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Darcy M, Crocker K, Wang Y, Le JV, Mohammadiroozbahani G, Abdelhamid MAS, Craggs TD, Castro CE, Bundschuh R, Poirier MG. High-Force Application by a Nanoscale DNA Force Spectrometer. ACS NANO 2022; 16:5682-5695. [PMID: 35385658 PMCID: PMC9048690 DOI: 10.1021/acsnano.1c10698] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/28/2022] [Indexed: 05/06/2023]
Abstract
The ability to apply and measure high forces (>10 pN) on the nanometer scale is critical to the development of nanomedicine, molecular robotics, and the understanding of biological processes such as chromatin condensation, membrane deformation, and viral packaging. Established force spectroscopy techniques including optical traps, magnetic tweezers, and atomic force microscopy rely on micron-sized or larger handles to apply forces, limiting their applications within constrained geometries including cellular environments and nanofluidic devices. A promising alternative to these approaches is DNA-based molecular calipers. However, this approach is currently limited to forces on the scale of a few piconewtons. To study the force application capabilities of DNA devices, we implemented DNA origami nanocalipers with tunable mechanical properties in a geometry that allows application of force to rupture a DNA duplex. We integrated static and dynamic single-molecule characterization methods and statistical mechanical modeling to quantify the device properties including force output and dynamic range. We found that the thermally driven dynamics of the device are capable of applying forces of at least 20 piconewtons with a nanometer-scale dynamic range. These characteristics could eventually be used to study other biomolecular processes such as protein unfolding or to control high-affinity interactions in nanomechanical devices or molecular robots.
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Affiliation(s)
- Michael Darcy
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kyle Crocker
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuchen Wang
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jenny V. Le
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Golbarg Mohammadiroozbahani
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Timothy D. Craggs
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K.
| | - Carlos E. Castro
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ralf Bundschuh
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G. Poirier
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Yadav R, Senanayake KB, Comstock MJ. High-Resolution Optical Tweezers Combined with Multicolor Single-Molecule Microscopy. Methods Mol Biol 2022; 2478:141-240. [PMID: 36063322 DOI: 10.1007/978-1-0716-2229-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present an instrument that combines high-resolution optical tweezers and multicolor confocal fluorescence spectroscopy. Biological macromolecules exhibit complex conformation and stoichiometry changes in coordination with their motion and activity. To further our understanding of the complex machinery of life, we need methods that can simultaneously probe more than one degree of freedom of single molecules and complexes. Fluorescence optical tweezers, or "fleezers," combine the capabilities of optical tweezers and single-molecule fluorescence microscopy into a single instrument. Here we present the latest generation of a high-resolution fleezers instrument integrated with multicolor fluorescence spectroscopy. The tweezers portion of the instrument can manipulate biological macromolecules with pN scale forces while measuring subnanometer distances. Simultaneous with tweezers measurements, the multicolor fluorescence capability allows the direct observation of multiple molecules or multiple degrees of freedom which allows, for example, the observation of multiple proteins simultaneously within a complex. The instrument incorporates three fluorescence excitation lasers, all sourced from a single-mode optical fiber allowing a reliable alignment scheme, that allows, for example, three independent fluorescent probes or fluorescence resonance energy transfer (FRET) measurements and also increases flexibility in the choice of fluorescent probes. To avoid photobleaching and improve tweezers stability, the instrument implements a timesharing (using a single trap laser to produce a pair of traps via rapid switching between two locations) and interlacing (turning the trapping beam off when the fluorescence excitation beams are on and vice versa) scheme using acousto-optic modulators (AOM) to rapidly and precisely modulate lasers. Our latest "random phase" trap AOM control method obliterates previous residual trap positioning and bead position measurement errors. Here we present the general design principles and detailed construction and testing protocols for the instrument.
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Affiliation(s)
- Rajeev Yadav
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA
| | - Kasun B Senanayake
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA
| | - Matthew J Comstock
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA.
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3
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Jeong J, Kim HD. Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Res 2020; 48:5147-5156. [PMID: 32282905 PMCID: PMC7229855 DOI: 10.1093/nar/gkaa207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.
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Affiliation(s)
- Jiyoun Jeong
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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4
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Bao Y, Luo Z, Cui S. Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials. Chem Soc Rev 2020; 49:2799-2827. [PMID: 32236171 DOI: 10.1039/c9cs00855a] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.
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Affiliation(s)
- Yu Bao
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China.
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5
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Ma G, Hu C, Li S, Gao X, Li H, Hu X. Simultaneous, hybrid single-molecule method by optical tweezers and fluorescence. NANOTECHNOLOGY AND PRECISION ENGINEERING 2019. [DOI: 10.1016/j.npe.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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7
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Multi-parameter measurements of conformational dynamics in nucleic acids and nucleoprotein complexes. Methods 2019; 169:69-77. [PMID: 31228549 DOI: 10.1016/j.ymeth.2019.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/15/2019] [Accepted: 06/18/2019] [Indexed: 11/20/2022] Open
Abstract
Biological macromolecules undergo dynamic conformational changes. Single-molecule methods can track such structural rearrangements in real time. However, while the structure of large macromolecules may change along many degrees of freedom, single-molecule techniques only monitor a limited number of these axes of motion. Advanced single-molecule methods are being developed to track multiple degrees of freedom in nucleic acids and nucleoprotein complexes at high resolution, to enable better manipulation and control of the system under investigation, and to collect measurements in massively parallel fashion. Combining complementary single-molecule methods within the same assay also provides unique measurement opportunities. Implementations of magnetic and optical tweezers combined with fluorescence and FRET have demonstrated results unattainable by either technique alone. Augmenting other advanced single-molecule methods with fluorescence detection will allow us to better capture the multidimensional dynamics of nucleic acids and nucleoprotein complexes central to biology.
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8
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Xiao S, Liang H, Wales DJ. The Contribution of Backbone Electrostatic Repulsion to DNA Mechanical Properties is Length-Scale-Dependent. J Phys Chem Lett 2019; 10:4829-4835. [PMID: 31380654 DOI: 10.1021/acs.jpclett.9b01960] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mechanics of DNA bending is crucially related to many vital biological processes. Recent experiments reported anomalous flexibility for DNA on short length scales, calling into doubt the validity of the harmonic worm-like chain (WLC) model in this region. In the present work, we systematically probed the bending dynamics of DNA at different length scales. In contrast to the remarkable deviation from the WLC description for DNA duplexes of less than three helical turns, our atomistic studies indicate that the neutral "null isomer" behaves in accord with the ideal elastic WLC and exhibits a uniform decay for the directional correlation of local bending. The backbone neutralization weakens the anisotropy in the effective bending preference and the helical periodicity of bend correlation that have previously been observed for normal DNA. The contribution of electrostatic repulsion to stretching cooperativity and the mechanical properties of DNA strands is length-scale-dependent: the phosphate neutralization increases the stiffness of DNA below two helical turns, but it is decreased for longer strands. We find that DNA rigidity is largely determined by base pair stacking, with electrostatic interactions contributing only around 10% of the total persistence length.
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Affiliation(s)
- Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Nomidis SK, Skoruppa E, Carlon E, Marko JF. Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. Phys Rev E 2019; 99:032414. [PMID: 30999490 DOI: 10.1103/physreve.99.032414] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 12/12/2022]
Abstract
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here the effect of G on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness C_{eff} for small twist-bend coupling. We find that the "bare" G is "screened" by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with G=0 but with long-wavelength bending and twisting rigidities that are shifted by G-dependent amounts. Using results for torsional and bending rigidities for freely fluctuating DNA, we show how our perturbative results can be extended to a nonperturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo "triad" and molecular dynamics "oxDNA" models, characterized by different degrees of coarse graining, validating the perturbative and nonperturbative analyses. While our theory is in generally good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely used coarse-grained models.
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Affiliation(s)
- Stefanos K Nomidis
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium.,Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - Enrico Skoruppa
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - John F Marko
- Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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10
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Choudhary D, Mossa A, Jadhav M, Cecconi C. Bio-Molecular Applications of Recent Developments in Optical Tweezers. Biomolecules 2019; 9:E23. [PMID: 30641944 PMCID: PMC6359149 DOI: 10.3390/biom9010023] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 12/17/2022] Open
Abstract
In the past three decades, the ability to optically manipulate biomolecules has spurred a new era of medical and biophysical research. Optical tweezers (OT) have enabled experimenters to trap, sort, and probe cells, as well as discern the structural dynamics of proteins and nucleic acids at single molecule level. The steady improvement in OT's resolving power has progressively pushed the envelope of their applications; there are, however, some inherent limitations that are prompting researchers to look for alternatives to the conventional techniques. To begin with, OT are restricted by their one-dimensional approach, which makes it difficult to conjure an exhaustive three-dimensional picture of biological systems. The high-intensity trapping laser can damage biological samples, a fact that restricts the feasibility of in vivo applications. Finally, direct manipulation of biological matter at nanometer scale remains a significant challenge for conventional OT. A significant amount of literature has been dedicated in the last 10 years to address the aforementioned shortcomings. Innovations in laser technology and advances in various other spheres of applied physics have been capitalized upon to evolve the next generation OT systems. In this review, we elucidate a few of these developments, with particular focus on their biological applications. The manipulation of nanoscopic objects has been achieved by means of plasmonic optical tweezers (POT), which utilize localized surface plasmons to generate optical traps with enhanced trapping potential, and photonic crystal optical tweezers (PhC OT), which attain the same goal by employing different photonic crystal geometries. Femtosecond optical tweezers (fs OT), constructed by replacing the continuous wave (cw) laser source with a femtosecond laser, promise to greatly reduce the damage to living samples. Finally, one way to transcend the one-dimensional nature of the data gained by OT is to couple them to the other large family of single molecule tools, i.e., fluorescence-based imaging techniques. We discuss the distinct advantages of the aforementioned techniques as well as the alternative experimental perspective they provide in comparison to conventional OT.
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Affiliation(s)
- Dhawal Choudhary
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy.
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.
| | - Alessandro Mossa
- Istituto Statale di Istruzione Superiore "Leonardo da Vinci", Via del Terzolle 91, 50127 Firenze, Italy.
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, Via Giovanni Sansone 1, 50019 Sesto Fiorentino, Italy.
| | - Milind Jadhav
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy.
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy.
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.
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