51
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Kim JM, Doyle PS. Brownian Dynamics Simulations of a DNA Molecule Colliding with a Small Cylindrical Post. Macromolecules 2007. [DOI: 10.1021/ma0710434] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ju Min Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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52
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Mohan A, Doyle PS. Stochastic Modeling and Simulation of DNA Electrophoretic Separation in a Microfluidic Obstacle Array. Macromolecules 2007. [DOI: 10.1021/ma071354e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aruna Mohan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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53
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Mohan A, Doyle PS. Effect of disorder on DNA electrophoresis in a microfluidic array of obstacles. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:040903. [PMID: 17994929 DOI: 10.1103/physreve.76.040903] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Indexed: 05/25/2023]
Abstract
The size-based separation of electrophoresing DNA chains of varying lengths has been experimentally achieved in microfluidic obstacle arrays. The separation is actuated by the occurrence of size-dependent chain-obstacle collisions and the subsequent formation of hooked chain configurations in the array. We investigate the role played by disorder in array geometry in determining chain dynamics in the array. As a prototypical example of a disordered post array, we select a self-assembled array of magnetic colloids, wherein the degree of disorder may be varied by varying the magnetic field strength under which the array is generated. We employ Brownian dynamics simulations of chain electrophoresis in the array to compute the mobility, dispersivity, chain-obstacle collision probability, and mean chain stretch in the device, and demonstrate the link between the orientational order of the array and the resulting chain dynamics.
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Affiliation(s)
- Aruna Mohan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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54
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Laval P, Lisai N, Salmon JB, Joanicot M. A microfluidic device based on droplet storage for screening solubility diagrams. LAB ON A CHIP 2007; 7:829-34. [PMID: 17594000 DOI: 10.1039/b700799j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This work describes a new microfluidic device developed for the rapid screening of solubility diagrams. In several parallel channels, hundreds of nanolitre volume droplets of a given solution are first stored with a gradual variation in the solute concentration. Then, the application of a temperature gradient along these channels enables us to read directly and quantitatively phase diagrams, concentration vs. temperature. We show, using a solution of adipic acid, that we can measure ten points of the solubility curve in less than 1 hr and with only 250 microL of solution.
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Affiliation(s)
- Philippe Laval
- LOF, unité mixte Rhodia-CNRS-Bordeaux 1, 178 avenue du Docteur Schweitzer, F-33608 Pessac cedex, France.
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55
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Nagasaki Y, Kobayashi H, Katsuyama Y, Jomura T, Sakura T. Enhanced immunoresponse of antibody/mixed-PEG co-immobilized surface construction of high-performance immunomagnetic ELISA system. J Colloid Interface Sci 2007; 309:524-30. [PMID: 17368469 DOI: 10.1016/j.jcis.2006.12.079] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 12/15/2006] [Accepted: 12/15/2006] [Indexed: 10/23/2022]
Abstract
Poly(ethylene glycol) possessing pentaethylenehexamine at one end (N6-PEG) was prepared via a reductive amination reaction of aldehyde-ended PEG with pentaethylenehexamine. Using N6-PEG, an antibody/PEG co-immobilized surface was constructed on magnetic particles via an active ester reaction method. After immobilization of the antibody on the active ester surface, N6-PEG was reacted on the magnetic beads. A sandwich enzyme-linked immunosorbent assay (ELISA) system was newly constructed using PEG/antibody co-immobilized magnetic beads combined with an alkaline phosphatase (ALP)-assisted fluorescent detection system using alpha-fetoprotein (AFP) as a model antigen. The co-immobilization of both antibody and PEG on the magnetic bead surfaces reduced the nonspecific adsorption of proteins from cell lysates. Especially, when the magnetic particle surface was modified by N6-PEG mixtures with different molecular weights of 6000 and 2500 (6 kDa:2.5 kDa=9:1 w/w), the nonspecific adsorption of proteins was strongly suppressed. It is rather surprising for us that the sensitivity of the antibody on the surface was enhanced significantly when the PEG tethered chain was constructed in between the surface antibodies. Consequently, the mixed N6-PEG treatment showed a much higher S/N ratio than for the corresponding beads treated with bovine serum albumin (BSA), a conventional blocking reagent. Actually, when alpha-fetoprotein was analyzed by the magnetic bead-assisted ELISA thus constructed, the S/N ratio was about 20-fold higher for the mixed coating with PEG (6 kDa):PEG (2.5 kDa)=9:1, compared to the conventional BSA.
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Affiliation(s)
- Yukio Nagasaki
- Tsukuba Research Center for Interdisciplinary Materials Science, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8573, Japan.
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56
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Regtmeier J, Duong TT, Eichhorn R, Anselmetti D, Ros A. Dielectrophoretic Manipulation of DNA: Separation and Polarizability. Anal Chem 2007; 79:3925-32. [PMID: 17444613 DOI: 10.1021/ac062431r] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although separation of polymers based on the combination of dielectrophoretic trapping and electrophoretic forces was proposed 15 years ago, experimental proof has not yet been reported. Here, we address this problem for long DNA fragments in a simple and easy-to-fabricate microfluidic device, in which the DNA is manipulated by electrophoresis and by electrodeless dielectrophoresis. By slowly increasing the strength of the dielectrophoretic traps in the course of the separation experiments, we are able to perform efficient and fast DNA separation according to length for two different DNA conformations: linear DNA (lambda (48.5-kbp) and T2 (164-kbp) DNA) and supercoiled covalently closed circular plasmid DNA (7 and 14 kbp). The underlying migration mechanism-thermally induced escape processes out of the dielectrophoretic traps in the direction of the electrophoretic force-is sensitive to different DNA fragments because of length-dependent DNA polarizabilities. This is analyzed in a second series of experiments, where the migration mechanism is exploited for the quantitative measurement of the DNA polarizabilities. This new and simple technique allows for the systematic characterization of the polarizability not only for DNA but also for other biomolecules like proteins. Furthermore, our results have direct implications to future biotechnological applications such as gene therapy and DNA vaccination.
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Affiliation(s)
- Jan Regtmeier
- Experimental Biophysics and Applied Nanoscience and Condensed Matter Theory, Physics Department, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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57
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Teclemariam NP, Beck VA, Shaqfeh ESG, Muller SJ. Dynamics of DNA Polymers in Post Arrays: Comparison of Single Molecule Experiments and Simulations. Macromolecules 2007. [DOI: 10.1021/ma062892e] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nerayo P. Teclemariam
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Victor A. Beck
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Eric S. G. Shaqfeh
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Susan J. Muller
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
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58
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Kim JM, Doyle PS. Design and numerical simulation of a DNA electrophoretic stretching device. LAB ON A CHIP 2007; 7:213-25. [PMID: 17268624 DOI: 10.1039/b612021k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
DNA stretching is now a key technology in emerging DNA mapping devices such as direct linear analysis (DLA), though DNA stretching in a high throughput manner is still a challenging problem. In this work, we present a new microfluidic channel design to enhance DNA stretching using kinematic analysis and Brownian dynamics-finite element method (BD-FEM). Our group recently showed in experiments that the extensional electrophoretic field arising from a hyperbolic microcontraction can be utilized to stretch T4-DNA. We demonstrate the reliability of our BD-FEM model for the present problem by showing that the numerical predictions are consistent with the experimental data for the hyperbolic channel. We then investigate DNA stretching for four different funnel shapes. Surprisingly the maximum mean DNA stretch is quite similar in all four designs. Finally, we propose a new design with a side-feeding branch to enhance stretching based on a kinematic analysis along different feeding locations. Our numerical simulation predicted that DNA stretching can be dramatically enhanced using side-feeding.
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Affiliation(s)
- Ju Min Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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59
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Okamoto Y, Ikawa Y, Kitagawa F, Otsuka K. Preparation of fritless capillary using avidin immobilized magnetic particles for electrochromatographic chiral separation. J Chromatogr A 2007; 1143:264-9. [PMID: 17240386 DOI: 10.1016/j.chroma.2007.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 12/26/2006] [Accepted: 01/02/2007] [Indexed: 10/23/2022]
Abstract
In capillary electrochromatography (CEC), magnetic particles (MPs) were packed in a fused silica capillary by using the magnetic field to be retained without frits. For a chiral CEC separation, avidin was immobilized onto the surface of the MPs (AVI-MPs) as a stationary phase by using the physical adsorption technique. The injected AVI-MPs into the capillary were stably captured with the magnet (surface magnetic flux density, 250 mT) under the separation voltage of 10 kV (190 V/cm). By employing the fritless AVI-MPs packed capillary, the chiral separation of ketoprofen was successfully attained with the packing length of only 5 cm. Effects of the modification condition of avidin, pH of background solution, and the packing length on the enantioseparation were also investigated. Under the optimal condition, furthermore, the repeatability for the retention time of ketoprofen was better than 1.5% in the relative standard deviation and the capillary-to-capillary reproducibility was also acceptable in the prepared fritless capillaries.
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Affiliation(s)
- Yukihiro Okamoto
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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60
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Zeng Y, Harrison DJ. Confinement effects on electromigration of long DNA molecules in an ordered cavity array. Electrophoresis 2006; 27:3747-52. [PMID: 16960918 DOI: 10.1002/elps.200600233] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Confinement effects on the electromigration of long dsDNA molecules in an array of well-ordered, molecular sized cavities interconnected by nanopores are described. The array was prepared by replicating the structure of a colloidal crystal of microspheres in a polymer matrix. Both conformation and mobility studies show that the electrophoretic behavior of large DNA molecules is distinct from that in gels and other microfabricated sieves, showing a peak in mobility versus electric field, and an inversion in the separation order with field strength. A simple model was proposed to interpret this unexpected observation qualitatively. We conclude that the molecular behavior of DNA can be modified by the combination of entropic effect and electric trapping as a consequence of both unique geometry and conductivity of this cavity array material. This approach provides insights for design and optimization of on-chip molecular sieving structures for rapid separation of long DNA molecules. It may lead to a promising material for manipulation and size fractionation of other biological macromolecules.
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Affiliation(s)
- Yong Zeng
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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61
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Affiliation(s)
- Greg C. Randall
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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62
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Kenward M, Slater GW. Molecular-dynamics simulations with explicit hydrodynamics II: on the collision of polymers with molecular obstacles. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2006; 20:125-41. [PMID: 16779525 DOI: 10.1140/epje/i2006-10008-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Accepted: 04/26/2006] [Indexed: 05/10/2023]
Abstract
We present a study of the dynamics of single polymers colliding with molecular obstacles using Molecular-dynamics simulations. In concert with these simulations we present a generalized polymer-obstacle collision model which is applicable to a number of collision scenarios. The work focusses on three specific problems: i) a polymer driven by an external force colliding with a fixed microscopic post; ii) a polymer driven by a (plug-like) fluid flow colliding with a fixed microscopic post; and iii) a polymer driven by an external force colliding with a free polymer. In all three cases, we present a study of the length-dependent dynamics of the polymers involved. The simulation results are compared with calculations based on our generalized collision model. The generalized model yields analytical results in the first two instances (cases i) and ii)), while in the polymer-polymer collision example (case iii)) we obtain a series solution for the system dynamics. For the case of a polymer-polymer collision we find that a distinct V-shaped state exists as seen in experimental systems, though normally associated with collisions with multiple polymers. We suggest that this V-shaped state occurs due to an effective hydrodynamic counter flow generated by a net translational motion of the two-chain system.
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Affiliation(s)
- M Kenward
- Department of Physics, University of Ottawa, 150 Louis-Pasteur Ottawa, K1N 6N5, Ontario, Canada.
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63
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Dorfman KD. DNA electrophoresis in microfluidic post arrays under moderate electric fields. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:061922. [PMID: 16906879 DOI: 10.1103/physreve.73.061922] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Indexed: 05/11/2023]
Abstract
The dynamics of long DNA moving through microfluidic arrays of micron-sized posts under a moderate electric field are modeled by a Scher-Lax continuous-time random walk. The microscale model consists of a repetitive sequence of three steps: (i) collision with the post and extension into two arms, (ii) electric-field-driven unhooking from the post, and (iii) uniform translation until the next collision. The model features two random variables: the initial offset between the two arms of the polymer during a given collision and the distance traveled between collisions. For experimentally realistic values of the electric field strength and DNA molecular weight, scaling laws indicate that the chain will generally be in a stem-flower conformation when unhooking from the post. Compared to a taut-chain model at the same field strength, the stem-flower conformation reduces the time engaged with the post and increases the collision frequency. Analytical expressions for the mean velocity and dispersivity are derived as a function of the post density, post spacing, free-solution mobility, Kuhn length, and sequence length. The incomplete extension of the chain does not strongly affect the mean velocity, but tends to increase the dispersivity relative to a taut chain. As a result, the separation resolution decreases as the field decreases for a moderate field, in agreement with experiments. The quantitative agreement between the model and experimental data is satisfactory, especially considering that the model contains no adjustable parameters.
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Affiliation(s)
- Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA.
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64
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Abstract
Magnetic forces are now being utilised in an amazing variety of microfluidic applications. Magnetohydrodynamic flow has been applied to the pumping of fluids through microchannels. Magnetic materials such as ferrofluids or magnetically doped PDMS have been used as valves. Magnetic microparticles have been employed for mixing of fluid streams. Magnetic particles have also been used as solid supports for bioreactions in microchannels. Trapping and transport of single cells are being investigated and recently, advances have been made towards the detection of magnetic material on-chip. The aim of this review is to introduce and discuss the various developments within the field of magnetism and microfluidics.
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Affiliation(s)
- Nicole Pamme
- National Institute for Materials Science (NIMS), International Centre for Young Scientists (ICYS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
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65
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Slovakova M, Minc N, Bilkova Z, Smadja C, Faigle W, Fütterer C, Taverna M, Viovy JL. Use of self assembled magnetic beads for on-chip protein digestion. LAB ON A CHIP 2005; 5:935-42. [PMID: 16100577 DOI: 10.1039/b504861c] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The use of grafted trypsin magnetic beads in a microchip for performing protein digestion is described. The PDMS device uses strong magnets to create a magnetic field parallel to the flow with a strong gradient pointing through the center of the chip channel. This allows for the formation of a low-hydrodynamic resistance plug of magnetic trypsin beads that serves as a matrix for protein digestion. This device represents an inexpensive way of fabricating a multi open-tubular-like column with an appropriate pore size for proteins. Kinetics studies of the hydrolysis of a model peptide show a 100-fold increase in digestion speed obtained by the microsystem when compared to a batch wise system. This system also offers the great advantage of easy replacement, as the bead matrix is easily washed out and replaced. High performance and reproducibility for digesting recombinant human growth hormone are confirmed by analysing the digest products in both CE and MALDI-TOF MS. Similar sequence coverage (of about 44%) is obtained from MS analysis of products after 10 minutes on-chip and 4 h with soluble trypsin in bulk.
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Affiliation(s)
- Marcela Slovakova
- Laboratoire Physicochimie-Curie, UMR/CNRS 168, Institut Curie, 75248 Paris Cedex 5, France
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66
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Lee JH, Kim Y, Ha MY, Lee EK, Choo J. Immobilization of aminophenylboronic acid on magnetic beads for the direct determination of glycoproteins by matrix assisted laser desorption ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1456-1460. [PMID: 16023361 DOI: 10.1016/j.jasms.2005.04.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 03/31/2005] [Accepted: 04/08/2005] [Indexed: 05/03/2023]
Abstract
Aminophenylboronic acid (APBA) has been immobilized on magnetic beads for the direct determination of glycoprotein by matrix assisted laser desorption/ionizaton time of flight mass spectrometry (MALDI-TOF-MS). An APBA layer was formed on the surface of carboxylic acid terminated magnetic beads by coupling with carbodiimide and subsequently reacted with an N-hydroxysuccinimide moiety. The immobilized APBA was identified by MALDI-TOF-MS without a matrix. Glycoproteins, such as HbA1c, fibrinogen, or RNase B were separated and desalted using APBA magnetic beads by simply washing the magnetic beads and then separating them by external magnet. Proteins can be identified by direct determination of proteins on beads on MALDI plate and confirmed again by peptide mass finger printing after digestion of proteins on magnetic beads by trypsin. Fluorescence image with a FITC tagging protein using confocal laser microscopy showed the difference of immobilization efficiency between glycoproteins and nonglycoproteins. The methods developed within this work allow the simple treatment and enrichment of glycoproteins as well as direct determination of proteins on beads by MALDI-TOF-MS.
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Affiliation(s)
| | - Yangsun Kim
- Proteonik Research Laboratory, Ansan, South Korea.
| | - Mi Young Ha
- Microbiochip Center, Hanyang University, Ansan, South Korea
| | - Eun Kyu Lee
- Microbiochip Center, Hanyang University, Ansan, South Korea
| | - Jaebum Choo
- Department of Applied Chemistry, Hanyang University, Ansan, South Korea
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67
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Haghgooie R, Doyle PS. Structure and dynamics of repulsive magnetorheological colloids in two-dimensional channels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:011405. [PMID: 16089959 DOI: 10.1103/physreve.72.011405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 05/07/2005] [Indexed: 05/03/2023]
Abstract
We study a system of colloidal spheres with induced magnetic dipoles confined in two-dimensional (2D) hard-wall channels using Brownian dynamics simulations. The external magnetic field is directed normal to the 2D plane and therefore the colloids interact with a purely repulsive r(-3) potential. The effects of confinement between parallel walls are determined by analyzing the structure and dynamics of these confined systems and comparing to the unbounded (infinite) 2D plane limit. The bond-order correlation function is analyzed as a function of time and exhibits unique characteristics associated with the channel-like confinement. The existence of a plateau in this correlation function is observed over an intermediate time scale and the fate of the plateau (decay or persistence) depends upon the channel width, the strength of the external magnetic field, and the number density. The plateau is analyzed in further detail and an explanation is put forth for its existence and subsequent long time behavior. Additionally, re-entrant behavior with respect to dimensionless channel width is observed in the structural properties and an associated state-diagram is presented for these systems.
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Affiliation(s)
- Ramin Haghgooie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, 02139, USA
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68
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Minc N, Bokov P, Zeldovich KB, Fütterer C, Viovy JL, Dorfman KD. Motion of single long DNA molecules through arrays of magnetic columns. Electrophoresis 2005; 26:362-75. [PMID: 15657884 DOI: 10.1002/elps.200410115] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a videomicroscopy study of T4 DNA (169 kbp) in microfluidic arrays of posts formed by the self-assembly of magnetic beads. We observe DNA moving through an area of 10 000 microm(2), typically containing 100-600 posts. We determine the distribution of the contact times with the posts and the distribution of passage times across the field of view for hundreds of DNA per experiment. The contact time is well approximated by a Poisson process, scaling like the inverse of the field strength, independent of the density of the array. The distribution of passage times allows us to estimate the mean velocity and dispersivity of the DNA during its motion over distances long compared to our field of view. We compare these values with those computed from a lattice Monte Carlo model and geometration theory. We find reasonable quantitative agreement between the lattice Monte Carlo model and experiment, with the error increasing with increasing post density. The deviation between theory and experiment is attributed to the high mobility of DNA after disengaging from the posts, which leads to a difference between the contact time and the total time lost by colliding. Classical geometration theory furnishes surprisingly good agreement for the dispersivity, while geometration theory with a mean free path significantly overestimates the dispersivity.
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Affiliation(s)
- Nicolas Minc
- Laboratoire Physicochimie-Curie, Institut Curie, Paris, France
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69
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Minc N, Viovy JL, Dorfman KD. Non-markovian transport of DNA in microfluidic post arrays. PHYSICAL REVIEW LETTERS 2005; 94:198105. [PMID: 16090219 DOI: 10.1103/physrevlett.94.198105] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Indexed: 05/03/2023]
Abstract
We present an analytically solvable model for the transport of long DNA through microfluidic arrays of posts. The motion is a repetitive three-part cycle: (i) collision with the post and extension of the arms; (ii) rope-over-pulley post disengagement; and (iii) a random period of uniform translation before the next collision. This cycle, inspired by geometration, is a nonseparable (Scher-Lax) continuous-time random walk on a lattice defined by the posts. Upon adopting a simple model for the transition probability density on the lattice, we analytically compute the mean DNA velocity and dispersivity in the long-time limit without any adjustable parameters. The results compare favorably with the limited amount of experimental data on separations in self-assembled arrays of magnetic beads. The Scher-Lax formalism provides a template for incorporating more sophisticated microscale models.
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Affiliation(s)
- Nicolas Minc
- Laboratoire Physicochimie-Curie, CNRS/UMR 168, Institut Curie, Paris, France
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70
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Korneva G, Ye H, Gogotsi Y, Halverson D, Friedman G, Bradley JC, Kornev KG. Carbon nanotubes loaded with magnetic particles. NANO LETTERS 2005; 5:879-84. [PMID: 15884887 DOI: 10.1021/nl0502928] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We describe a simple and versatile technique to produce magnetic tubes by filling carbon nanotubes (CNTs) with paramagnetic iron oxide particles ( approximately 10 nm diameter). Commercial ferrofluids were used to fill CNTs with an average outer diameter of 300 nm made via chemical vapor deposition into alumina membranes. Transmission electron microscopy study shows a high density of particles inside the CNT. Experiments using external magnetic fields demonstrate that almost 100% of the nanotubes become magnetic and can be easily manipulated in magnetic field. These one-dimensional magnetic nanostructures can find numerous applications in nanotechnology, memory devices, optical transducers for wearable electronics, and in medicine.
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Affiliation(s)
- Guzeliya Korneva
- Chemistry Department, A. J. Drexel Nanotechnology Institute, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
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71
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Kan CW, Fredlake CP, Doherty EAS, Barron AE. DNA sequencing and genotyping in miniaturized electrophoresis systems. Electrophoresis 2004; 25:3564-88. [PMID: 15565709 DOI: 10.1002/elps.200406161] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Advances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far-reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high-resolution size- and/or conformation-based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high-quality, low-cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high-throughput and high-resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high-throughput DNA sequencing and genotyping technologies.
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Affiliation(s)
- Cheuk-Wai Kan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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Randall GC, Doyle PS. Electrophoretic collision of a DNA molecule with an insulating post. PHYSICAL REVIEW LETTERS 2004; 93:058102. [PMID: 15323733 DOI: 10.1103/physrevlett.93.058102] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Indexed: 05/24/2023]
Abstract
We study the dynamics of single DNA molecules driven by an electric field into a stationary obstacle. These collisions are broadly classified as "hook" and "roll-off" events. We show that obstacle-induced electric field gradients stretch impacting DNA and thus greatly influence the hooking probability. Consequently, in addition to collision geometry, determination of the hooking probability depends on the Deborah number (De) for 0.5<De<40. Individual DNA impact dynamics are highly configuration sensitive, characteristic of polymers in elongational flows and fields.
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Affiliation(s)
- Greg C Randall
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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