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García de la Torre J, Hernández Cifre J. Hydrodynamic Properties of Biomacromolecules and Macromolecular Complexes: Concepts and Methods. A Tutorial Mini-review. J Mol Biol 2020; 432:2930-2948. [DOI: 10.1016/j.jmb.2019.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 01/08/2023]
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2
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Dorfman KD. The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics. J Biomech Eng 2018; 140:2653367. [PMID: 28857114 PMCID: PMC5816256 DOI: 10.1115/1.4037790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/16/2017] [Indexed: 12/28/2022]
Abstract
The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.
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Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and
Materials Science,
University of Minnesota—Twin Cities,
421 Washington Ave SE,
Minneapolis, MN 55455
e-mail:
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3
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Vargas-Lara F, Stavis SM, Strychalski EA, Nablo BJ, Geist J, Starr FW, Douglas JF. Dimensional reduction of duplex DNA under confinement to nanofluidic slits. SOFT MATTER 2015; 11:8273-8284. [PMID: 26353028 DOI: 10.1039/c5sm01580d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency. Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.
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Affiliation(s)
- Fernando Vargas-Lara
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Samuel M Stavis
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Elizabeth A Strychalski
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Brian J Nablo
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jon Geist
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Francis W Starr
- Department of Physics and Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Jack F Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Tree DR, Muralidhar A, Doyle PS, Dorfman KD. Is DNA a Good Model Polymer? Macromolecules 2013; 46:10.1021/ma401507f. [PMID: 24347685 PMCID: PMC3859536 DOI: 10.1021/ma401507f] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit "ideal" scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.
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Affiliation(s)
- Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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Nepal M, Yaniv A, Shafran E, Krichevsky O. Structure of DNA coils in dilute and semidilute solutions. PHYSICAL REVIEW LETTERS 2013; 110:058102. [PMID: 23414049 DOI: 10.1103/physrevlett.110.058102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 10/10/2012] [Indexed: 06/01/2023]
Abstract
We apply scanning fluorescence correlation spectroscopy to study the structure of individual DNA coils in dilute and semidilute solutions. In dilute solutions, over two decades in length, from 0.6 to 46 μm, DNA behave as ideal chains, in agreement with theoretical predictions and in disagreement with prior experiments. In semidilute solutions, up to very high densities, the structures of individual DNA coils are independent of concentration, unlike flexible coils that shrink with increasing density. Our experimental findings are consistent with the marginal solution theory of semiflexible polymers.
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Affiliation(s)
- Manish Nepal
- Physics Department, Ben-Gurion University, Beer-Sheva 84105, Israel
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7
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Tsortos A, Papadakis G, Gizeli E. The intrinsic viscosity of linear DNA. Biopolymers 2011; 95:824-32. [PMID: 21638275 DOI: 10.1002/bip.21684] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 04/07/2011] [Accepted: 05/20/2011] [Indexed: 11/05/2022]
Abstract
We measured the intrinsic viscosity of very small synthetic DNA molecules, of 20-395 base pairs, and incorporated them in a nearly complete picture for the whole span of molecular weights reported in the literature to date. A major transition is observed at M approximately 2 × 10(6) . It is found that in the range of approximately 7 × 10(3) ≤ M ≤ 2 × 10(6) , the intrinsic viscosity scales as [η] approximately M(1.05) , suggesting that short DNA chains are not as rigid as generally thought. The corresponding scaling for the range of 2 × 10(6) ≤ M ≤ 8 × 10(10) is [η] approximately M(0.69) . A comparison of our results with existing equations, for much narrower data distributions, is made, and the agreement is very satisfactory considering the huge range of data analyzed here. Experimental concerns such as the effect of ionic strength, polydispersity, temperature, and shear rate are discussed in detail. Some issues concerning the Huggins coefficient, polymer chain stiffness, and the relationship between the Mark-Houwink constants K, α are also presented; it is found that log K = 1.156 - 6.19α.
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research & Technology - Hellas (FO.R.T.H), Vassilika Vouton, 70013 Heraklion, Greece.
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de la Torre JG, Ortega Á, Amorós D, Schmidt RR, Cifre JGH. Methods and Tools for the Prediction of Hydrodynamic Coefficients and Other Solution Properties of Flexible Macromolecules in Solution. A Tutorial Minireview. Macromol Biosci 2010; 10:721-30. [DOI: 10.1002/mabi.200900464] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Shafran E, Yaniv A, Krichevsky O. Marginal nature of DNA solutions. PHYSICAL REVIEW LETTERS 2010; 104:128101. [PMID: 20366566 DOI: 10.1103/physrevlett.104.128101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Indexed: 05/29/2023]
Abstract
We adapt a scanning fluorescence correlation spectroscopy technique to measure the structure factor of complex fluid systems and present the first measurements of the structure of semidilute solutions of long DNA polymers. The measured structure factors exhibit screening effects which, as expected for semidilute polymer solutions, grow stronger with increasing DNA concentration c. The measured concentration dependence of the screening length xi proportional to c{0.53+/-0.02} is unusual, but can be understood within the framework of a marginal solutions theory for semiflexible polymers.
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Affiliation(s)
- Eyal Shafran
- Physics Department, Ben-Gurion University, Beer-Sheva 84105, Israel
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10
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Niu S, Singh G, Saraf RF. Label-less fluorescence-based method to detect hybridization with applications to DNA micro-array. Biosens Bioelectron 2007; 23:714-20. [PMID: 17888648 DOI: 10.1016/j.bios.2007.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 08/07/2007] [Indexed: 10/22/2022]
Abstract
By coupling scattered light from DNA to excite fluorescence in a polymer, we describe a quantitative, label-free assay for DNA hybridization detection. Since light scattering is intrinsically proportional to number of molecules, the change in (scattering coupled) fluorescence is highly linear with respect to percent binding of single stranded DNA (ssDNA) target with the immobilized ssDNA probes. The coupling is achieved by immobilizing ssDNA on a fluorescent polymer film at optimum thickness in nanoscale. The fluorescence from the underlining polymer increases due to proportionate increase in scattering from double stranded DNA (dsDNA) (i.e., probe-target binding) compared to ssDNA (i.e., probe). Because the scattering is proportional to fourth power of refractive index, the detection of binding is an order of magnitude more sensitive compared to other label-free optical methods, such as, reflectivity, interference, ellipsometry and surface-plasmon resonance. Remarkably, polystyrene film of optimum thickness 30 nm is the best fluorescent agent since its excitation wavelength matches (within 5 nm) with wavelength for the maximum refractive index difference between ssDNA and dsDNA. A quantitative model (with no fitting parameters) explains the observations. Potential dynamic range is 1 in 10(4) at signal-to-noise ratio of 3:1.
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Affiliation(s)
- Sanjun Niu
- Department of Chemical Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Henshaw JW, Zaharoff DA, Mossop BJ, Yuan F. A single molecule detection method for understanding mechanisms of electric field-mediated interstitial transport of genes. Bioelectrochemistry 2006; 69:248-53. [PMID: 16713747 DOI: 10.1016/j.bioelechem.2006.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 03/20/2006] [Accepted: 03/22/2006] [Indexed: 10/24/2022]
Abstract
The interstitial space is a rate limiting physiological barrier to non-viral gene delivery. External pulsed electric fields have been proposed to increase DNA transport in the interstitium, thereby improving non-viral gene delivery. In order to characterize and improve the interstitial transport, we developed a reproducible single molecule detection method to observe the electromobility of DNA in a range of pulsed, high field strength electric fields typically used during electric field-mediated gene delivery. Using agarose gel as an interstitium phantom, we investigated the dependence of DNA electromobility on field magnitude, pulse duration, pulse interval, and pore size in the interstitial space. We observed that the characteristic electromobility behavior, exhibited under most pulsing conditions, consisted of three distinct phases: stretching, reptation, and relaxation. Electromobility depended strongly on the field magnitude, pulse duration, and pulse interval of the applied pulse sequences, as well as the pore size of the fibrous matrix through which the DNA migrated. Our data also suggest the existence of a minimum pulse amplitude required to initiate electrophoretic transport. These results are useful for understanding the mechanisms of DNA electromobility and improving interstitial transport of genes during electric field-mediated gene delivery.
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Affiliation(s)
- Joshua W Henshaw
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall, Durham, NC 27708, USA
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12
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Robertson RM, Laib S, Smith DE. Diffusion of isolated DNA molecules: dependence on length and topology. Proc Natl Acad Sci U S A 2006; 103:7310-4. [PMID: 16648255 PMCID: PMC1450111 DOI: 10.1073/pnas.0601903103] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The conformation and dynamics of circular polymers is a subject of considerable theoretical and experimental interest. DNA is an important example because it occurs naturally in different topological states, including linear, relaxed circular, and supercoiled circular forms. A fundamental question is how the diffusion coefficients of isolated polymers scale with molecular length and how they vary for different topologies. Here, diffusion coefficients D for relaxed circular, supercoiled, and linear DNA molecules of length L ranging from approximately 6 to 290 kbp were measured by tracking the Brownian motion of single molecules. A topology-independent scaling law D approximately L(-nu) was observed with nu(L) = 0.571 +/- 0.014, nu(C) = 0.589 +/- 0.018, and nu(S) = 0.571 +/- 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with the scaling exponent of nu congruent with 0.588 predicted by renormalization group theory for polymers with significant excluded volume interactions. Our findings thus provide evidence in support of several theories that predict an effective diameter of DNA much greater than the Debye screening length. In addition, the measured ratio D(Circular)/D(Linear) = 1.32 +/- 0.014 was closer to the value of 1.45 predicted by using renormalization group theory than the value of 1.18 predicted by classical Kirkwood hydrodynamic theory and agreed well with a value of 1.31 predicted when incorporating a recently proposed expression for the radius of gyration of circular polymers into the Zimm model.
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Affiliation(s)
- Rae M. Robertson
- Department of Physics, University of California at San Diego, Mail Code 0379, 9500 Gilman Drive, La Jolla, CA 92093
| | - Stephan Laib
- Department of Physics, University of California at San Diego, Mail Code 0379, 9500 Gilman Drive, La Jolla, CA 92093
| | - Douglas E. Smith
- Department of Physics, University of California at San Diego, Mail Code 0379, 9500 Gilman Drive, La Jolla, CA 92093
- *To whom correspondence should be addressed. E-mail:
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Karlsson M, Nolkrantz K, Davidson MJ, Strömberg A, Ryttsén F, Akerman B, Orwar O. Electroinjection of colloid particles and biopolymers into single unilamellar liposomes and cells for bioanalytical applications. Anal Chem 2000; 72:5857-62. [PMID: 11128948 DOI: 10.1021/ac0003246] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A combined electroporation and pressure-driven microinjection method for efficient loading of biopolymers and colloidal particles into single-cell-sized unilamellar liposomes was developed. Single liposomes were positioned between a approximately 2-microm tip diameter solute-filled glass micropipet, equipped with a Pt electrode, and a 5-microm-diameter carbon fiber electrode. A transient, 1-10 ms, rectangular waveform dc voltage pulse (10-40 V/cm) was applied between the electrodes, thus focusing the electric field over the liposome. Dielectric membrane breakdown induced by the applied voltage pulse caused the micropipet tip to enter the liposome and a small volume (typically 50-500 x 10(-15) L) of fluorescein, YOYO-intercalated T7-phage DNA, 100-nm-diameter unilamellar liposomes, or fluorescent latex spheres could be injected into the intraliposomal compartment. We also demonstrate initiation of a chemical intercalation reaction between T2-phage DNA and YOYO-1 by dual injection into a single giant unilamellar liposome. The method was also successfully applied for loading of single cultured cells.
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Affiliation(s)
- M Karlsson
- Department of Chemistry, Göteborg University, Sweden
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Sobel ES, Harpst JA. Effects of Na+ on the persistence length and excluded volume of T7 bacteriophage DNA. Biopolymers 1991; 31:1559-64. [PMID: 1814504 DOI: 10.1002/bip.360311311] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Total intensity, Rayleigh light scattering has been used to measure the rms radius, second virial coefficient, persistence length, and excluded volume of homogeneous T7 bacteriophage DNA as a function of Na+ concentration (0.005 to 3.0 M). All parameters decrease sharply as [Na+] increases, and tend to level off at high Na+. The variation of persistence length with [Na+] is consistent with predictions from counterion condensation theory.
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Affiliation(s)
- E S Sobel
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106-4935
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Harpst JA, Jamieson AM, Dawson JR. Polydispersity and excluded volume effects in sheared DNA fragments. Biophys J 1991; 60:513-8. [PMID: 1912285 PMCID: PMC1260090 DOI: 10.1016/s0006-3495(91)82079-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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