical treatments. Anal Chim Acta 2007; 602:229-35. [DOI: 10.1016/j.aca.2007.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 08/31/2007] [Accepted: 09/08/2007] [Indexed: 10/22/2022]
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16
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Isailovic S, Li HW, Yeung ES. Adsorption of single DNA molecules at the water/fused-silica interface. J Chromatogr A 2007; 1150:259-66. [PMID: 17054967 DOI: 10.1016/j.chroma.2006.09.093] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 09/25/2006] [Accepted: 09/27/2006] [Indexed: 11/20/2022]
Abstract
We applied total internal reflection fluorescence microscopy (TIRFM) to study intermolecular interactions at the water/fused-silica interface at the single-molecule level. Real-time molecular motion at the interface was recorded to reveal adsorption behavior and conformational dynamics of three DNAs with sticky ends of different numbers of unpaired bases. Features of DNA motion at the interface, such as evanescent-field residence time, linear velocity and frequency of adsorption/desorption events were measured to assess the relative affinities of the oligonucleotides for the surface. The general trend of stronger interaction with the surface for longer sticky ends confirmed hydrophobic interaction and hydrogen bonding as the driving forces of DNA adsorption to fused-silica at pH 5. For DNAs of different sizes, different conformational dynamics and the accessibility of sticky ends give rise to a nonlinear relationship with respect to affinity. Such information may prove valuable for chromatography studies as well as for the design of DNA microarrays and drug delivery systems.
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Affiliation(s)
- Slavica Isailovic
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, IA 50011, United States
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Fletcher KA, Fakayode SO, Lowry M, Tucker SA, Neal SL, Kimaru IW, McCarroll ME, Patonay G, Oldham PB, Rusin O, Strongin RM, Warner IM. Molecular fluorescence, phosphorescence, and chemiluminescence spectrometry. Anal Chem 2006; 78:4047-68. [PMID: 16771540 PMCID: PMC2662353 DOI: 10.1021/ac060683m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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18
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Park HY, Li HW, Yeung ES, Porter MD. Single molecule adsorption at compositionally patterned self-assembled monolayers on gold: role of domain boundaries. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:4244-9. [PMID: 16618171 DOI: 10.1021/la053100x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
This paper examines the single-molecule adsorption of YOYO-I-labeled lambda-DNA at compositionally patterned self-assembled monolayers (SAMs). The interactions of fluorescently labeled lambda-DNA molecule with the patterned SAMs, which are comprised of different functional groups (i.e., amine-, alcohol-, and acid-terminated thiolates), were monitored at optically transparent gold films using total internal reflection fluorescence microscopy. The role of solution pH, lambda-DNA concentration, and domain size was investigated. In addition to delineation of the relative adsorption strength as a function of terminal group identity (NH2 > COOH > OH), the potential importance of structural defects was also revealed. The latter result, found both at the disordered boundaries between domains and at adlayers in which structural order was affected by the length of the alkyl chain, points to the subtle but preferential adsorption of the "sticky ends" of lambda-DNA. These experiments also detected an intriguing dependence of adsorption with respect to domain size.
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Affiliation(s)
- Hye-Young Park
- Ames Laboratory-USDOE, Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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