1
|
Radhakrishnan K, Singh SP. Compression of a confined semiflexible polymer under direct and oscillating fields. Phys Rev E 2023; 108:014501. [PMID: 37583203 DOI: 10.1103/physreve.108.014501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/19/2023] [Indexed: 08/17/2023]
Abstract
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is contrary to the previously reported stretching of the chain. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. In the case of a semiflexible polymer chain, the inhomogeneous hydrodynamic drag from the center to the periphery of the coil couples with the chain bending to cause a swirling movement of the chain segments, leading to structural intertwining and compaction. Contrarily, a flexible chain of the same length lacks such structural deformation and forms a well-established tadpole structure. While bending rigidity profoundly influences the chain's folding favorability, we also found that subject to the direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk where such compaction is absent. However, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. This field-induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures even for shorter chains, unlike other spontaneous knotting experiments where it happens exclusively for longer chains.
Collapse
Affiliation(s)
- Keerthi Radhakrishnan
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
| |
Collapse
|
2
|
Radhakrishnan K, Singh SP. Collapse of a Confined Polyelectrolyte Chain under an AC Electric Field. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keerthi Radhakrishnan
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Sunil P. Singh
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| |
Collapse
|
3
|
Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| |
Collapse
|
4
|
Wang X, Boire TC, Bronikowski C, Zachman AL, Crowder SW, Sung HJ. Decoupling polymer properties to elucidate mechanisms governing cell behavior. TISSUE ENGINEERING PART B-REVIEWS 2012; 18:396-404. [PMID: 22536977 DOI: 10.1089/ten.teb.2012.0011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Determining how a biomaterial interacts with cells ("structure-function relationship") reflects its eventual clinical applicability. Therefore, a fundamental understanding of how individual material properties modulate cell-biomaterial interactions is pivotal to improving the efficacy and safety of clinically translatable biomaterial systems. However, due to the coupled nature of material properties, their individual effects on cellular responses are difficult to understand. Structure-function relationships can be more clearly understood by the effective decoupling of each individual parameter. In this article, we discuss three basic decoupling strategies: (1) surface modification, (2) cross-linking, and (3) combinatorial approaches (i.e., copolymerization and polymer blending). Relevant examples of coupled material properties are briefly reviewed in each section to highlight the need for improved decoupling methods. This follows with examples of more effective decoupling techniques, mainly from the perspective of three primary classes of synthetic materials: polyesters, polyethylene glycol, and polyacrylamide. Recent strides in decoupling methodologies, especially surface-patterning and combinatorial techniques, offer much promise in further understanding the structure-function relationships that largely govern the success of future advancements in biomaterials, tissue engineering, and drug delivery.
Collapse
Affiliation(s)
- Xintong Wang
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA
| | | | | | | | | | | |
Collapse
|
5
|
Abstract
Capillary electrophoresis with a polymer solution support medium is a well-established powerful analytical tool. This paper discusses a possible alternative application of capillary electrophoresis, namely a path for studying the dynamics of polymer solutions. The key to the approach is an inversion of perspective. Instead of treating the migrating species as the object of experimental importance and the support medium as being of importance only because it facilitates separations, one treats the polymer solution as being of experimental importance, and the choice of migrating species as being of interest only because different species may probe different aspects of polymer dynamics.
Collapse
Affiliation(s)
- George D J Phillies
- Department of Physics, Worcester Polytechnic Institute, Worcester, MA 01609, USA.
| |
Collapse
|
6
|
Liu H, Zhu Y, Maginn E. Molecular Simulation of Polyelectrolye Conformational Dynamics under an AC Electric Field. Macromolecules 2010. [DOI: 10.1021/ma100354f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hongjun Liu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556
| | - Yingxi Zhu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556
| | - Edward Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556
| |
Collapse
|
7
|
|
8
|
You S, Van Winkle DH. Single Molecule Observation of DNA Electrophoresis in Pluronic F127. J Phys Chem B 2010; 114:4171-7. [DOI: 10.1021/jp911183m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seungyong You
- Department of Physics and Martech, The Florida State University, Tallahassee, Florida, 32306-4351
| | - David H. Van Winkle
- Department of Physics and Martech, The Florida State University, Tallahassee, Florida, 32306-4351
| |
Collapse
|
9
|
Santoso Y, Kapanidis AN. Probing biomolecular structures and dynamics of single molecules using in-gel alternating-laser excitation. Anal Chem 2010; 81:9561-70. [PMID: 19863108 DOI: 10.1021/ac901423e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gel electrophoresis is a standard biochemical technique used for separating biomolecules on the basis of size and charge. Despite the use of gels in early single-molecule experiments, gel electrophoresis has not been widely adopted for single-molecule fluorescence spectroscopy. We present a novel method that combines gel electrophoresis and single-molecule fluorescence spectroscopy to simultaneously purify and analyze biomolecules in a gel matrix. Our method, in-gel alternating-laser excitation (ALEX), uses nondenaturing gels to purify biomolecular complexes of interest from free components, aggregates, and nonspecific complexes. The gel matrix also slows down translational diffusion of molecules, giving rise to long, high-resolution time traces without surface immobilization, which allow extended observations of conformational dynamics in a biologically friendly environment. We demonstrated the compatibility of this method with different types of single molecule spectroscopy techniques, including confocal detection and fluorescence-correlation spectroscopy. We demonstrated that in-gel ALEX can be used to study conformational dynamics at the millisecond time scale; by studying a DNA hairpin in gels, we directly observed fluorescence fluctuations due to conformational interconversion between folded and unfolded states. Our method is amenable to the addition of small molecules that can alter the equilibrium and dynamic properties of the system. In-gel ALEX will be a versatile tool for studying structures and dynamics of complex biomolecules and their assemblies.
Collapse
Affiliation(s)
- Yusdi Santoso
- Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford, OX1 3PU, United Kingdom.
| | | |
Collapse
|
10
|
Forster RE, Hert DG, Chiesl TN, Fredlake CP, Barron AE. DNA migration mechanism analyses for applications in capillary and microchip electrophoresis. Electrophoresis 2009; 30:2014-24. [PMID: 19582705 DOI: 10.1002/elps.200900264] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In 2009, electrophoretically driven DNA separations in slab gels and capillaries have the sepia tones of an old-fashioned technology in the eyes of many, even while they remain ubiquitously used, fill a unique niche, and arguably have yet to reach their full potential. For comic relief, what is old becomes new again: agarose slab gel separations are used to prepare DNA samples for "next-gen" sequencing platforms (e.g. the Illumina and 454 machines) - dsDNA molecules within a certain size range are "cut out" of a gel and recovered for subsequent "massively parallel" pyrosequencing. In this review, we give a Barron lab perspective on how our comprehension of DNA migration mechanisms in electrophoresis has evolved, since the first reports of DNA separations by CE ( approximately 1989) until now, 20 years later. Fused-silica capillaries and borosilicate glass and plastic microchips quietly offer increasing capacities for fast (and even "ultra-fast"), efficient DNA separations. While the channel-by-channel scaling of both old and new electrophoresis platforms provides key flexibility, it requires each unique DNA sample to be prepared in its own micro or nanovolume. This Achilles' heel of electrophoresis technologies left an opening through which pooled sample, next-gen DNA sequencing technologies rushed. We shall see, over time, whether sharpening understanding of transitions in DNA migration modes in crosslinked gels, nanogel solutions, and uncrosslinked polymer solutions will allow electrophoretic DNA analysis technologies to flower again. Microchannel electrophoresis, after a quiet period of metamorphosis, may emerge sleeker and more powerful, to claim its own important niche applications.
Collapse
Affiliation(s)
- Ryan E Forster
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | | | | | | | | |
Collapse
|
11
|
Stellwagen NC, Stellwagen E. Effect of the matrix on DNA electrophoretic mobility. J Chromatogr A 2009; 1216:1917-29. [PMID: 19100556 PMCID: PMC2643323 DOI: 10.1016/j.chroma.2008.11.090] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/24/2008] [Accepted: 11/27/2008] [Indexed: 11/18/2022]
Abstract
DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.
Collapse
Affiliation(s)
- Nancy C Stellwagen
- Department of Biochemistry, University of Iowa, 4403 Bowen Science Building, Iowa City, IA 52242, USA.
| | | |
Collapse
|
12
|
Wang R, Wang JS, Liu GR, Han J, Chen YZ. Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse-grained hybrid molecular dynamics approach. J Comput Chem 2009; 30:505-13. [DOI: 10.1002/jcc.21081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
13
|
Kuroda D, Zhang Y, Wang J, Kaji N, Tokeshi M, Baba Y. A viscosity-tunable polymer for DNA separation by microchip electrophoresis. Anal Bioanal Chem 2008; 391:2543-9. [DOI: 10.1007/s00216-008-2196-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 05/12/2008] [Accepted: 05/20/2008] [Indexed: 10/21/2022]
|
14
|
Fredlake CP, Hert DG, Kan CW, Chiesl TN, Root BE, Forster RE, Barron AE. Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes. Proc Natl Acad Sci U S A 2008; 105:476-81. [PMID: 18184818 PMCID: PMC2206561 DOI: 10.1073/pnas.0705093105] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Indexed: 01/17/2023] Open
Abstract
To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require approximately 70 min to deliver approximately 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between repeating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.
Collapse
Affiliation(s)
| | | | | | | | - Brian E. Root
- Materials Science and Engineering, Northwestern University, Evanston, IL 60208
| | - Ryan E. Forster
- Materials Science and Engineering, Northwestern University, Evanston, IL 60208
| | | |
Collapse
|
15
|
Lam L, Sakakihara S, Ishizuka K, Takeuchi S, Noji H. An integrated system for enzymatic cleavage and electrostretching of freely-suspended single DNA molecules. LAB ON A CHIP 2007; 7:1738-1745. [PMID: 18030395 DOI: 10.1039/b711826k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A novel polyacrylamide gel-based femtolitre microchamber system for performing single-molecule restriction enzyme assay on freely-suspended DNA molecules and subsequent DNA electrostretching by applying an alternating electric field has been developed. We attempted the integration by firstly initiating restriction enzyme reaction on a fluorescent-stained lambdaDNA molecule, encapsulated in a microchamber, using magnesium as an external trigger. Upon complete digestion, the cleaved DNA fragments were electrostretched to analyze the DNA lengths optically. The critical parameters for electrostretching of encapsulated DNA were investigated and optimum stretching was achieved by using 1.5 kHz pulses with electric field strength in the order of 10(3) V cm(-1) in 7% linear polyacrylamide (LPA) solution. LPA was adopted to minimize the adverse effects of ionic thermal agitation on molecular dielectrophoretic elongation in the microchamber. In our experiments, as the fragments were not immobilized throughout the entire protocol, it was found from repeated tests that digestion always occurred, producing the expected number of cleaved fragments. This versatile microchamber approach realized direct observation of these biological reactions on real-time basis at a single-molecule level. Furthermore, with the employment of porous polyacrylamide gel, the effective manipulation of DNA assays and the ability to combine conventionally independent bioanalytical processes have been demonstrated.
Collapse
Affiliation(s)
- Liza Lam
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, 8-1, Ibaraki, 567-0047, Japan.
| | | | | | | | | |
Collapse
|
16
|
Chiesl TN, Forster RE, Root BE, Larkin M, Barron AE. Stochastic Single-Molecule Videomicroscopy Methods To Measure Electrophoretic DNA Migration Modalities in Polymer Solutions above and below Entanglement. Anal Chem 2007; 79:7740-7. [PMID: 17874850 DOI: 10.1021/ac071160x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have studied the effects of polymer molar mass and concentration on the electrophoretic migration modalities of individual molecules of DNA in LPA, HEC, and PEO solutions via epifluorescent videomicroscopy. While both transient entanglement coupling (TEC) and reptation have been studied in the past, the transition between them has not. Understanding this transition will allow for polymer network properties to be optimized to enhance the speed and resolution of DNA separations in microfluidic devices. Near the overlap threshold concentration, C*, TEC is the dominant observed mode of DNA migration, and the observation frequency of TEC increases with increasing polymer molar mass. As polymer concentration is increased, observed TEC events reduce to zero while DNA reptation events become the only detected mechanism. Individual DNA molecules undergoing both migration mechanisms were counted in solutions of varying polymer molar masses and concentrations and were plotted against a dimensionless polymer concentration, C/C*. The data for LPA reduce to form universal curves with a sharp increase in DNA reptation at approximately 6.5C*. Analogous transition concentrations for PEO and HEC were observed at 5C* and 3.5C*, respectively, reflecting the different physical properties of these polymers. This transition correlates closely with the polymer network entanglement concentration, Ce, as measured by rheological techniques. The electrophoretic mobility of lambda-DNA in LPA polymer solutions was also measured and shows how a balance can be struck between DNA resolution and separation speed by choosing the desired prevalence of DNA reptation.
Collapse
Affiliation(s)
- Thomas N Chiesl
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | | | | | | | | |
Collapse
|
17
|
Vailaya A. Fundamentals of Reversed Phase Chromatography: Thermodynamic and Exothermodynamic Treatment. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-200052969] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Anant Vailaya
- a Merck Research Laboratories , Rahway, New Jersey, USA
| |
Collapse
|
18
|
Saha S, Heuer DM, Archer LA. Electrophoretic mobility of linear and star-branched DNA in semidilute polymer solutions. Electrophoresis 2006; 27:3181-94. [PMID: 16850503 DOI: 10.1002/elps.200500836] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Electrophoresis of large linear T2 (162 kbp) and 3-arm star-branched (N(Arm) = 48.5 kbp) DNA in linear polyacrylamide (LPA) solutions above the overlap concentration c* has been investigated using a fluorescence visualization technique that allows both the conformation and mobility mu of the DNA to be determined. LPA solutions of moderate polydispersity index (PI approximately 1.7-2.1) and variable polymer molecular weight Mw (0.59-2.05 MDa) are used as the sieving media. In unentangled semidilute solutions (c* < c < c(e)), we find that the conformational dynamics of linear and star-branched DNA in electric fields are strikingly different; the former migrating in predominantly U- or I-shaped conformations, depending on electric field strength E, and the latter migrating in a squid-like profile with the star-arms outstretched in the direction opposite to E and dragging the branch point through the sieving medium. Despite these visual differences, mu for linear and star-branched DNA of comparable size are found to be nearly identical in semidilute, unentangled LPA solutions. For LPA concentrations above the entanglement threshold (c > c(e)), the conformation of migrating linear and star-shaped DNA manifest only subtle changes from their unentangled solution features, but mu for the stars decreases strongly with increasing LPA concentration and molecular weight, while mu for linear DNA becomes nearly independent of c and Mw. These findings are discussed in the context of current theories for electrophoresis of large polyelectrolytes.
Collapse
Affiliation(s)
- Sourav Saha
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | | | | |
Collapse
|
19
|
Randall GC, Schultz KM, Doyle PS. Methods to electrophoretically stretch DNA: microcontractions, gels, and hybrid gel-microcontraction devices. LAB ON A CHIP 2006; 6:516-25. [PMID: 16572214 DOI: 10.1039/b515326c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The ability to controllably and continuously stretch large DNA molecules in a microfluidic format is important for gene mapping technologies such as Direct Linear Analysis (DLA). We have recently shown that electric field gradients can be readily generated in a microfluidic device and the resulting field is purely elongational. We present a single molecule fluorescence microscopy analysis of T4 DNA (169 kbp) stretching in the electric field gradients in a hyperbolic contraction microchannel. In addition, we are able to selectively pattern a crosslinked gel anywhere inside the microchannel. With an applied electric field, DNA molecules are forced to reptate through the gel and they moderately stretch as they exit the gel. By placing a gel immediately in front of the hyperbolic contraction, we bypass "molecular individualism" and achieve highly uniform and complete stretching of T4 DNA.
Collapse
Affiliation(s)
- Greg C Randall
- Department of Chemical Engineering, Massachusetts Institute of Technology, MIT Room 66-456, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | | | | |
Collapse
|
20
|
Chu AKH. Transport control within a microtube. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 70:061902. [PMID: 15697397 DOI: 10.1103/physreve.70.061902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 05/03/2004] [Indexed: 05/24/2023]
Abstract
Investigation of the entrainment of gases induced by a surface wave propagating along the wall of a microtube is conducted by using a relaxed model with slip velocity boundary conditions. Flow patterns tuned by critical reflux values a0, Knudsen numbers, Reynolds numbers, and the wave number are demonstrated. Results show that once the cross section of the microtube is narrowed down (slip velocity increasing) there are earlier backward flows and the flow pattern is much more complicated. Our results should be useful for the design of micro total analytical systems.
Collapse
Affiliation(s)
- A Kwang-Hua Chu
- Department of Physics, Xinjiang University, Wulumuqi 830046, People's Republic of China and P. O. Box 30-15, Shanghai 200030, People's Republic of China
| |
Collapse
|
21
|
Chiu TC, Chang HT. Comparison of the separation of large DNA fragments in the presence and absence of electroosmotic flow at high pH. J Chromatogr A 2002; 979:299-306. [PMID: 12498261 DOI: 10.1016/s0021-9673(02)01438-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This paper describes the analysis of large DNA fragments at pH > 10.0 by capillary electrophoresis (CE) in the presence of electroosmotic flow (EOF) using hydroxyethylcellulose (HEC) solution. HEC solution in the anodic reservoir enters the capillaries filled with high-pH buffer by EOF after sample injection. With respect to resolution, sensitivity, and speed, separation conducted under discontinuous conditions (different pH values of HEC solutions and buffer filling the capillary) is appropriate. Using HEC solution at concentrations higher than its entanglement threshold ensures a good separation of large DNA fragments in the presence of EOF at high pH. In addition to pH and HEC, the electrolyte species, dimethylamine, methylamine, and piperidine, play different roles in determining the resolution. The separation of DNA fragments ranging in size from 5 to 40 kilo base pairs was completed in 6 min using 1.5% HEC prepared in 20 mM methylamine-borate, pH 12.0, and the capillary filled with 40 mM dimethylamine-borate, pH 10.0. In comparison, this method allows faster separations of large DNA fragments compared with that conducted in the absence of EOF using dilute HEC solutions.
Collapse
Affiliation(s)
- Tai-Chia Chiu
- Department of Chemistry, National Taiwan University, Section 4, Roosevelt Road, Taipei, Taiwan
| | | |
Collapse
|
22
|
Abstract
A novel technique that can rapidly separate long-strand polymers according to length is presented. The separation mechanism is mediated by a confinement-induced entropic force at the abrupt interface between regions of vastly different configuration entropy. To demonstrate this technique, DNA molecules were partially inserted into a dense array of nanopillars (an entropically unfavorable region) using a pulsed electric field and allowed to relax to their natural state by removal of the field. Molecules of dissimilar lengths (T2 and T7 coliphage DNA) were inserted into this region in such a way that shorter molecules were fully inserted in this region, while longer molecules remained partially across the interface. The longer T2 molecules were observed to recoil entirely out of the pillar array, leaving the shorter T7 molecules inserted, and effecting separation of the two species in a single step. To show how this method can be used for separation of unknown samples, the inserting electric field was pulsed for progressively longer times, allowing passage of progressively longer molecules and producing the equivalent of a conventional electropherogram. The effects limiting resolution in this device are discussed, and the expected separating power of a multistage device is reported. The extracted resolution and running separation time compare favorably with current conventional separation techniques.
Collapse
Affiliation(s)
- Mario Cabodi
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.
| | | | | |
Collapse
|
23
|
Nkodo AE, Tinland B. Simultaneous measurements of the electrophoretic mobility, diffusion coefficient and orientation of dsDNA during electrophoresis in polymer solutions. Electrophoresis 2002; 23:2755-65. [PMID: 12210180 DOI: 10.1002/1522-2683(200208)23:16<2755::aid-elps2755>3.0.co;2-#] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We determined simultaneously the electrophoretic mobility, diffusion coefficient D and molecular orientation during electrophoresis of dsDNAs in polymer solutions ranging from the dilute to the semidilute regime. We established, for the first time, master scaling laws for the diffusion coefficient showing a universal behavior. A model found in the literature designed for the dilute regime allows, surprisingly, to describe the mobility data over the whole range of concentrations studied and at the same time the biased reptation with fluctuations (BRF) failed for the semidilute regime, even when constraint release of the network was taken into account. These quantitative determinations of D are of practical interest to evaluate band broadening during capillary electrophoresis and provide data for stimulating investigation of the physics of DNA electrophoretic motion.
Collapse
Affiliation(s)
- Axel Ekani Nkodo
- Institut Charles Sadron, Centre National de la Recherche Scientifique, 6 rue Boussingault, F-67083 Strasbourg Cedex, France
| | | |
Collapse
|
24
|
Abstract
Recently, a microfabricated entropic trap array was demonstrated to be useful in separating large (5-200 kbp) DNA molecules efficiently (within approximately 30 min), by dc electrophoresis, on a microchip platform without a sieving matrix. This paper reports further development of the technique, with emphasis on optimizing separation selectivity and resolution. The interaction of DNA molecules with regularly spaced entropic barriers was modeled in order to predict the effect of changing various structural parameters. The selectivity (differential mobility) was shown to be dependent on the depth of deep and shallow channel regions, applied electric field, and number of entropic barriers. Experimental data were compared with the prediction of the model. It was expected from the model that, in the low-field (severe trapping) limit, separation resolution should depend only on the number of entropic traps. However, in reality, resolution did depend on the applied field because the relaxation of DNA is not achieved at high fields. The requirement and feasibility of megabase pair DNA separation with the entropic trap array device was discussed.
Collapse
Affiliation(s)
- Jongyoon Han
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.
| | | |
Collapse
|
25
|
Serwer P, Hayes SJ. Partially condensed DNA conformations observed by single molecule fluorescence microscopy. Biophys J 2001; 81:3398-408. [PMID: 11721002 PMCID: PMC1301796 DOI: 10.1016/s0006-3495(01)75972-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
To detect partially condensed conformations of a double-stranded DNA molecule, single molecule fluorescence microscopy is performed here. The single DNA molecules are ethidium stained, 670 kilobase pair bacteriophage G genomes that are observed both during and after expulsion from capsids. Expulsion occurs in an agarose gel. Just after expulsion, the entire G DNA molecule typically has a partially condensed conformation not previously described (called a balloon). A balloon subsequently extrudes a filamentous segment of DNA. The filamentous segment becomes gently elongated via diffusion into the network that forms the agarose gel. The elongated DNA molecule usually has bright spots that undergo both appearance/disappearance and apparent motion. These spots are called dynamic spots. A dynamic spot is assumed to be the image of a zone of partially condensed DNA segments (globule). The positions of globules along an elongated DNA molecule 1) are restricted primarily to time-stable regions with comparatively high thermal motion-induced, micrometer-scale bending of the DNA molecule and 2) move within a given region on a time scale smaller than the time scale of recording. Less mobile globules are observed when either magnesium cation or ethanol is added before gel-embedding DNA molecules. These observations are explained by globules induced at equilibrium by a bending-dependent, inter-DNA segment force. Theory has previously predicted that globules are induced by electrostatic forces along an electrically charged polymer at equilibrium. The hypothesis is proposed that intracellular DNA globules assist action-at-a-distance during DNA metabolism.
Collapse
Affiliation(s)
- P Serwer
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA.
| | | |
Collapse
|
26
|
de Carmejane O, Yamaguchi Y, Todorov TI, Morris MD. Three-dimensional observation of electrophoretic migration of dsDNA in semidilute hydroxyethylcellulose solution. Electrophoresis 2001; 22:2433-41. [PMID: 11519947 DOI: 10.1002/1522-2683(200107)22:12<2433::aid-elps2433>3.0.co;2-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Three-dimensional (3-D) video fluorescence microscopy is demonstrated for the investigation of biopolymer electrophoretic migration using double-stranded (ds)DNA in semidilute hydroxyethylcellulose (HEC) as a test system. It is shown that 3-D imaging enables visualization of segmental motion with greater detail than is available in conventional video microscopy. A high frame rate (50-110 frames per second (fps)) intensified progressive scan camera is used to acquire fifteen axial sections focused at different depths through the DNA molecule. A 3-D DNA image is generated from these sections using blind deconvolution image reconstruction and motion is represented as a succession of volume images. A 3-D extension of the Doi/Oana ellipsoidal model is used to fit the DNA envelope, allowing simple quantitative descriptions of the changing shape of the DNA as it interacts with the sieving polymer solution. With 3-D views of migrating DNA molecules we observe U-shaped conformations oriented at an angle to the microscope plane. We are also able to resolve ambiguities and artifacts resulting from loss of information from DNA segments that are not in focus.
Collapse
Affiliation(s)
- O de Carmejane
- Department of Chemistry, University of Michigan, Ann Arbor 48109-1055, USA
| | | | | | | |
Collapse
|
27
|
Noguchi H, Takasu M. Dynamics of DNA in entangled polymer solutions: An anisotropic friction model. J Chem Phys 2001. [DOI: 10.1063/1.1359481] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
28
|
Abstract
Nanofabrication is playing an ever increasing role in science and technology on the nanometer scale and will soon allow us to build systems of the same complexity as found in nature. Conventional methods that emerged from microelectronics are now used for the fabrication of structures for integrated circuits, microelectro-mechanical systems, microoptics and microanalytical devices. Nonconventional or alternative approaches have changed the way we pattern very fine structures and have brought about a new appreciation of simple and low-cost techniques. We present an overview of some of these methods, paying particular attention to those which enable large-scale production of lithographic patterns. We preface the review with a brief primer on lithography and pattern transfer concepts. After reviewing the various patterning techniques, we discuss some recent application issues in the fields of microelectronics, optoelectronics, magnetism as well as in biology and biochemistry.
Collapse
Affiliation(s)
- Y Chen
- Laboratoire de Microstructures et de Microélectronique, CNRS, Bagneux, France.
| | | |
Collapse
|
29
|
Slater GW, Desruisseaux C, Hubert SJ, Mercier JF, Labrie J, Boileau J, Tessier F, Pépin MP. Theory of DNA electrophoresis: A look at some current challenges. Electrophoresis 2000. [DOI: 10.1002/1522-2683(200012)21:18%3c3873::aid-elps3873%3e3.0.co;2-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
30
|
Slater GW, Desruisseaux C, Hubert SJ, Mercier JF, Labrie J, Boileau J, Tessier F, Pépin MP. Theory of DNA electrophoresis: a look at some current challenges. Electrophoresis 2000; 21:3873-87. [PMID: 11192112 DOI: 10.1002/1522-2683(200012)21:18<3873::aid-elps3873>3.0.co;2-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although electrophoresis is one of the basic methods of the modern molecular biology laboratory, new ideas are being suggested at an accelerated rate, in large part because of the pressing demands of the biomedical community. Although we now have, at least for some methods, a fairly good theoretical understanding of the physical mechanisms that lead to the observed peak spacings, widths and shapes, this knowledge is often too qualitative to be used to guide further technical developments and improvements. In this article, we review some selected elements of the current state of our theoretical ignorance, focusing mostly on DNA electrophoresis, and we offer several suggestions for further theoretical investigations.
Collapse
Affiliation(s)
- G W Slater
- Department of Physics, University of Ottawa, Ontario, Canada.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Imaging of a band for DNA fragment migrating in microchannel on integrated microchip. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2000. [DOI: 10.1016/s0928-4931(00)00154-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
32
|
Noguchi H. Dynamics of DNA electrophoresis in dilute and entangled polymer solutions. J Chem Phys 2000. [DOI: 10.1063/1.481583] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
33
|
|
34
|
Hearn MT. Physicochemical factors in polypeptide and protein purification and analysis by high-performance liquid chromatographic techniques: current status and challenges for the future. HANDBOOK OF BIOSEPARATIONS 2000. [DOI: 10.1016/s0149-6395(00)80050-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
35
|
Ueda M. Dynamics of long DNA confined by linear polymers. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1999; 41:153-65. [PMID: 10626773 DOI: 10.1016/s0165-022x(99)00045-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We studied the electrophoretic behavior of long DNA molecules in a linear polymer [polyacrylamide (PA)] solution through direct observation by means of fluorescence microscopy. DNA migrates in an I-shaped conformation in concentrated polymer solutions under steady electric fields, but it is not stretched up to its natural contour length in this I-shaped conformation under such fields. The stretching of DNA is induced under alternating current fields through the entanglement effect between DNA and host polymers. We experimentally investigated the conditions required for this stretching phenomenon and found that DNA can be stretched at a concentration of around 7% PA, under a field of around 10 Hz. These conditions do not depend on the length of the DNA chains. It is expected that DNA stretching will be useful in the optical mapping of specific sites along an individual DNA chain.
Collapse
Affiliation(s)
- M Ueda
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, The University of Tokushima, Japan.
| |
Collapse
|
36
|
Ueda M, Yoshikawa K, Doi M. Molecular Motion of Long Deoxyribonucleic Acid Chains in a Concentrated Polymer Solution Depending on the Frequency of Alternating Electric Field. Polym J 1999. [DOI: 10.1295/polymj.31.637] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
37
|
Schwinefus JJ, Hammond RW, Oana H, Wang SC, De Carmejane O, Bonadio J, Morris MD. Comparative Conformational Dynamics of Supercoiled Plasmids and Linear DNA during Capillary Electrophoresis. Macromolecules 1999. [DOI: 10.1021/ma990129x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeffrey J. Schwinefus
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Department of Physics, Kyoto University, Kyoto, 606-8502, Japan, and Selective Genetics, Inc., San Diego, California 92121
| | - Richard W. Hammond
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Department of Physics, Kyoto University, Kyoto, 606-8502, Japan, and Selective Genetics, Inc., San Diego, California 92121
| | - Hidehiro Oana
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Department of Physics, Kyoto University, Kyoto, 606-8502, Japan, and Selective Genetics, Inc., San Diego, California 92121
| | - Shau-Chun Wang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Department of Physics, Kyoto University, Kyoto, 606-8502, Japan, and Selective Genetics, Inc., San Diego, California 92121
| | - Olivia De Carmejane
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Department of Physics, Kyoto University, Kyoto, 606-8502, Japan, and Selective Genetics, Inc., San Diego, California 92121
| | - Jeffrey Bonadio
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Department of Physics, Kyoto University, Kyoto, 606-8502, Japan, and Selective Genetics, Inc., San Diego, California 92121
| | - Michael D. Morris
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, Department of Physics, Kyoto University, Kyoto, 606-8502, Japan, and Selective Genetics, Inc., San Diego, California 92121
| |
Collapse
|
38
|
Schwinefus JJ, Morris MD. Periodicity of λ DNA Motions during Field Inversion Electrophoresis in Dilute Hydroxyethyl Cellulose Visualized by High-Speed Video Fluorescence Microscopy. Macromolecules 1999. [DOI: 10.1021/ma9819384] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Michael D. Morris
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|