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Qiao L, Slater GW. Capture and translocation of a rod-like molecule by a nanopore: orientation, charge distribution and hydrodynamics. Phys Chem Chem Phys 2022; 24:6444-6452. [PMID: 35244666 DOI: 10.1039/d2cp00313a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the translocation of rods with different charge distributions using hybrid Langevin dynamics and lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the P3M algorithm to model the electrohydrodynamic interactions (EHI). We first examine the free-solution electrophoretic properties of rods with various charge distributions. Our translocation simulation results suggest that the order parameter is asymmetric during the capture and escape processes despite the symmetric electric field lines, while the impacts of the charge distribution on rod orientation are more significant during the capture process. The capture/threading/escape times are under the combined effects of charge screening, rod orientation, and charge distributions. We also show that the mean capture time of a rod is shorter when it is launched near the wall because rods tend to align along the wall and hence with the local field lines. Remarkably, the orientational capture radius we proposed previously for uniformly charged rods is still valid in the presence of EHI.
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Affiliation(s)
- Le Qiao
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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Affiliation(s)
- Mykyta V. Chubynsky
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario K1N 6N5, Canada
| | - Gary W. Slater
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario K1N 6N5, Canada
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Chubynsky MV, Slater GW. Theory of end-labeled free-solution electrophoresis: is the end effect important? Electrophoresis 2014; 35:596-604. [PMID: 24375057 DOI: 10.1002/elps.201300419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/24/2013] [Accepted: 11/29/2013] [Indexed: 11/12/2022]
Abstract
In the theory of free-solution electrophoresis of a polyelectrolyte (such as the DNA) conjugated with a "drag-tag," the conjugate is divided into segments of equal hydrodynamic friction and its electrophoretic mobility is calculated as a weighted average of the mobilities of individual segments. If all the weights are assumed equal, then for an electrically neutral drag-tag, the elution time t is predicted to depend linearly on the inverse DNA length 1/M. While it is well-known that the equal-weights assumption is approximate and in reality the weights increase toward the ends, this "end effect" has been assumed to be small, since in experiments the t(1/M) dependence seems to be nearly perfectly linear. We challenge this assumption pointing out that some experimental linear fits do not extrapolate to the free (i.e. untagged) DNA elution time in the limit 1/M→0, indicating nonlinearity outside the fitting range. We show that a theory for a flexible polymer taking the end effect into account produces a nonlinear curve that, however, can be fitted with a straight line over a limited range of 1/M typical of experiments, but with a "wrong" intercept, which explains the experimental results without additional assumptions. We also study the influence of the flexibilities of the charged and neutral parts.
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Hickey OA, Holm C. Electrophoretic mobility reversal of polyampholytes induced by strong electric fields or confinement. J Chem Phys 2013; 138:194905. [PMID: 23697439 DOI: 10.1063/1.4804620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the mobility of polyampholytes consisting of both negatively and positively charged sections. The simulations are carried out using molecular dynamics simulations with electrohydrodynamical effects taken into account via a simple coupling scheme to a lattice-Boltzmann fluid. Our results show a previously predicted mobility reversal of the polyampholytes as the applied electric field is increased due to stretching of the polyampholytes. Further, we show that a similar mobility reversal can be induced due to confinement between parallel plates. At high electric field strengths, the polyampholytes' electrophoretic mobility is a non-monotonic function of the distance between the plates. These results help to clarify the role of deformation and confinement on the electrophoretic mobility of polyampholytes.
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Affiliation(s)
- Owen A Hickey
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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Shendruk T, Hickey O, Slater G, Harden J. Electrophoresis: When hydrodynamics matter. Curr Opin Colloid Interface Sci 2012. [DOI: 10.1016/j.cocis.2011.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Grass K, Holm C, Slater GW. Optimizing End-Labeled Free-Solution Electrophoresis by Increasing the Hydrodynamic Friction of the Drag Tag. Macromolecules 2009. [DOI: 10.1021/ma9003067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Grass
- Frankfurt Institute for Advanced Studies, Goethe University, Ruth-Moufang-Strasse 1, D-60438 Frankfurt am Main, Germany
| | - Christian Holm
- Frankfurt Institute for Advanced Studies, Goethe University, Ruth-Moufang-Strasse 1, D-60438 Frankfurt am Main, Germany
- Institute for Computational Physics, University of Stuttgart, Pfaffenwaldring 27, D-70569 Stuttgart, Germany
| | - Gary W. Slater
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario K1N 6N5, Canada
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Araya F, Huchet G, McGroarty I, Skellern GG, Waigh RD. Capillary electrophoresis for studying drug–DNA interactions. Methods 2007; 42:141-9. [PMID: 17472896 DOI: 10.1016/j.ymeth.2006.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 09/21/2006] [Accepted: 09/25/2006] [Indexed: 11/24/2022] Open
Abstract
The development of new drugs to treat disease by binding directly to DNA offers much promise but is reliant on methods to determine the relative affinity of the putative drug for different DNA sequences. Such methods should ideally be rapid and inexpensive as well as reliable. Use of capillary electrophoresis in simple silica columns offers such a method. The development of systems in which the solvent carries a soluble polymer allows the reliable separation of DNA oligomers, of 12-20 bp in length, which can then be titrated with the ligand in competition experiments. The results obtained are comparable with those obtained by footprinting and give direct graphical output, easily analysed for relative binding affinity.
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Affiliation(s)
- Fitsumbirhan Araya
- Department of Pharmaceutical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, UK
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McCormick LC, Slater GW. Molecular deformation and free-solution electrophoresis of DNA-uncharged polymer conjugates at high field strengths: Theoretical predictions. Part 1: Hydrodynamic segregation. Electrophoresis 2007; 28:674-82. [PMID: 17245697 DOI: 10.1002/elps.200600590] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent advancements in DNA sequencing by end-labeled free-solution electrophoresis (ELFSE) show the promise of this novel technique which overcomes the need for a gel by using a label (or drag-tag) to render the free solution mobility of the DNA size-dependent. It is the attachment of an uncharged drag-tag molecule of a set size to various lengths of DNA in the sample that selectively slows down smaller DNA chains which have less force to pull the drag-tag than larger DNA. So far, only globally random coil conformations have been associated with ELFSE, i.e., the DNA and the label together form a single, undeformed hydrodynamic unit. This paper investigates the conditions under which the DNA and label will segregate into two hydrodynamically distinct units, based on a theoretical approach developed for the electrophoresis of polyampholytes. Optimal experimental conditions tailored to the available label sizes and voltages are predicted along with insight into ideal label architecture.
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Abstract
In the present study, we simulated a model system, PE in biphenyl, to gain the insight into the detailed solvation structures and the molecular mechanism of polymer chain solvation. Using atomistic molecular dynamics (MD) simulation, it was found that when the biphenyl is far from PE chain or in the bulk, the dihedral angle of the two rings in the solvent molecule are approximately 32 degrees. But, the dihedral angel is about 27 degrees when the biphenyls are very close to the PE chain. In the first solvation shell, the orientation angle of the biphenyl long axis to the chain segment backbone was found to be enhanced around two values: approximately 0 and approximately 60 degrees. The detailed solvation structures found here include all dyad conformations (TT, TG, TG', GT, GG, GG', G'T, G'G, and G'G') and vary as a function of the distance between PE chain and biphenyls in the first solvation shell. The closer the the solvent molecule to the PE segment, the higher the TT conformation fraction response is. The other dyad conformations such as TG, GG', etc. undergo different decreases, respectively. This study shows that the solvation even in the Theta condition makes the overall size expansion or the chain stretched. Such a cooperative change was examined here and found not due to generating or losing a conformational state but due to a change in conformational distribution. This change occurs in the middle location of the chain instead of the chain end locations.
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Affiliation(s)
- Qing Ji
- Polymer Physics Laboratory, National Laboratory of Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China
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Meagher RJ, McCormick LC, Haynes RD, Won JI, Lin JS, Slater GW, Barron AE. Free-solution electrophoresis of DNA modified with drag-tags at both ends. Electrophoresis 2006; 27:1702-12. [PMID: 16645947 DOI: 10.1002/elps.200500554] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In end-labeled free-solution electrophoresis (ELFSE), DNA molecules are labeled with a frictional modifier or "drag-tag", allowing their size-based electrophoretic separation in free solution. Among the interesting observations from early work with dsDNA using streptavidin as a drag-tag was that the drag induced by including a streptavidin label at both ends was significantly more than double that from a single streptavidin (Heller, C. et al.., J. Chromatogr. A 1998, 806, 113-121). This finding was assumed to be in error, and subsequent work focused on experiments in which only a single drag-tag is appended to one end of the DNA molecule. Recent theoretical work (McCormick, L. C., Slater, G. W., Electrophoresis 2005, 26, 1659-1667) has examined the contribution of end-effects to the free-solution electrophoretic mobility of charged-uncharged polymer conjugates, reopening the question of enhanced drag from placing a drag-tag at both ends. In this study, this effect is investigated experimentally, using custom-synthesized ssDNA oligonucleotides allowing the attachment of drag-tags to one or both ends, as well as dsDNA PCR products generated with primers appropriate for the attachment of drag-tags at one or both ends. A range of sizes of drag-tags are used, including synthetic polypeptoid drag-tags as well as genetically engineered protein polymer drag-tags. The enhanced drag arising from labeling both ends has been confirmed, with 6-9% additional drag for the ssDNA and 10-23% additional drag for the dsDNA arising from labeling both ends than would be expected from simply doubling the size of the drag-tag at one end. The experimental results for ssDNA labeled at both ends are compared to the predictions of the recent theory of end-effects, with reasonably good quantitative agreement. These experimental findings demonstrate the feasibility of enhancing ELFSE separations by labeling both ends of the DNA molecule, leading to greater resolving power and a wider range of applications for this technique.
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Affiliation(s)
- Robert J Meagher
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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Nedelcu S, Slater GW. Branched polymeric labels used as drag-tags in free-solution electrophoresis of ssDNA. Electrophoresis 2005; 26:4003-15. [PMID: 16252324 DOI: 10.1002/elps.200500471] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In the framework of the classical blob theory of end-labeled free-solution electrophoresis of ssDNA, and based on recent experimental data with linear and branched polymeric labels (or drag-tags), the present study puts forward design principles for the optimal type of branching that would give, for a given total number of monomers, the highest effective frictional drag for ssDNA sequencing purposes. The hydrodynamic radii of the linear and branched labels are calculated using standard models like the freely jointed chain model and the Kratky-Porod worm-like chain model. Based on comparisons of the theory with the experimental data, we propose that the design of new branched labels should use either side chains whose length is comparable to the distance between the branching points or two long branches located near the ends of the molecule's backbone.
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Affiliation(s)
- Sorin Nedelcu
- Department of Physics, University of Ottawa, Ottawa, Canada
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