1
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Hui K, Yan L, Schneider JW. Electrophoretically Snagging Viral Genomes in Wormlike Micelle Networks Using Peptide Nucleic Acid Amphiphiles and dsDNA Oligomers. Biomacromolecules 2024. [PMID: 39017713 DOI: 10.1021/acs.biomac.4c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
We demonstrate that the attachment of 30-170 bp dsDNA oligomers to ssDNA viral genomes gives a significant additional mobility shift in micelle-tagging electrophoresis (MTE). In MTE, a modified peptide nucleic acid amphiphile is attached to the viral genome to bind drag-inducing micelles present in capillary electrophoresis running buffers. Further attachment of 30-170 bp dsDNA oligomers drastically shifts the mobility of the 5.1 kB ssDNA genome of mouse minute virus (MMV), providing a new mechanism to improve resolution in CE-based analysis of kilobase nucleic acids. A model based on biased-reptation electrophoresis, end-labeled free-solution electrophoresis, and Ferguson gel-filtration theory is presented to describe the observed mobility shifts.
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Affiliation(s)
- Kimberly Hui
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lingxiao Yan
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - James W Schneider
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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2
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Li Z, Liu B, Guo Y, Bi L, Hu H, Zeng T, Li R, Theodorakis PE. Evaporation Dynamics of Macro- and Nanodroplets on Heated Hydrophilic Rough Substrates: The Effect of Roughness and Scale. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38321753 DOI: 10.1021/acs.langmuir.3c03147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Droplet evaporation on rough substrates plays an essential role in cooling and micro/nanoparticle assembly. Currently, there are numerous macroscopic experiments and theoretical models to investigate the droplet evaporation behavior on rough substrates. However, due to the complexity of this phenomenon, understanding its mechanisms solely through macroscale studies is difficult. To this end, molecular dynamics simulations of the models with distinct roughness factors are performed, and the obtained results are compared with those of relevant experiments of droplet evaporation on three hydrophilic substrates with different roughness average of 0.1, 0.15, and 0.2 μm, respectively. In this way, we assess the evaporation on these rough systems and the effect of scale on macro- and nanodroplets, which allows us to explore deeper the mechanism of droplet evaporation on rough hydrophilic substrates. In particular, we find that in the case of macroscale droplets, the evaporation mode remains the same with increasing roughness, pointing to a combined mixed and constant-contact-radius (CCR) mode. In the case of nanoscale droplets, the evaporation model is the constant-contact-angle mode when the roughness factor r = 1, while the mixed and CCR modes are found for r = 1.5 and 2, respectively. The scale effect has significant influence on the evaporation pattern of droplets on rough hydrophilic substrates. Moreover, it is also found that increasing the roughness of substrates expands the substrate-droplet contact area on both the macro- and nanoscale, which in turn enhances the heat transfer from the substrate toward the droplet. We anticipate that this first systematic analysis of scale effects provides further insights into the evaporation dynamics of droplets on rough hydrophilic substrates and has significant implications for the advancement of nanotechnology.
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Affiliation(s)
- Zhuorui Li
- Tianjin Key Laboratory of Refrigeration Technology, Tianjin University of Commerce, Tianjin 300134, China
| | - Bin Liu
- Tianjin Key Laboratory of Refrigeration Technology, Tianjin University of Commerce, Tianjin 300134, China
- International Centre in Fundamental and Engineering Thermophysics, Tianjin University of Commerce, Tianjin 300134, China
- Key Lab of Agricultural Products Low Carbon Cold Chain of Ministry of Agriculture and Rural Affairs, Tianjin University of Commerce, Tianjin 300134, China
| | - Yali Guo
- Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education, Dalian University of Technology, Dalian 116024, China
| | - Lisen Bi
- Tianjin Key Laboratory of Refrigeration Technology, Tianjin University of Commerce, Tianjin 300134, China
| | - Hengxiang Hu
- Tianjin Key Laboratory of Refrigeration Technology, Tianjin University of Commerce, Tianjin 300134, China
| | - Tao Zeng
- Tianjin Key Laboratory of Refrigeration Technology, Tianjin University of Commerce, Tianjin 300134, China
| | - Rui Li
- Tianjin Key Laboratory of Refrigeration Technology, Tianjin University of Commerce, Tianjin 300134, China
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3
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Coll De Peña A, Li N, Vaduva M, Bwanali L, Tripathi A. A microfluidic electrophoretic dual dynamic staining method for the identification and relative quantitation of dsRNA contaminants in mRNA vaccines. Analyst 2023; 148:3758-3767. [PMID: 37439498 DOI: 10.1039/d3an00281k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
mRNA vaccines (i.e., COVID-19 vaccine) offer various advantages over traditional vaccines in preventing and reducing disease and shortening the time between pathogen discovery and vaccine creation. Production of mRNA vaccines results in several nucleic acid and enzymatic by-products, most of which can be detected and removed; however, double-stranded RNA (dsRNA) contaminants pose a particular challenge. Current purification and detection platforms for dsRNA vary in effectiveness, with problems in scalability for mass mRNA vaccine production. Effectively detecting dsRNA is crucial in ensuring the safety and efficacy of the vaccines, as these strands can cause autoimmune reactions with length-symptom dependency and enhance mRNA degradation. We present a new microfluidics method to rapidly identify and quantify dsRNA fragments in mRNA samples. Our innovation exploits the differences in the dynamic staining behavior between mRNA and dsRNA molecules to detect dsRNA contaminants in a high throughput approach. The limit of detection of the system for dsRNA was estimated to be between 17.7-76.6 pg μL-1 with a maximum loading capacity of mRNA of 12.99 ng μL-1. Based on these estimated values, our method allows for the detection of dsRNA contaminants present in percentages as low as 0.14-0.59% compared to the total mRNA concentration. Here, we discuss the molecular mechanism of the dynamic staining behavior of dsRNA and mRNA for two different stains. We believe our method will accelerate the mRNA vaccine development from initial development to quality control workflows.
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Affiliation(s)
- Adriana Coll De Peña
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
| | - Nina Li
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
| | - Matei Vaduva
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
| | | | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
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4
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Jomova K, Cvik M, Lauro P, Valko M, Cizmar E, Alomar SY, Alwasel SH, Oleksak P, Chrienova Z, Nepovimova E, Kuca K, Rhodes CJ. The role of redox active copper(II) on antioxidant properties of the flavonoid baicalein: DNA protection under Cu(II)-Fenton reaction and Cu(II)-ascorbate system conditions. J Inorg Biochem 2023; 245:112244. [PMID: 37178556 DOI: 10.1016/j.jinorgbio.2023.112244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/17/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
The antioxidant properties of flavonoids are mediated by their functional hydroxyl groups, which are capable of both chelating redox active metals such as iron, copper and scavenging free radicals. In this paper, the antioxidant vs. prooxidant and DNA protecting properties of baicalein and Cu(II)-baicalein complexes were studied under the conditions of the Copper-Fenton reaction and of the Copper-Ascorbate system. From the relevant EPR spectra, the interaction of baicalein with Cu(II) ions was confirmed, while UV-vis spectroscopy demonstrated a greater stability over time of Cu(II)-baicalein complexes in DMSO than in methanol and PBS and Phosphate buffers. An ABTS study confirmed a moderate ROS scavenging efficiency, at around 37%, for both free baicalein and Cu(II)-baicalein complexes (in the ratios 1:1 and 1:2). The results from absorption titrations are in agreement with those from viscometric studies and confirmed that the binding mode between DNA and both free baicalein and Cu-baicalein complexes, involves hydrogen bonds and van der Waals interactions. The DNA protective effect of baicalein has been investigated by means of gel electrophoresis under the conditions of the Cu-catalyzed Fenton reaction and of the Cu-Ascorbate system. In both cases, it was found that, at sufficiently high concentrations, baicalein offers some protection to cells from DNA damage caused by ROS (singlet oxygen, hydroxyl radicals and superoxide radical anions). Accordingly, baicalein may be useful as a therapeutic agent in diseases with a disturbed metabolism of redox metals such as copper, for example Alzheimer's disease, Wilson's disease and various cancers. While therapeutically sufficient concentrations of baicalein may protect neuronal cells from Cu-Fenton-induced DNA damage in regard to neurological conditions, conversely, in the case of cancers, low concentrations of baicalein do not inhibit the pro-oxidant effect of copper ions and ascorbate, which can, in turn, deliver an effective damage to DNA in tumour cells.
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Affiliation(s)
- Klaudia Jomova
- Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University in Nitra, Nitra 949 74, Slovakia.
| | - Marcel Cvik
- Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University in Nitra, Nitra 949 74, Slovakia
| | - Peter Lauro
- Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University in Nitra, Nitra 949 74, Slovakia
| | - Marian Valko
- Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava 812 37, Slovakia; King Saud University, Zoology Department, College of Science, Riyadh 11451, Saudi Arabia
| | - Erik Cizmar
- Department of Condensed Matter Physics, Faculty of Science, University of P. J. Safarik, Park Angelinum 9, Kosice 040 01, Slovakia
| | - Suliman Y Alomar
- King Saud University, Zoology Department, College of Science, Riyadh 11451, Saudi Arabia
| | - Saleh H Alwasel
- King Saud University, Zoology Department, College of Science, Riyadh 11451, Saudi Arabia
| | - Patrik Oleksak
- Department of Chemistry, Faculty of Sciences, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic
| | - Zofia Chrienova
- Department of Chemistry, Faculty of Sciences, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Sciences, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Sciences, University of Hradec Kralove, 50005 Hradec Kralove, Czech Republic; Biomedical Research Centre, University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic
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5
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Wang Z, Wang ZG, Shi AC, Lu Y, An L. Behaviors of a Polymer Chain in Channels: From Zimm to Rouse Dynamics. Macromolecules 2023. [DOI: 10.1021/acs.macromol.3c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Affiliation(s)
- Zhenhua Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - An-Chang Shi
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
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6
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Hettiarachchi S, Cha H, Ouyang L, Mudugamuwa A, An H, Kijanka G, Kashaninejad N, Nguyen NT, Zhang J. Recent microfluidic advances in submicron to nanoparticle manipulation and separation. LAB ON A CHIP 2023; 23:982-1010. [PMID: 36367456 DOI: 10.1039/d2lc00793b] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Manipulation and separation of submicron and nanoparticles are indispensable in many chemical, biological, medical, and environmental applications. Conventional technologies such as ultracentrifugation, ultrafiltration, size exclusion chromatography, precipitation and immunoaffinity capture are limited by high cost, low resolution, low purity or the risk of damage to biological particles. Microfluidics can accurately control fluid flow in channels with dimensions of tens of micrometres. Rapid microfluidics advancement has enabled precise sorting and isolating of nanoparticles with better resolution and efficiency than conventional technologies. This paper comprehensively studies the latest progress in microfluidic technology for submicron and nanoparticle manipulation. We first summarise the principles of the traditional techniques for manipulating nanoparticles. Following the classification of microfluidic techniques as active, passive, and hybrid approaches, we elaborate on the physics, device design, working mechanism and applications of each technique. We also compare the merits and demerits of different microfluidic techniques and benchmark them with conventional technologies. Concurrently, we summarise seven standard post-separation detection techniques for nanoparticles. Finally, we discuss current challenges and future perspectives on microfluidic technology for nanoparticle manipulation and separation.
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Affiliation(s)
- Samith Hettiarachchi
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
| | - Haotian Cha
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
| | - Lingxi Ouyang
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
| | | | - Hongjie An
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
| | - Gregor Kijanka
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
| | - Navid Kashaninejad
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
| | - Jun Zhang
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
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7
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Qiao L, Szuttor K, Holm C, Slater GW. Ratcheting Charged Polymers through Symmetric Nanopores Using Pulsed Fields: Designing a Low Pass Filter for Concentrating Polyelectrolytes. NANO LETTERS 2023; 23:1343-1349. [PMID: 36705546 DOI: 10.1021/acs.nanolett.2c04588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation, and pulsed fields. Using Langevin dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency. The process itself can be performed with many pores in parallel, and it should be possible to integrate it directly into nanopore sequencing devices, increasing its potential utility.
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Affiliation(s)
- Le Qiao
- Physics Department, University of Ottawa, Ottawa, OntarioK1N 6N5, Canada
| | - Kai Szuttor
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, OntarioK1N 6N5, Canada
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8
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Rehel DA, Polson JM. Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries. SOFT MATTER 2023; 19:1092-1108. [PMID: 36625101 DOI: 10.1039/d2sm01413k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules in box-like cavities with strong confinement in one direction and with square and elliptical cross sections in the lateral plane. Motivated by these experiments, we employ Monte Carlo and Brownian dynamics simulations to study the physical behaviour of two polymers confined to small cavities with shapes comparable to those used in the experiments. We quantify the effects of varying the following polymer properties and confinement dimensions on the organization and dynamics of the polymers: the polymer width, the polymer contour length ratio, the cavity cross-sectional area, and the degree of cavity elongation for cavities with rectangular and elliptical cross sections. We find that the tendency for polymers to segregate is enhanced by increasing polymer width. For sufficiently small cavities, increasing cavity elongation promotes segregation and localization of identical polymers to opposite sides of the cavity along its long axis. A free-energy barrier controls the rate of polymers swapping positions, and the observed dynamics are roughly in accord with predictions of a simple theoretical model. Increasing the contour length difference between polymers significantly affects their organization in the cavity. In the case of a large linear polymer co-trapped with a small ring polymer in an elliptical cavity, the small polymer tends to lie near the lateral confining walls, and especially at the cavity poles for highly elongated ellipses.
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Affiliation(s)
- Desiree A Rehel
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada.
| | - James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada.
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9
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Chen H, Poitzsch ME. Dynamics of Polymers Flowing through Porous Media: Interplay of Solvent Properties, Flow Rates, and Wetting. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hsieh Chen
- Aramco Americas: Aramco Research Center-Boston, Cambridge, Massachusetts02139, United States
| | - Martin E. Poitzsch
- Aramco Americas: Aramco Research Center-Boston, Cambridge, Massachusetts02139, United States
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10
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Magill M, Nagel AM, de Haan HW. Parallel computing for mobilities in periodic geometries. Phys Rev E 2022; 106:045304. [PMID: 36397582 DOI: 10.1103/physreve.106.045304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.
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Affiliation(s)
- Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Andrew M Nagel
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, Ontario L1H7K4, Canada
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11
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Zhao L, He X, Liu Y, Wei M, Jin H. Development of a simple and rapid fluorescent aptasensor based on
DNA
tweezer. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luyang Zhao
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
| | - Xing He
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
| | - Yong Liu
- College of Chemistry and Chemical Engineering Henan University Kaifeng People's Republic of China
| | - Min Wei
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
| | - Huali Jin
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control Henan University of Technology Zhengzhou People's Republic of China
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12
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Sateesh J, Guha K, Dutta A, Sengupta P, Yalamanchili D, Donepudi NS, Surya Manoj M, Sohail SS. A comprehensive review on advancements in tissue engineering and microfluidics toward kidney-on-chip. BIOMICROFLUIDICS 2022; 16:041501. [PMID: 35992641 PMCID: PMC9385224 DOI: 10.1063/5.0087852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
This review provides a detailed literature survey on microfluidics and its road map toward kidney-on-chip technology. The whole review has been tailored with a clear description of crucial milestones in regenerative medicine, such as bioengineering, tissue engineering, microfluidics, microfluidic applications in biomedical engineering, capabilities of microfluidics in biomimetics, organ-on-chip, kidney-on-chip for disease modeling, drug toxicity, and implantable devices. This paper also presents future scope for research in the bio-microfluidics domain and biomimetics domain.
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Affiliation(s)
| | - Koushik Guha
- Department of Electronics and Communication Engineering, National MEMS Design Centre, National Institute of Technology Silchar, Assam 788010, India
| | - Arindam Dutta
- Urologist, RG Stone Urology and Laparoscopic Hospital, Kolkata, West Bengal, India
| | | | | | - Nanda Sai Donepudi
- Medical Interns, Government Siddhartha Medical College, Vijayawada, India
| | - M. Surya Manoj
- Department of Electronics and Communication Engineering, National MEMS Design Centre, National Institute of Technology Silchar, Assam 788010, India
| | - Sk. Shahrukh Sohail
- Department of Electronics and Communication Engineering, National MEMS Design Centre, National Institute of Technology Silchar, Assam 788010, India
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13
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Hidema R, Fujito KY, Suzuki H. Drag force of polyethyleneglycol in flows of polymer solutions measured using a scanning probe microscope. SOFT MATTER 2022; 18:455-464. [PMID: 34918726 DOI: 10.1039/d1sm01305j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The drag force of polyethyleneglycol thiol (mPEG-SH) attached to a cantilever probe in the flows of glycerol and polyethyleneglycol (PEG) solutions was measured. The effects of the molecular weights of mPEG-SH, solute, and molecular weights of PEGs in the flows on the drag force were investigated. The drag force of mPEG-SH with any molecular weight in the flows of glycerol solutions was described well by the stem and ellipsoidal-flower model proposed in a previous study. However, the drag force further increased in the flow of the PEG solutions. To describe the increment, an assumption of polymer entanglement with mPEG-SH attached to the probe in the flow was employed. The modified stem and ellipsoidal-flower model that employed polymer entanglements fit well to the drag force of mPEG-SH with any molecular weight in the flow of the polymer solution.
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Affiliation(s)
- Ruri Hidema
- Department of Chemical Science and Engineering, Kobe University, Kobe 657-8501, Japan.
| | - Ken-Ya Fujito
- Department of Chemical Science and Engineering, Kobe University, Kobe 657-8501, Japan.
| | - Hiroshi Suzuki
- Department of Chemical Science and Engineering, Kobe University, Kobe 657-8501, Japan.
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14
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Chen J, Sun L, Wang S, Tian F, Zhu H, Zhang R, Dai L. Crowding-induced polymer trapping in a channel. Phys Rev E 2021; 104:054502. [PMID: 34942690 DOI: 10.1103/physreve.104.054502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/20/2021] [Indexed: 11/07/2022]
Abstract
In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, ϕ^{*}, which scales as ϕ^{*}∼(a_{c}/L_{p})^{1/3} for a_{c}≫a_{m} and ϕ^{*}∼(a_{c}/L_{p})^{1/3}(a_{c}/a_{m})^{1/2} for a_{c}≪a_{m}, where a_{c} is the crowder diameter, a_{m} is the monomer diameter, and L_{p} is the polymer persistence length. For DNA, ϕ^{*} is estimated to be around 0.25 for crowders with a_{c}=2nm. We find that ϕ^{*} also strongly depends on the shape of the channel cross section, and ϕ^{*} is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.
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Affiliation(s)
- Jialu Chen
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong, China
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15
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Takao J, Endo T, Hisamoto H, Sueyoshi K. Direct Measurement of Initial Rate of Enzyme Reaction by Electrokinetic Filtration Using a Hydrogel-plugged Capillary Device. ANAL SCI 2021; 37:1439-1446. [PMID: 33840683 DOI: 10.2116/analsci.21p067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A novel electrokinetic filtration device using a plugged hydrogel was developed to directly measure the initial rate of enzyme reactions. In the proposed method, the enzyme reaction proceeded only for a short time when the substrate was passed through a thin layer of enzyme trapped by the hydrogel without any lag times for mixing and detection. In experimental conditions, alkaline phosphatase (enzyme) was filtrated at a cathodic-side interface of the plugged hydrogel by molecular sieving effect, providing the thin enzyme zone whose thickness was approximately 100 μm. When 4-methylumberiferyl phosphate (substrate) was electrokinetically introduced into the device after trapping the enzyme, 4-methylumberiferone (product) was generated by the enzyme reaction for only 1.26 s as the substrate passed through the trapped enzyme zone. As a result, the initial rate of the enzyme reaction could be directly calculated to 31.0 μM/s by simply dividing the concentration of the product by the tunable reaction time. Compared to the initial rate obtained by mixing the enzyme and substrate solutions, the value of the maximum velocity of the enzyme reaction was 30-fold larger than that in the mixing method due to the preconcentration of the enzyme by trapping. The Michaelis-Menten constant in the proposed method was 2.7-fold larger than that in the mixing method, suggesting the variation of changes in the equilibrium of complex formation under the experimental conditions.
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Affiliation(s)
- Junku Takao
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University.,Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO)
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16
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Abstract
AbstractThe outbreak of new viral strains promotes advances in universal diagnostic techniques for detecting infectious diseases with unknown viral sequence. Long double-stranded RNA (dsRNA), a hallmark of infections, serves as a virus marker for prompt detection of viruses with unknown genomes. Here, we report on-chip paper electrophoresis for ultrafast screening of infectious diseases. Negatively charged RNAs pass through the micro and nanoscale pores of cellulose in order of size under an external electric field applied to the paper microfluidic channel. Quantitative separation of long dsRNA mimicking poly I:C was analyzed from 1.67 to 33 ng·μL−1, which is close to the viral dsRNA concentration in infected cells. This paper-based capillary electrophoresis chip (paper CE chip) can provide a new diagnostic platform for ultrafast viral disease detection at the point-of-care (POC) level.
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17
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Hu SY, Chu JJ, Shelley MJ, Zhang J. Lévy Walks and Path Chaos in the Dispersal of Elongated Structures Moving across Cellular Vortical Flows. PHYSICAL REVIEW LETTERS 2021; 127:074503. [PMID: 34459633 DOI: 10.1103/physrevlett.127.074503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/19/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
In cellular vortical flows, namely arrays of counterrotating vortices, short but flexible filaments can show simple random walks through their stretch-coil interactions with flow stagnation points. Here, we study the dynamics of semirigid filaments long enough to broadly sample the vortical field. Using simulation, we find a surprising variety of long-time transport behavior-random walks, ballistic transport, and trapping-depending upon the filament's relative length and effective flexibility. Moreover, we find that filaments execute Lévy walks whose diffusion exponents generally decrease with increasing filament length, until transitioning to Brownian walks. Lyapunov exponents likewise increase with length. Even completely rigid filaments, whose dynamics is finite dimensional, show a surprising variety of transport states and chaos. Fast filament dispersal is related to an underlying geometry of "conveyor belts." Evidence for these various transport states is found in experiments using arrays of counterrotating rollers, immersed in a fluid and transporting a flexible ribbon.
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Affiliation(s)
- Shi-Yuan Hu
- Applied Mathematics Lab, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- Department of Physics, New York University, New York, New York 10003, USA
| | - Jun-Jun Chu
- School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
| | - Michael J Shelley
- Applied Mathematics Lab, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- Center for Computational Biology, Flatiron Institute, New York, New York 10010, USA
| | - Jun Zhang
- Applied Mathematics Lab, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- Department of Physics, New York University, New York, New York 10003, USA
- NYU-ECNU Institute of Physics at NYU Shanghai, Shanghai 200062, China
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18
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Samarasinghe TN, Zeng Y, Johnson CK. Microchip Electrophoresis Assay for Calmodulin Binding Proteins. J Sep Sci 2021; 44:895-902. [PMID: 34321981 DOI: 10.1002/jssc.202000884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The calcium signaling protein calmodulin regulates numerous intracellular processes. We introduce a sensitive microchip assay to separate and detect calmodulin binding proteins. The assay utilizes an optimized microchip electrophoresis protein separation platform with laser-induced fluorescence detection. Fluorescence-labeled calmodulin modified with a photoreactive diazirine crosslinker allowed selective detection of calmodulin binding proteins. We demonstrate successful in-vitro crosslinking of calmodulin with two calmodulin binding proteins, calcineurin and nitric oxide synthase. We compare the efficacy of commonly applied electrophoretic separation modes: microchip capillary zone electrophoresis, microchip micellar electrokinetic chromatography/gel electrophoresis, and nanoparticle colloidal arrays. Out of the methods tested, polydymethylsiloxane/glass chips with microchip zone electrophoresis gave the poorest separation, whereas sieving methods in which electro-osmotic flow was suppressed gave the best separation of photoproducts of calmodulin conjugated with calmodulin binding proteins.
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Affiliation(s)
| | - Yong Zeng
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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19
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Ohmatsuzawa A, Kikuchi M, Kawaguchi S, Kumaki J. Molecular Combing of Various Poly( n-Alkyl Acrylate) Chains on Mica by the Dipping Method. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7556-7564. [PMID: 34110164 DOI: 10.1021/acs.langmuir.1c01054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
If polymer chains could be deposited on a substrate as a fully extended chain, a procedure known as "molecular combing," the chain structure could be characterized by atomic force microscopy in more detail than has been possible with the measurements available today. We show here, for the first time, that flexible polymers can be molecularly combed to fully extended chains by the dipping method. We studied the molecular combing of a series of poly(n-alkyl acrylate)s on mica from a chloroform solution by the dipping method and found that poly(n-alkyl acrylate)s with an alkyl group longer than n-octyl can be molecularly combed into straight chains under optimized conditions. With increasing alkyl lengths, the number of chains deposited decreases by four orders of magnitude, and chains become molecularly combed under a wider range of conditions. The length of the molecularly combed chains is ∼80% for poly(n-octyl acrylate) but ∼100% of the all-trans conformation for poly(n-alkyl acrylate)s with an alkyl length longer than n-nonyl.
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Affiliation(s)
- Akihiro Ohmatsuzawa
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Moriya Kikuchi
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Seigou Kawaguchi
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Jiro Kumaki
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
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20
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Polson JM, Rehel DA. Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement. SOFT MATTER 2021; 17:5792-5805. [PMID: 34028486 DOI: 10.1039/d1sm00308a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as flexible bead-spring chains, and the box has a square cross-section of side length L and a height that is small enough to compress the polymers in that dimension. For sufficiently large L, the system behaviour approaches that of an isolated polymer in a slit. However, the combined effects of crowding and confinement on the polymer organization, conformation and equilibrium dynamics become significant when where is the transverse radius of gyration for a slit geometry. In this regime, the centre-of-mass probability distribution in the transverse plane exhibits a depletion zone near the centre of the cavity (except at very small L) and a 4-fold symmetry with quasi-discrete positions. Reduction in polymer size with decreasing L arises principally from confinement rather than inter-polymer crowding. By contrast, polymer diffusion and internal motion are strongly affected by inter-polymer crowding. The two polymers tend to occupy opposite positions relative to the box centre, about which they diffuse relatively freely. Qualitatively, this static and dynamical behaviour differs significantly from that previously observed for confinement of two polymers to a narrow channel. The simulation results for a suitably chosen box width are qualitatively consistent with results from a recent experimental study of two λ-DNA chains confined to a nanofluidic cavity.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.
| | - Desiree A Rehel
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.
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21
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Chen H, Poitzsch ME. Emergent slow dynamics of collapsed polymers flowing through porous media. Phys Rev E 2021; 103:L040501. [PMID: 34005983 DOI: 10.1103/physreve.103.l040501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/08/2021] [Indexed: 11/07/2022]
Abstract
Using hydrodynamic simulations, we study the single polymers flowing through model porous media (close-packed colloidal crystal). In good solvent or high flow rates, the polymer transport is similar to gel electrophoresis, with size-dependent sieving for L_{c}/L≲1 and size-independent biased reptation for L_{c}/L≳1 (L_{c} is the polymer contour length and L is the diameter of colloids forming the porous media). Importantly, in bad solvent and low flow rates, the polymers show an extra window of size-dependent velocity for 1≲L_{c}/L≲2, where the polymer transport is controlled by a globule-stretch transition at pore throats, and the transport velocity is much slower than reptation.
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Affiliation(s)
- Hsieh Chen
- Aramco Services Company: Aramco Research Center-Boston, Cambridge, Massachusetts 02139, USA
| | - Martin E Poitzsch
- Aramco Services Company: Aramco Research Center-Boston, Cambridge, Massachusetts 02139, USA
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22
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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23
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On-site processing of single chromosomal DNA molecules using optically driven microtools on a microfluidic workbench. Sci Rep 2021; 11:7961. [PMID: 33846479 PMCID: PMC8042024 DOI: 10.1038/s41598-021-87238-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/22/2021] [Indexed: 11/08/2022] Open
Abstract
We developed optically driven microtools for processing single biomolecules using a microfluidic workbench composed of a microfluidic platform that functions under an optical microscope. The optically driven microtools have enzymes immobilized on their surfaces, which catalyze chemical reactions for molecular processing in a confined space. Optical manipulation of the microtools enables them to be integrated with a microfluidic device for controlling the position, orientation, shape of the target sample. Here, we describe the immobilization of enzymes on the surface of microtools, the microfluidics workbench, including its microtool storage and sample positioning functions, and the use of this system for on-site cutting of single chromosomal DNA molecules. We fabricated microtools by UV lithography with SU-8 and selected ozone treatments for immobilizing enzymes. The microfluidic workbench has tool-stock chambers for tool storage and micropillars to trap and extend single chromosomal DNA molecules. The DNA cutting enzymes DNaseI and DNaseII were immobilized on microtools that were manipulated using optical tweezers. The DNaseI tool shows reliable cutting for on-site processing. This pinpoint processing provides an approach for analyzing chromosomal DNA at the single-molecule level. The flexibility of the microtool design allows for processing of various samples, including biomolecules and single cells.
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24
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Driven Transport of Dilute Polymer Solutions through Porous Media Comprising Interconnected Cavities. COLLOIDS AND INTERFACES 2021. [DOI: 10.3390/colloids5020022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Driven transport of dilute polymer solutions through porous media has been simulated using a recently proposed novel dissipative particle dynamics method satisfying the no-penetration and no-slip boundary conditions. The porous media is an array of overlapping spherical cavities arranged in a simple cubic lattice. Simulations were performed for linear, ring, and star polymers with 12 arms for two cases with the external force acting on (I) both polymer and solvent beads to model a pressure-driven flow; (II) polymer beads only, similar to electrophoresis. When the external force is in the direction of a principal axis, the extent of change in the polymers’ conformation and their alignment with the driving force is more significant for case I. These effects are most pronounced for linear chains, followed by rings and stars at the same molecular weight. Moreover, the polymer mean velocity is affected by its molecular weight and architecture as well as the direction and strength of the imposed force.
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25
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Nikoubashman A. Ordering, phase behavior, and correlations of semiflexible polymers in confinement. J Chem Phys 2021; 154:090901. [DOI: 10.1063/5.0038052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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26
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Samarasinghe TN, Zeng Y, Johnson CK. Comparison of separation modes for microchip electrophoresis of proteins. J Sep Sci 2020; 44:744-751. [PMID: 33226183 DOI: 10.1002/jssc.202000883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Separation of a set of model proteins was tested on a microchip electrophoresis analytical platform capable of sample injection by two different electrokinetic mechanisms. A range of separation modes-microchip capillary zone electrophoresis, microchip micellar electrokinetic chromatography, and nanoparticle-based sieving-was tested on glass and polydimethylsiloxane/glass microchips and with silica-nanoparticle colloidal arrays. The model proteins calmodulin (18 kiloDalton), bovine serum albumin (66 kDa), and concanavalin (106 kDa) were labeled with Alexa Fluor 647 for laser-induced fluorescence detection. The best separation and resolution were obtained in a silica-nanoparticle colloidal array chip.
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Affiliation(s)
| | - Yong Zeng
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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27
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Polson JM, Hastie CG. Free energy of a knotted polymer confined to narrow cylindrical and conical channels. Phys Rev E 2020; 102:052502. [PMID: 33327190 DOI: 10.1103/physreve.102.052502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally satisfied. For cylindrical confinement, we examine polymers with a single knot of topology 3_{1}, 4_{1}, or 5_{1}, as well as unknotted polymers that are capable of forming S loops. We measure the variation of the free energy F with the end-to-end polymer extension length X and examine the effect of varying the polymer topology, persistence length P, and cylinder diameter D on the free-energy functions. Similarly, we characterize the behavior of the knot span along the channel. We find that increasing the knot complexity increases the typical size of the knot. In the regime of low X, where the knot/S-loop size is large, the conformational behavior is independent of polymer topology. In addition, the scaling properties of the free energy and knot span are in agreement with predictions from a theoretical model constructed using known properties of interacting polymers in the Odijk regime. We also examine the variation of F with the position of a knot in conical channels for various values of the cone angle α. The free energy decreases as the knot moves in a direction where the cone widens, and it also decreases with increasing α and with increasing knot complexity. The behavior is in agreement with predictions from a theoretical model in which the dominant contribution to the change in F is the change in the size of the hairpins as the knot moves to the wider region of the channel.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada
| | - Cameron G Hastie
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada
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28
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Chakrabarti B, Gaillard C, Saintillan D. Trapping, gliding, vaulting: transport of semiflexible polymers in periodic post arrays. SOFT MATTER 2020; 16:5534-5544. [PMID: 32507870 DOI: 10.1039/d0sm00390e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the dynamics of semiflexible polymers under the influence of an imposed flow in a structured two-dimensional lattice serving as an idealization of a porous medium. This problem has received much attention in the limit of reptation and for long-chain polymer molecules such as DNA that are transported through micropost arrays for electrophoretic chromatographic separation. In contrast to long entropic molecules, the dynamics of elastic polymers results from a combination of scattering with the obstacles and flow-induced buckling instabilities. We identify three dominant modes of transport that involve trapping, gliding and vaulting of the polymers around the obstacles, and we reveal their essential features using tools from dynamical systems theory. The interplay of these scattering dynamics with transport and deformations in the imposed flow results in the long-time asymptotic dispersion of the center of mass, which we quantify in terms of a hydrodynamic dispersion tensor. We then discuss a simple yet efficient chromatographic device that exploits the competition between different modes of transport to sort filaments in a dilute suspension according to their lengths.
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Affiliation(s)
- Brato Chakrabarti
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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29
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Wang H, de Haan HW, Slater GW. Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field. Electrophoresis 2020; 41:621-629. [DOI: 10.1002/elps.201900299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/29/2019] [Accepted: 11/28/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Hanyang Wang
- Department of PhysicsUniversity of OttawaOttawa Ontario K1N 6N5 Canada
| | - Hendrick W. de Haan
- Faculty of ScienceUniversity of Ontario Institute of TechnologyOshawa Ontario L1H 7K4 Canada
| | - Gary W. Slater
- Department of PhysicsUniversity of OttawaOttawa Ontario K1N 6N5 Canada
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30
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Wang C, Wu F, Zhao B, Chen YC, Luo MB. Spontaneous Injection of Polymer into a Spherical Cavity from a Narrow Tube. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chao Wang
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Fan Wu
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Bin Zhao
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Ying-Cai Chen
- Department of Physics, Taizhou University, Taizhou 318000, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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31
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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32
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Viefhues M. Analytics in Microfluidic Systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:191-209. [DOI: 10.1007/10_2020_131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Li M, Wang J. Stretching Wormlike Chains in Narrow Tubes of Arbitrary Cross-Sections. Polymers (Basel) 2019; 11:E2050. [PMID: 31835594 PMCID: PMC6960511 DOI: 10.3390/polym11122050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 12/06/2019] [Indexed: 12/03/2022] Open
Abstract
We considered the stretching of semiflexible polymer chains confined in narrow tubes with arbitrary cross-sections. Based on the wormlike chain model and technique of normal mode decomposition in statistical physics, we derived a compact analytical expression on the force-confinement-extension relation of the chains. This single formula was generalized to be valid for tube confinements with arbitrary cross-sections. In addition, we extended the generalized bead-rod model for Brownian dynamics simulations of confined polymer chains subjected to force stretching, so that the confinement effects to the chains applied by the tubes with arbitrary cross-sections can be quantitatively taken into account through numerical simulations. Extensive simulation examples on the wormlike chains confined in tubes of various shapes quantitatively justified the theoretically derived generalized formula on the force-confinement-extension relation of the chains.
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Affiliation(s)
| | - Jizeng Wang
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou 730000, China;
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34
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Ou X, Chen P, Huang X, Li S, Liu B. Microfluidic chip electrophoresis for biochemical analysis. J Sep Sci 2019; 43:258-270. [DOI: 10.1002/jssc.201900758] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023]
Affiliation(s)
- Xiaowen Ou
- Hubei Key Laboratory of Purification and Application of Plant Anti‐Cancer Active IngredientsCollege of Chemistry and Life ScienceHubei University of Education Wuhan P. R. China
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics‐Hubei Bioinformatics & Molecular Imaging Key LaboratorySystems Biology ThemeDepartment of Biomedical EngineeringCollege of Life Science and TechnologyHuazhong University of Science and Technology Wuhan P. R. China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics‐Hubei Bioinformatics & Molecular Imaging Key LaboratorySystems Biology ThemeDepartment of Biomedical EngineeringCollege of Life Science and TechnologyHuazhong University of Science and Technology Wuhan P. R. China
| | - Xizhi Huang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics‐Hubei Bioinformatics & Molecular Imaging Key LaboratorySystems Biology ThemeDepartment of Biomedical EngineeringCollege of Life Science and TechnologyHuazhong University of Science and Technology Wuhan P. R. China
| | - Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics‐Hubei Bioinformatics & Molecular Imaging Key LaboratorySystems Biology ThemeDepartment of Biomedical EngineeringCollege of Life Science and TechnologyHuazhong University of Science and Technology Wuhan P. R. China
| | - Bi‐Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics‐Hubei Bioinformatics & Molecular Imaging Key LaboratorySystems Biology ThemeDepartment of Biomedical EngineeringCollege of Life Science and TechnologyHuazhong University of Science and Technology Wuhan P. R. China
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Conformational Properties of Comb-shaped Polyelectrolytes with Negatively Charged Backbone and Neutral Side Chains Studied by a Generic Coarse-grained Bead-and-Spring Model. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-020-2350-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Wang Z, Zhai Q, Chen W, Wang X, Lu Y, An L. Mechanism of Nonmonotonic Increase in Polymer Size: Comparison between Linear and Ring Chains at High Shear Rates. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zhenhua Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Qilong Zhai
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- School of Mathematical Sciences, Peking University, Beijing 100871, P. R. China
| | - Wei Chen
- School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093, P. R. China
| | - Xiaoliang Wang
- School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093, P. R. China
| | - Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei 230026, P. R. China
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37
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Bogdan MJ, Savin T. Errors in Energy Landscapes Measured with Particle Tracking. Biophys J 2019; 115:139-149. [PMID: 29972805 DOI: 10.1016/j.bpj.2018.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/28/2018] [Accepted: 05/01/2018] [Indexed: 01/29/2023] Open
Abstract
Tracking Brownian particles is often employed to map the energy landscape they explore. Such measurements have been exploited to study many biological processes and interactions in soft materials. Yet video tracking is irremediably contaminated by localization errors originating from two imaging artifacts: the "static" errors come from signal noise, and the "dynamic" errors arise from the motion blur due to finite frame-acquisition time. We show that these errors result in systematic and nontrivial biases in the measured energy landscapes. We derive a relationship between the true and the measured potential that elucidates, among other aberrations, the presence of false double-well minima in the apparent potentials reported in recent studies. We further assess several canonical trapping and pair-interaction potentials by using our analytically derived results and Brownian dynamics simulations. In particular, we show that the apparent spring stiffness of harmonic potentials (such as optical traps) is increased by dynamic errors but decreased by static errors. Our formula allows for the development of efficient corrections schemes, and we also present in this work a provisional method for reconstructing true potentials from the measured ones.
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Affiliation(s)
- Michał J Bogdan
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Thierry Savin
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom.
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38
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Soh BW, Klotz AR, Dai L, Doyle PS. Conformational State Hopping of Knots in Tensioned Polymer Chains. ACS Macro Lett 2019; 8:905-911. [PMID: 35619478 DOI: 10.1021/acsmacrolett.9b00462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We use Brownian dynamics simulations to study the conformational states of knots on tensioned chains. Focusing specifically on the 81 knot, we observe knot conformational state hopping and show that the process can be described by a two-state kinetic model in the presence of an external force. The distribution of knot conformational states depends on the applied chain tension, which leads to a force-dependent distribution of knot untying pathways. We generalize our findings by considering the untying pathways of other knots and find that the way knots untie is generally governed by the force applied to the chain. From a broader perspective, being able to influence how a knot unties via external force can potentially be useful for applications of single-molecule techniques in which knots are unwanted.
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Affiliation(s)
- Beatrice W Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander R Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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39
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Li P, Shen Y, Wang L, Lu W, Li W, Chen K, Zhou Y, Shen L, Wei F, Zheng W. The electric double layer structure modulates poly-dT 25 conformation and adsorption kinetics at the cationic lipid bilayer interface. SOFT MATTER 2019; 15:4445-4453. [PMID: 31011740 DOI: 10.1039/c9sm00321e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The conformation and adsorption kinetics of oligonucleotides at lipid membrane interfaces are crucial to their biological functions, but are yet not clearly understood. Poly-dT oligonucleotide molecules have been widely used as primers for reverse translation of RNA molecules, as well as a surface recognition agent for mRNA purification and extraction. In this research, the adsorption processes of poly-dT25 on lipid membranes in different ionic solutions were investigated by sum frequency generation vibrational spectroscopy (SFG-VS) together with a single molecule tracking technique in situ and in real time. These systematic studies provide us with molecular insight into the chemical and physical nature of oligonucleotide-membrane interactions, and show us how the electric double layer (EDL) structure changes the conformation and adsorption kinetics of oligonucleotides. The SFG-VS results indicate that an increase of ionic concentration not only decreases the adsorption density of oligonucleotides but also changes the conformation of oligonucleotides from an elongated conformation to a coiled conformation, causing stronger thermodynamic interactions with membranes, as demonstrated by single molecule tracking techniques. It is also shown that the ionic solution can tune the balance between the surface diffusion rate and solution diffusion rate of oligonucleotides significantly. These results demonstrated that the spectra and kinetics collected by in situ label-free SFG-VS detection and the single molecular tracking technique can provide new molecular insights into the mechanisms of oligonucleotide-membrane interactions. These new understandings may help researchers to control the assembly of oligonucleotide-liposome complexes and to improve the efficiency of transportation and delivery of oligonucleotide molecules.
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Affiliation(s)
- PengHua Li
- Institution for Interdisciplinary Research, & Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Jianghan University, Wuhan, Hubei 430056, China.
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40
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Hu X, Lu D. Intensification of chemical separation engineering by nanostructured channels and nanofluidics: From theories to applications. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2019.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Kim YS, Dincau BM, Kwon YT, Kim JH, Yeo WH. Directly Accessible and Transferrable Nanofluidic Systems for Biomolecule Manipulation. ACS Sens 2019; 4:1417-1423. [PMID: 31062586 DOI: 10.1021/acssensors.9b00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular detection and manipulation via nanofluidic systems offers new routes for single-molecule analysis to study epigenetic mechanisms and genetic mutation of disease. For detection of single biological molecule, many types of nanomicrofluidic systems have been utilized. Typically, mechanical tethering, fluidic pressure, chemical interactions, or electrical forces allow controllable attraction, enrichment, confinement, and elongation of target molecules. The currently available methods, however, are unable to offer both molecular manipulation and direct and concurrent assessment of target molecules in the system due to the nature of enclosed channels and associated fluidic components. Here, we introduce a wafer-scale nanofluidic system that incorporates an array of accessible open nanochannels and nano-microtrappers to enrich and elongate target molecules (DNA) via the combination of an electric field and hydrodynamic force. The open nanofluidic system allows easy access, direct observation, and manipulation of molecules in the nanochannels. The presence of a stretched single DNA and the efficacy of the nanofluidic system are studied by fluorescence microscopy and atomic force microscopy. Hybrid integration of the nanodevice fabrication with a material transfer printing technique enables to design a highly flexible and transferrable nanofluidic system after molecular concentration.
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Affiliation(s)
| | - Brian M. Dincau
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
| | | | - Jong-Hoon Kim
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
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43
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Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels. Polymers (Basel) 2019; 11:polym11030488. [PMID: 30960472 PMCID: PMC6473708 DOI: 10.3390/polym11030488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 12/14/2022] Open
Abstract
Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular dynamics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained.
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44
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Wang J, Li K. Statistical Behaviors of Semiflexible Polymer Chains Stretched in Rectangular Tubes. Polymers (Basel) 2019; 11:E260. [PMID: 30960244 PMCID: PMC6419070 DOI: 10.3390/polym11020260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/27/2019] [Accepted: 01/31/2019] [Indexed: 11/23/2022] Open
Abstract
We investigated the statistical behaviors of semiflexible polymer chains, which were simultaneously subjected to force stretching and rectangular tube confinement. Based on the wormlike chain model and Odijk deflection theory, we derived a new deflection length, by using which new compact formulas were obtained for the confinement free energy and force⁻confinement⁻extension relations. These newly derived formulas were justified by numerical solutions of the eigenvalue problem associated with the Fokker⁻Planck governing equation and extensive Brownian dynamics simulations based on the so-called generalized bead-rod (GBR) model. We found that, compared to classical deflection theory, these new formulas were valid for a much more extended range of the confinement size/persistence length ratio and had no adjustable fitting parameters for sufficiently long semiflexible chains in the whole deflection regime.
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Affiliation(s)
- Jizeng Wang
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Kai Li
- Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou 730000, Gansu, China.
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Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T. Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis. J Chem Phys 2019; 149:215101. [PMID: 30525714 DOI: 10.1063/1.5051319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.
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Affiliation(s)
- Jens Krog
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Erik Werner
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Bernhard Mehlig
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Michael A Lomholt
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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Lee S, Lee Y, Kim Y, Wang C, Park J, Jung GY, Chen Y, Chang R, Ikeda S, Sugiyama H, Jo K. Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations. Polymers (Basel) 2018; 11:E15. [PMID: 30959999 PMCID: PMC6401831 DOI: 10.3390/polym11010015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yelin Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yongkyun Kim
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Cong Wang
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Jungyul Park
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Gun Young Jung
- School of Material Science and Engineering, GIST, Gwangju 61005, Korea.
| | - Yenglong Chen
- Institute of Physics, Academia Sinica and Department of Chemical Engineering, National Tsing-Hua University and Department of Physics, National Taiwan University, Taipei 10617, Taiwan.
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 01897, Korea.
| | - Shuji Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
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47
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Soh BW, Klotz AR, Doyle PS. Untying of Complex Knots on Stretched Polymers in Elongational Fields. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01879] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander R. Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Wongkaew N, Simsek M, Griesche C, Baeumner AJ. Functional Nanomaterials and Nanostructures Enhancing Electrochemical Biosensors and Lab-on-a-Chip Performances: Recent Progress, Applications, and Future Perspective. Chem Rev 2018; 119:120-194. [DOI: 10.1021/acs.chemrev.8b00172] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Nongnoot Wongkaew
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Marcel Simsek
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Christian Griesche
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Antje J. Baeumner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
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49
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Polson JM. Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- James M. Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada
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50
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Hopgood JR, Connelly M, McHoull B, Troy D. Multi-Snapshot Imaging for Chromatographic Peak Analysis. IEEE Trans Biomed Eng 2018; 66:119-129. [PMID: 29993422 DOI: 10.1109/tbme.2018.2826144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Snapshot imaging has several advantages in automated gel electrophoresis compared with the finish-line method in capillary electrophoresis; this comes at the expense of resolution. A novel signal processing algorithm is proposed enabling a multisnapshot imaging (MSI) modality whose objective is to substantially improve resolution. MSI takes multiple-captures in time as macromolecules are electrophoresed. Peaks from latter snapshots have high resolution, but low signal-to-noise ratio (SNR), while earlier snapshots have low resolution, but high SNR. METHODS Signals at different capture-times are related by a scale-in-separation, shift-in-separation, and amplitude gain. The proposed method realigns the multiple captures using least-squares and fuses them. The algorithm accounts for the partial waveforms observed as the chromatic peaks exit the sensor's field-of-view. RESULTS MSI improves resolution by approximately [Formula: see text] on average per minute of additional electrophoresis. CONCLUSIONS Comprehensive analysis of the resolution quantified on several data sets demonstrates the effectiveness of MSI. SIGNIFICANCE MSI can double the resolution compared with traditional snap-shot imaging over a typical set of captures.
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