1
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Zheng CC, Chen YL, Dong HL, Zhang XH, Tan ZJ. Effect of ethanol on the elasticities of double-stranded RNA and DNA revealed by magnetic tweezers and simulations. J Chem Phys 2024; 161:075101. [PMID: 39145565 DOI: 10.1063/5.0211869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024] Open
Abstract
The elasticities of double-stranded (ds) DNA and RNA, which are critical to their biological functions and applications in materials science, can be significantly modulated by solution conditions such as ions and temperature. However, there is still a lack of a comprehensive understanding of the role of solvents in the elasticities of dsRNA and dsDNA in a comparative way. In this work, we explored the effect of ethanol solvent on the elasticities of dsRNA and dsDNA by magnetic tweezers and all-atom molecular dynamics simulations. We found that the bending persistence lengths and contour lengths of dsRNA and dsDNA decrease monotonically with the increase in ethanol concentration. Furthermore, the addition of ethanol weakens the positive twist-stretch coupling of dsRNA, while promotes the negative twist-stretch coupling of dsDNA. Counter-intuitively, the lower dielectric environment of ethanol causes a significant re-distribution of counterions and enhanced ion neutralization, which overwhelms the enhanced repulsion along dsRNA/dsDNA, ultimately leading to the softening in bending for dsRNA and dsDNA. Moreover, for dsRNA, ethanol causes slight ion-clamping across the major groove, which weakens the major groove-mediated twist-stretch coupling, while for dsDNA, ethanol promotes the stretch-radius correlation due to enhanced ion binding and consequently enhances the helical radius-mediated twist-stretch coupling.
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Affiliation(s)
- Chen-Chen Zheng
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yun-Long Chen
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hai-Long Dong
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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2
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Kretzer B, Herényi L, Csík G, Supala E, Orosz Á, Tordai H, Kiss B, Kellermayer M. TMPyP binding evokes a complex, tunable nanomechanical response in DNA. Nucleic Acids Res 2024; 52:8399-8418. [PMID: 38943349 PMCID: PMC11317170 DOI: 10.1093/nar/gkae560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.
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Affiliation(s)
- Balázs Kretzer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Eszter Supala
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Ádám Orosz
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
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3
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Chua GNL, Liu S. When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. Annu Rev Biophys 2024; 53:169-191. [PMID: 38237015 DOI: 10.1146/annurev-biophys-030822-032904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.
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Affiliation(s)
- Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
- Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
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4
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Dong HL, Zhang C, Dai L, Zhang Y, Zhang XH, Tan ZJ. The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations. Nucleic Acids Res 2024; 52:2519-2529. [PMID: 38321947 PMCID: PMC10954459 DOI: 10.1093/nar/gkae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead to significant variations in their biological roles and medical implications, largely due to their distinct biophysical properties, such as bending stiffness. Although it is well known that A-form dsRNA is stiffer than B-form dsDNA under physiological salt conditions, the underlying cause of this difference remains unclear. In this study, we employ high-precision magnetic-tweezer experiments along with molecular dynamics simulations and reveal that the relative bending stiffness between dsRNA and dsDNA is primarily determined by the structure- and salt-concentration-dependent ion distribution around their helical structures. At near-physiological salt conditions, dsRNA shows a sparser ion distribution surrounding its phosphate groups compared to dsDNA, causing its greater stiffness. However, at very high monovalent salt concentrations, phosphate groups in both dsRNA and dsDNA become fully neutralized by excess ions, resulting in a similar intrinsic bending persistence length of approximately 39 nm. This similarity in intrinsic bending stiffness of dsRNA and dsDNA is coupled to the analogous fluctuations in their total groove widths and further coupled to the similar fluctuation of base-pair inclination, despite their distinct A-form and B-form helical structures.
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Affiliation(s)
- Hai-Long Dong
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
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5
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Joshi J, McCauley MJ, Morse M, Muccio MR, Kanlong JG, Rocha MS, Rouzina I, Musier-Forsyth K, Williams MC. Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity. Int J Mol Sci 2024; 25:1410. [PMID: 38338688 PMCID: PMC10855526 DOI: 10.3390/ijms25031410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.
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Affiliation(s)
- Joha Joshi
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael R. Muccio
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Joseph G. Kanlong
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Márcio S. Rocha
- Department of Physics, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil;
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
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6
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Jung J, Kim S, Rah SH, Lee J, Shon MJ. Force-fluorescence setup for observing protein-DNA interactions under load. Methods Enzymol 2024; 694:137-165. [PMID: 38492949 DOI: 10.1016/bs.mie.2024.01.003] [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: 03/18/2024]
Abstract
This chapter explores advanced single-molecule techniques for studying protein-DNA interactions, particularly focusing on Replication Protein A (RPA) using a force-fluorescence setup. It combines magnetic tweezers (MT) with total internal reflection fluorescence (TIRF) microscopy, enabling detailed observation of DNA behavior under mechanical stress. The chapter details the use of DNA hairpins and bare DNA to examine RPA's binding dynamics and its influence on DNA's mechanical properties. This approach provides deeper insights into RPA's role in DNA replication, repair, and recombination, highlighting its significance in maintaining genomic stability.
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Affiliation(s)
- Jaehun Jung
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sang-Hyun Rah
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jayil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea; Institute of Basic Science Center for Genomic Integrity, Ulsan, Republic of Korea
| | - Min Ju Shon
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
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7
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Zou Z, Liang J, Jia Q, Bai D, Xie W, Wu W, Tan C, Ma J. A versatile and high-throughput flow-cell system combined with fluorescence imaging for simultaneous single-molecule force measurement and visualization. NANOSCALE 2023; 15:17443-17454. [PMID: 37859523 DOI: 10.1039/d3nr03214k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A flow-cell offers many advantages for single-molecule studies. But, its merit as a quantitative single-molecule tool has long been underestimated. In this work, we developed a gas-pumped fully calibrated flow-cell system combined with fluorescence imaging for simultaneous single-molecule force measurement and visualization. Such a flow-cell system has considered the hydrodynamic drags on biomolecules and hence can apply and measure force up to more than 100 pN in sub-pN precision with an ultra-high force stability (force drift <0.01 pN in 10 minutes) and tuning accuracy (∼0.04 pN). Meanwhile, it also allows acquiring force signals and fluorescence images at the same time, parallelly tracking hundreds of protein motors in real time as well as monitoring the conformational changes of biomolecules under a well-controlled force, as demonstrated by a series of single-molecule experiments in this work, including the studies of DNA overstretching dynamics, transcription under force and DNA folding/unfolding dynamics. Interesting findings, such as the very tight association of single-stranded binding (SSB) proteins with ssDNA and the reversed transcription, have also been made. These results together lay down an essential foundation for a flow-cell to be used as a versatile, quantitative and high-throughput tool for single-molecule manipulation and visualization.
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Affiliation(s)
- Zhenyu Zou
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Qian Jia
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, P.R. China
| | - Di Bai
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, P.R. China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, P.R. China
| | - Wenqiang Wu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, P.R. China
| | - Chuang Tan
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
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8
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Liang T, Yang C, Song X, Feng Y, Liu Y, Chen H. Quantification of macromolecule crowding at single-molecule level. Phys Rev E 2023; 108:014406. [PMID: 37583195 DOI: 10.1103/physreve.108.014406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/19/2023] [Indexed: 08/17/2023]
Abstract
Macromolecule crowding has a prominent impact on a series of biochemical processes in the cell. It is also expected to promote macromolecular complexation induced by excluded volume effects, which conflicts with recent advances in the thermodynamic interaction between inert, synthetic polymers, and nucleic acids. Along this line, a method combining high-resolution magnetic tweezers and extended crowder-oxDNA model was applied to resolve these discrepancies by systematically studying the kinetics and thermodynamics of the folding-unfolding transition for an individual DNA hairpin in a crowded environment. More specifically, from the magnetic tweezers-based experiments, the linear dependence of the critical force of the DNA hairpin on the polyethylene glycol (PEG) concentration was demonstrated, which is consistent with the results based on the crowder-oxDNA model in which the Lennard-Jones potential was adopted to express the interaction between the crowders and the DNA hairpin. These consistencies highlight that the excluded volume effects are mainly responsible for the interaction between PEG and the DNA hairpin, which is different from the interaction between dextran and the DNA hairpin. In the meantime, the dependence of the folding rate on the molecule weight of PEG, which was different from fluorescence resonance energy transfer-based results, was identified. The proposed method opens a path to detect the interaction between an inert, synthetic molecule, and the DNA hairpin, which is important to accurately mimic the cytosolic environments using mixtures of different inert molecules.
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Affiliation(s)
- Ting Liang
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Chao Yang
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Xiaoya Song
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Yuyu Feng
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Yanhui Liu
- College of Physics, Guizhou University, Guiyang 550025, China
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
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9
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Geyer VF, Diez S. Horizontal Magnetic Tweezers to Directly Measure the Force-Velocity Relationship for Multiple Kinesin Motors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2300558. [PMID: 37035988 DOI: 10.1002/smll.202300558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Transport of intracellular cargo along cytoskeletal filaments is often achieved by the concerted action of multiple motor molecules. While single-molecule studies have provided profound insight into the mechano-chemical principles and force generation of individual motors, studies on multi-motor systems are less advanced. Here, a horizontal magnetic-tweezers setup is applied, capable of producing up to 150 pN of horizontal force onto 2.8 µm superparamagnetic beads, to motor-propelled cytoskeletal filaments. It is found that kinesin-1 driven microtubules decorated with individual beads display frequent transitions in their gliding velocities which we attribute to dynamic changes in the number of engaged motors. Applying defined temporal force-ramps the force-velocity relationship is directly measured for multi-motor transport. It is found that the stall forces of individual motors are approximately additive and collective backward motion of the transport system under super-stall forces is observed. The magnetic-tweezers apparatus is expected to be readily applicable to a wide range of molecular and cellular motility assays.
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Affiliation(s)
- Veikko F Geyer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Arnoldstraße 18, 01307, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
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10
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Liu J, Le S, Yao M, Huang W, Tio Z, Zhou Y, Yan J. Tension Gauge Tethers as Tension Threshold and Duration Sensors. ACS Sens 2023; 8:704-711. [PMID: 36731861 PMCID: PMC9973368 DOI: 10.1021/acssensors.2c02218] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
Mechanotransduction, the process by which cells respond to tension transmitted through various supramolecular linkages, is important for understanding cellular behavior. Tension gauge tethers (TGTs), short fragments of double-stranded DNA that irreversibly break under shear-stretch conditions, have been used in live cell experiments to study mechanotransduction. However, our current understanding of TGTs' mechanical responses is limited, which limits the information that can be gleaned from experimental observations. In this study, we quantified the tension-dependent lifetime of TGTs to better understand their mechanical stability under various physiologically relevant stretching conditions. This work has broad applications for using TGTs as tension threshold and duration sensors and also suggests the need to revisit previous interpretations of experimental observations.
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Affiliation(s)
- Jingzhun Liu
- Mechanobiology
Institute, National University of Singapore, 117411Singapore
| | - Shimin Le
- Department
of Physics, Xiamen University, Xiamen361005, People’s Repbulic of China
| | - Mingxi Yao
- Department
of Biomedical Engineering, Southern University
of Science and Technology, Shenzhen518055, People’s Repbulic of China
| | - Wenmao Huang
- Department
of Physics, National University of Singapore, 117546Singapore
| | - Zhikai Tio
- Department
of Chemical and Biomolecular Engineering, National University of Singapore, 117585Singapore
| | - Yu Zhou
- Mechanobiology
Institute, National University of Singapore, 117411Singapore
| | - Jie Yan
- Mechanobiology
Institute, National University of Singapore, 117411Singapore
- Department
of Physics, National University of Singapore, 117546Singapore
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11
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Rico-Pasto M, Ritort F. Temperature-dependent elastic properties of DNA. BIOPHYSICAL REPORTS 2022; 2:100067. [PMID: 36425333 PMCID: PMC9680767 DOI: 10.1016/j.bpr.2022.100067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/20/2022] [Indexed: 06/02/2023]
Abstract
Knowledge of the elastic properties, e.g., the persistence length or interphosphate distance, of single-stranded (ss) and double-stranded (ds) DNA under different experimental conditions is critical to characterizing molecular reactions studied with single-molecule techniques. While previous experiments have addressed the dependence of the elastic parameters upon varying ionic strength and contour length, temperature-dependent effects are less studied. Here, we examine the temperature-dependent elasticity of ssDNA and dsDNA in the range 5°C-50°C using a temperature-jump optical trap. We find a temperature softening for dsDNA and a temperature stiffening for ssDNA. Our results highlight the need for a general theory explaining the phenomenology observed.
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Affiliation(s)
- Marc Rico-Pasto
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, Barcelona, Spain
| | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, Barcelona, Spain
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12
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The Development of Single Molecule Force Spectroscopy: From Polymer Biophysics to Molecular Machines. Q Rev Biophys 2022; 55:e9. [PMID: 35916314 DOI: 10.1017/s0033583522000087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Paul B, Chaubet L, Verver DE, Montoya G. Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA. Nucleic Acids Res 2022; 50:5208-5225. [PMID: 34951457 PMCID: PMC9122593 DOI: 10.1093/nar/gkab1272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Cas12a is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here, we selected a target site on bacteriophage λ-DNA and used optical tweezers combined with fluorescence to provide mechanistic insight into wild type Cas12a and three engineered variants, where the specific dsDNA and the unspecific ssDNA cleavage are dissociated (M1 and M2) and a third one which nicks the target DNA (M3). At low forces wtCas12a and the variants display two main off-target binding sites, while on stretched dsDNA at higher forces numerous binding events appear driven by the mechanical distortion of the DNA and partial matches to the crRNA. The multiple binding events onto dsDNA at high tension do not lead to cleavage, which is observed on the target site at low forces when the DNA is flexible. In addition, activity assays also show that the preferential off-target sites for this crRNA are not cleaved by wtCas12a, indicating that λ-DNA is only severed at the target site. Our single molecule data indicate that the Cas12a scaffold presents singular mechanical properties, which could be used to generate new endonucleases with biomedical and biotechnological applications.
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Affiliation(s)
- Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Loïc Chaubet
- LUMICKS, Pilotenstraat 41, 1059 CH, Amsterdam, The Netherlands
| | | | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
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14
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Shaheen C, Hastie C, Metera K, Scott S, Zhang Z, Chen S, Gu G, Weber L, Munsky B, Kouzine F, Levens D, Benham C, Leslie S. Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation. Nucleic Acids Res 2022; 50:2754-2764. [PMID: 35188541 PMCID: PMC8934633 DOI: 10.1093/nar/gkac101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 12/12/2022] Open
Abstract
Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
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Affiliation(s)
- Cynthia Shaheen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Cameron Hastie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Kimberly Metera
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Shane Scott
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Institute of Materials Science, Kiel University, 24142 Kiel, Germany
| | - Zhi Zhang
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Sitong Chen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Gracia Gu
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Lisa Weber
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Fedor Kouzine
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Levens
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Craig Benham
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Sabrina Leslie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
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15
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Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT. Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay. Methods Mol Biol 2022; 2478:273-312. [PMID: 36063324 DOI: 10.1007/978-1-0716-2229-2_10] [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
Single-molecule force spectroscopy can precisely probe the biomechanical interactions of proteins that unwind duplex DNA and bind to and wrap around single-stranded (ss)DNA. Yet assembly of the required substrates, which often contain a ssDNA segment embedded within a larger double-stranded (ds)DNA construct, can be time-consuming and inefficient, particularly when using a standard three-way hybridization protocol. In this chapter, we detail how to construct a variety of force-activated DNA substrates more efficiently. To do so, we engineered a dsDNA molecule with a designed sequence of specified GC content positioned between two enzymatically induced, site-specific nicks. Partially pulling this substrate into the overstretching transition of DNA (~65 pN) using an optical trap led to controlled dissociation of the ssDNA segment delineated by the two nicks. Here, we describe protocols for generating ssDNA of up to 1000 nucleotides as well as more complex structures, such as a 120-base-pair DNA hairpin positioned next to a 33-nucleotide ssDNA segment. The utility of the hairpin substrate was demonstrated by measuring the motion of E. coli. RecQ, a 3'-to-5' DNA helicase.
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Affiliation(s)
- Arnulf M K Taylor
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Stephen R Okoniewski
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA.
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16
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Moon HM, Park JS, Lee IB, Kang YI, Jung HJ, An D, Shin Y, Kim MJ, Kim HI, Song JJ, Kim J, Lee NK, Hong SC. Cisplatin fastens chromatin irreversibly even at a high chloride concentration. Nucleic Acids Res 2021; 49:12035-12047. [PMID: 34865121 PMCID: PMC8643659 DOI: 10.1093/nar/gkab922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/12/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
Cisplatin is one of the most potent anti-cancer drugs developed so far. Recent studies highlighted several intriguing roles of histones in cisplatin's anti-cancer effect. Thus, the effect of nucleosome formation should be considered to give a better account of the anti-cancer effect of cisplatin. Here we investigated this important issue via single-molecule measurements. Surprisingly, the reduced activity of cisplatin under [NaCl] = 180 mM, corresponding to the total concentration of cellular ionic species, is still sufficient to impair the integrity of a nucleosome by retaining its condensed structure firmly, even against severe mechanical and chemical disturbances. Our finding suggests that such cisplatin-induced fastening of chromatin can inhibit nucleosome remodelling required for normal biological functions. The in vitro chromatin transcription assay indeed revealed that the transcription activity was effectively suppressed in the presence of cisplatin. Our direct physical measurements on cisplatin-nucleosome adducts suggest that the formation of such adducts be the key to the anti-cancer effect by cisplatin.
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Affiliation(s)
- Hyeon-Min Moon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Jin-Sung Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
| | - Il-Buem Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Young-Im Kang
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Hae Jun Jung
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Dongju An
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yumi Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Min Ji Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Nam-Kyung Lee
- Department of Physics, Sejong University, Seoul 05006, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
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17
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Liang J, Li J, Zhong Z, Rujiralai T, Ma J. Quantifying the force in flow-cell based single-molecule stretching experiments. NANOSCALE 2021; 13:15916-15927. [PMID: 34522927 DOI: 10.1039/d1nr04748e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The flow-cell based single-molecule manipulation technique has found many applications in the study of DNA mechanics and protein-DNA interactions. However, the force in these experiments has not been fully characterized and is usually limited to a moderate force regime (<25 pN). In this work, using the "tethered-bead" assay, the hydrodynamic drag of DNA has been quantitatively evaluated based on a "bead-spring chain" model. The force derived from the Brownian motion of the bead thus contains both contributions from this equivalent hydrodynamic drag of DNA and the pulling force from the tethered bead. Next, using flow-cell based DNA pulling experiments, the linear relationship between the flow rate and total hydrodynamic force on the bead-DNA system has been demonstrated to be valid over a wide force range (0-110 pN). Consequently, the force can be directly converted from the flow rate by a linear factor that can be calibrated either by the bead's Brownian motion at low flow rates or using DNA overstretching transition. Furthermore, the hydrodynamic force and torque due to the shear flow on the bead as well as the equivalent stretching force on DNA are calculated based on theoretical models with the hydrodynamic drag on DNA also considered. The calculated force-extension curves show a good agreement with the measured ones. These results offer important insights into the force in flow-cell based single-molecule stretching experiments and provide a foundation for establishing flow-cells as a simple, low-cost, yet flexible and precise tool for single-molecule force measurements over a wide force range.
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Affiliation(s)
- Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Jiaxi Li
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhensheng Zhong
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Thitima Rujiralai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
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18
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Backer AS, King GA, Biebricher AS, Shepherd JW, Noy A, Leake MC, Heller I, Wuite GJL, Peterman EJG. Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy. J Phys Chem B 2021; 125:8351-8361. [PMID: 34309392 PMCID: PMC8350907 DOI: 10.1021/acs.jpcb.1c02708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/01/2021] [Indexed: 11/29/2022]
Abstract
The combination of DNA force spectroscopy and polarization microscopy of fluorescent DNA intercalator dyes can provide valuable insights into the structure of DNA under tension. These techniques have previously been used to characterize S-DNA-an elongated DNA conformation that forms when DNA overstretches at forces ≥ 65 pN. In this way, it was deduced that the base pairs of S-DNA are highly inclined, relative to those in relaxed (B-form) DNA. However, it is unclear whether and how topological constraints on the DNA may influence the base-pair inclinations under tension. Here, we apply polarization microscopy to investigate the impact of DNA pulling geometry, torsional constraint, and negative supercoiling on the orientations of intercalated dyes during overstretching. In contrast to earlier predictions, the pulling geometry (namely, whether the DNA molecule is stretched via opposite strands or the same strand) is found to have little influence. However, torsional constraint leads to a substantial reduction in intercalator tilting in overstretched DNA, particularly in AT-rich sequences. Surprisingly, the extent of intercalator tilting is similarly reduced when the DNA molecule is negatively supercoiled up to a critical supercoiling density (corresponding to ∼70% reduction in the linking number). We attribute these observations to the presence of P-DNA (an overwound DNA conformation). Our results suggest that intercalated DNA preferentially flanks regions of P-DNA rather than those of S-DNA and also substantiate previous suggestions that P-DNA forms predominantly in AT-rich sequences.
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Affiliation(s)
- Adam S. Backer
- Apple Inc, 1 Apple Park Way, Cupertino, California 95014, United States
| | - Graeme A. King
- Institute
of Structural and Molecular Biology, University
College London, Gower Street, London WC1E
6BT, U.K.
| | - Andreas S. Biebricher
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Jack W. Shepherd
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Agnes Noy
- Department
of Physics, University of York, York YO10 5DD, U.K.
| | - Mark C. Leake
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Iddo Heller
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Gijs J. L. Wuite
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Erwin J. G. Peterman
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
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19
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Guo Z, Hong H, Sun H, Zhang X, Wu CX, Li B, Cao Y, Chen H. SpyTag/SpyCatcher tether as a fingerprint and force marker in single-molecule force spectroscopy experiments. NANOSCALE 2021; 13:11262-11269. [PMID: 34155491 DOI: 10.1039/d1nr01907d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single molecule force spectroscopy has emerged as a powerful tool to study protein folding dynamics, ligand-receptor interactions, and various mechanobiological processes. High force precision does not necessarily lead to high force accuracy, as the uncertainties in calibration can bring serious systematic errors. In the case of magnetic tweezers, accurate determination of the applied forces for short biomolecular tethers, by measuring thermal fluctuations of inhomogeneous magnetic beads, remains difficult. Here we address this challenge by showing that the SpyTag/SpyCatcher complex is not only a convenient and genetically encodable covalent linker but also an ideal molecular fingerprint and force marker in single molecule force spectroscopy experiments. By stretching the N-termini of both SpyCatcher and SpyTag, the complex unfolds locally up to the isopeptide bond position in an unzipping geometry, resulting in equilibrium transitions at ∼30 pN with step sizes of ∼3.4 nm. This mechanical feature can be used as the fingerprint to identify single-molecular events. Moreover, the transitions occur with a fast exchange rate and in a narrow force range. Therefore, the real applied forces can be determined accurately based on the force-dependent transitions. The equilibrium forces are insensitive to buffer conditions and temperature, making the calibration applicable to many complicated experimental systems. We provide an example to calibrate protein unfolding forces using this force marker and expect that this method can greatly simplify force calibration in single-molecule force spectroscopy experiments and improve the force accuracy.
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Affiliation(s)
- Zilong Guo
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
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20
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Corsetti S, Dholakia K. Optical manipulation: advances for biophotonics in the 21st century. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210127-PER. [PMID: 34235899 PMCID: PMC8262092 DOI: 10.1117/1.jbo.26.7.070602] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/17/2021] [Indexed: 05/10/2023]
Abstract
SIGNIFICANCE Optical trapping is a technique capable of applying minute forces that has been applied to studies spanning single molecules up to microorganisms. AIM The goal of this perspective is to highlight some of the main advances in the last decade in this field that are pertinent for a biomedical audience. APPROACH First, the direct determination of forces in optical tweezers and the combination of optical and acoustic traps, which allows studies across different length scales, are discussed. Then, a review of the progress made in the direct trapping of both single-molecules, and even single-viruses, and single cells with optical forces is outlined. Lastly, future directions for this methodology in biophotonics are discussed. RESULTS In the 21st century, optical manipulation has expanded its unique capabilities, enabling not only a more detailed study of single molecules and single cells but also of more complex living systems, giving us further insights into important biological activities. CONCLUSIONS Optical forces have played a large role in the biomedical landscape leading to exceptional new biological breakthroughs. The continuous advances in the world of optical trapping will certainly lead to further exploitation, including exciting in-vivo experiments.
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Affiliation(s)
- Stella Corsetti
- University of St Andrews, SUPA, School of Physics and Astronomy, St. Andrews, United Kingdom
- Address all correspondence to Stella Corsetti,
| | - Kishan Dholakia
- University of St Andrews, SUPA, School of Physics and Astronomy, St. Andrews, United Kingdom
- University of Adelaide, School of Biological Sciences, Adelaide, South Australia, Australia
- Yonsei University, College of Science, Department of Physics, Seoul, Republic of Korea
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21
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Majumdar D. Elasticity of a DNA chain dotted with bubbles under force. Phys Rev E 2021; 103:052412. [PMID: 34134228 DOI: 10.1103/physreve.103.052412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 05/04/2021] [Indexed: 11/07/2022]
Abstract
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles, respectively, when the strands of the DNA are subjected to a force along the same direction, here called a stretching force. The force-temperature phase diagram shows the existence of a tricritical point, where the first-order force-induced zipping transition becomes continuous. On the other hand, when the forces are being applied in opposite directions, here called an unzipping force, the transition remains first order, with the possibility of vanishing of the low-temperature reentrant phase for a semiflexible DNA. Moreover, we found that the bulk elasticity changes only if an external force penetrates the bound phase and affects the bubble states.
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Affiliation(s)
- Debjyoti Majumdar
- Institute of Physics, Bhubaneswar, Odisha 751005, India and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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22
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Abstract
The precise measurement of thermodynamic and kinetic properties for biomolecules provides the detailed information for a multitude of applications in biochemistry, biosensing, and health care. However, sensitivity in characterizing the thermodynamic binding affinity down to a single molecule, such as the Gibbs free energy ([Formula: see text]), enthalpy ([Formula: see text]), and entropy ([Formula: see text]), has not materialized. Here, we develop a nanoparticle-based technique to probe the energetic contributions of single-molecule binding events, which introduces a focused laser of optical tweezer to an optical path of plasmonic imaging to accumulate and monitor the transient local heating. This single-molecule calorimeter uncovers the complex nature of molecular interactions and binding characterizations, which can be employed to identify the thermodynamic equilibrium state and determine the energetic components and complete thermodynamic profile of the free energy landscape. This sensing platform promises a breakthrough in measuring thermal effect at the single-molecule level and provides a thorough description of biomolecular specific interactions.
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23
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Xu W, Dunlap D, Finzi L. Energetics of twisted DNA topologies. Biophys J 2021; 120:3242-3252. [PMID: 33974883 DOI: 10.1016/j.bpj.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/30/2021] [Accepted: 05/05/2021] [Indexed: 11/30/2022] Open
Abstract
Our goal is to review the main theoretical models used to calculate free energy changes associated with common, torsion-induced conformational changes in DNA and provide the resulting equations hoping to facilitate quantitative analysis of both in vitro and in vivo studies. This review begins with a summary of work regarding the energy change of the negative supercoiling-induced B- to L-DNA transition, followed by a discussion of the energetics associated with the transition to Z-form DNA. Finally, it describes the energy changes associated with the formation of DNA curls and plectonemes, which can regulate DNA-protein interactions and promote cross talk between distant DNA elements, respectively. The salient formulas and parameters for each scenario are summarized in table format to facilitate comparison and provide a concise, user-friendly resource.
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Affiliation(s)
- Wenxuan Xu
- Emory University, Department of Physics, Atlanta, Georgia
| | - David Dunlap
- Emory University, Department of Physics, Atlanta, Georgia
| | - Laura Finzi
- Emory University, Department of Physics, Atlanta, Georgia.
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24
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Winogradoff D, Li P, Joshi H, Quednau L, Maffeo C, Aksimentiev A. Chiral Systems Made from DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003113. [PMID: 33717850 PMCID: PMC7927625 DOI: 10.1002/advs.202003113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA's chirality, from plasmonics and spintronics to biosensing.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Pin‐Yi Li
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Himanshu Joshi
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Lauren Quednau
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Christopher Maffeo
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Aleksei Aksimentiev
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
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25
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Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
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Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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26
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Singh J, Purohit PK. Statistical mechanics of a double-stranded rod model for DNA melting and elasticity. SOFT MATTER 2020; 16:7715-7726. [PMID: 32734998 PMCID: PMC7484343 DOI: 10.1039/d0sm00521e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The double-helical topology of DNA molecules observed at room temperature in the absence of any external loads can be disrupted by increasing the bath temperature or by applying tensile forces, leading to spontaneous strand separation known as DNA melting. Here, continuum mechanics of a 2D birod is combined with statistical mechanics to formulate a unified framework for studying both thermal melting and tensile force induced melting of double-stranded molecules: it predicts the variation of melting temperature with tensile load, provides a mechanics-based understanding of the cooperativity observed in melting transitions, and reveals an interplay between solution electrostatics and micromechanical deformations of DNA which manifests itself as an increase in the melting temperature with increasing ion concentration. This novel predictive framework sheds light on the micromechanical aspects of DNA melting and predicts trends that were observed experimentally or extracted phenomenologically using the Clayperon equation.
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Affiliation(s)
- Jaspreet Singh
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, 19104, USA.
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, 19104, USA.
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27
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Yang D, Liu W, Deng X, Xie W, Chen H, Zhong Z, Ma J. GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes. Biophys J 2020; 119:852-861. [PMID: 32738216 DOI: 10.1016/j.bpj.2020.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/22/2020] [Accepted: 06/18/2020] [Indexed: 01/25/2023] Open
Abstract
DNA:RNA hybrid duplex plays important roles in various biological processes. Both its structural stability and interactions with proteins are highly sequence dependent. In this study, we utilize homebuilt optical tweezers to investigate how GC contents in the sequence influence the structural and mechanical properties of DNA:RNA hybrid by measuring its contour length, elasticities, and overstretching dynamics. Our results support that the DNA:RNA hybrid adopts a conformation between the A- and B-form helix, and the GC content does not affect its structural and elastic parameters obviously when varying from 40 to 60% before the overstretching transition of DNA:RNA hybrid occurs. In the overstretching transition, however, our study unravels significant heterogeneity and strong sequence dependence, suggesting the presence of a highly dynamic competition between the two processes, namely the S-form duplex formation (nonhysteretic) and the unpeeling (hysteretic). Analyzing the components left in DNA:RNA hybrid after the overstretching transition suggests that the RNA strand is more easily unpeeled than the DNA strand, whereas an increase in the GC content from 40 to 60% can significantly reduce unpeeling. Large hysteresis is observed between the stretching and relaxation processes, which is also quantitatively correlated with the percentage of unpeeling in the DNA:RNA duplex. Increasing in both the salt concentration and GC content can effectively reduce the hysteresis with the latter being more significant. Together, our study reveals that the mechanical properties of DNA:RNA hybrid duplexes are significantly different from double-stranded DNA and double-stranded RNA, and its overstretching behavior is highly sequence dependent. These results should be taken into account in the future studies on DNA:RNA-hybrid-related functional structures and motor proteins.
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Affiliation(s)
- Dongni Yang
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenzhao Liu
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiangyu Deng
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei Xie
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen, Fujian, China
| | - Zhensheng Zhong
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou, Guangdong, China; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou, Guangdong, China.
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28
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Jiang Y, Feldman T, Bakx JA, Yang D, Wong WP. Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping. LAB ON A CHIP 2020; 20:1780-1791. [PMID: 32301470 PMCID: PMC7239757 DOI: 10.1039/c9lc01028a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-molecule force spectroscopy has brought many new insights into nanoscale biology, from the functioning of molecular motors to the mechanical response of soft materials within the cell. To expand the single-molecule toolbox, we have developed a surface-free force spectroscopy assay based on a high-speed hydrodynamic trap capable of applying extremely high tensions for long periods of time. High-speed single-molecule trapping is enabled by a rigid and gas-impermeable microfluidic chip, rapidly and inexpensively fabricated out of glass, double-sided tape and UV-curable adhesive. Our approach does not require difficult covalent attachment chemistries, and enables simultaneous force application and single-molecule fluorescence. Using this approach, we have induced a highly extended state with twice the contour length of B-DNA in regions of partially intercalated double-stranded (dsDNA) by applying forces up to 250 pN. This highly extended state resembles the hyperstretched state of dsDNA, which was initially discovered as a structure fully intercalated by dyes under high tension. It has been hypothesized that hyperstretched DNA could also be induced without the aid of intercalators if high-enough forces were applied, which matches our observation. Combining force application with single-molecule fluorescence imaging is critical for distinguishing hyperstretched DNA from single-stranded DNA that can result from peeling. High-speed hydrodynamic trapping is a powerful yet accessible force spectroscopy method that enables the mechanics of biomolecules to be probed in previously difficult to access regimes.
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Affiliation(s)
- Yan Jiang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Theodore Feldman
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Julia A.M. Bakx
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Wesley P. Wong
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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29
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Li F, Mao X, Li F, Li M, Shen J, Ge Z, Fan C, Zuo X. Ultrafast DNA Sensors with DNA Framework-Bridged Hybridization Reactions. J Am Chem Soc 2020; 142:9975-9981. [PMID: 32369359 DOI: 10.1021/jacs.9b13737] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intracellular DNA-based hybridization reactions generally occur under tension rather than in free states, which are spatiotemporally controlled in physiological conditions. However, how nanomechanical forces affect DNA hybridization efficiencies in in-vitro DNA assays, for example, biosensors or biochips, remains largely elusive. Here, we design DNA framework-based nanomechanical handles that can control the stretching states of DNA molecules. Using a pair of tetrahedral DNA framework (TDF) nanostructured handles, we develop bridge DNA sensors that can capture target DNA with ultrafast speed and high efficiency. We find that the rigid TDF handles bind two ends of a single-stranded DNA (ssDNA) and hold it in a stretched state, with an apparent stretching length comparable to its counterpart of double-stranded DNA (dsDNA) via atomic force microscopy measurement. The DNA stretching effect of ssDNA is then monitored using single-molecule fluorescence energy transfer (FRET), resulting in decreased FRET efficiency in the stretched ssDNA. By controlling the stretching state of ssDNA, we obtained significantly improved hybridization kinetics (within 1 min) and hybridization efficiency (∼98%) under the target concentration of 500 nM. The bridge DNA sensors demonstrated high sensitivity (1 fM), high specificity (single mismatch mutation discrimination), and high selectivity (suitable for the detection in serum and blood) under the target concentration of 10 nM. Controlling the stretching state of ssDNA shows great potential in biosensors, bioimaging, and biochips applications.
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Affiliation(s)
- Fengqin Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianlei Shen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhilei Ge
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
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30
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Papini FS, Seifert M, Dulin D. High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments. Nucleic Acids Res 2020; 47:e144. [PMID: 31584079 PMCID: PMC6902051 DOI: 10.1093/nar/gkz851] [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: 06/05/2019] [Revised: 08/20/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022] Open
Abstract
Single molecule biophysics experiments have enabled the observation of biomolecules with a great deal of precision in space and time, e.g. nucleic acids mechanical properties and protein–nucleic acids interactions using force and torque spectroscopy techniques. The success of these experiments strongly depends on the capacity of the researcher to design and fabricate complex nucleic acid structures, as the outcome and the yield of the experiment also strongly depend on the high quality and purity of the final construct. Though the molecular biology techniques involved are well known, the fabrication of nucleic acid constructs for single molecule experiments still remains a difficult task. Here, we present new protocols to generate high quality coilable double-stranded DNA and RNA, as well as DNA and RNA hairpins with ∼500–1000 bp long stems. Importantly, we present a new approach based on single-stranded DNA (ssDNA) annealing and we use magnetic tweezers to show that this approach simplifies the fabrication of complex DNA constructs, such as hairpins, and converts more efficiently the input DNA into construct than the standard PCR-digestion-ligation approach. The protocols we describe here enable the design of a large range of nucleic acid construct for single molecule biophysics experiments.
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Affiliation(s)
- Flávia S Papini
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Cauerstrasse 3, 91058 Erlangen, Germany
| | - Mona Seifert
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Cauerstrasse 3, 91058 Erlangen, Germany
| | - David Dulin
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Cauerstrasse 3, 91058 Erlangen, Germany
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31
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Yang YJ, Dong HL, Qiang XW, Fu H, Zhou EC, Zhang C, Yin L, Chen XF, Jia FC, Dai L, Tan ZJ, Zhang XH. Cytosine Methylation Enhances DNA Condensation Revealed by Equilibrium Measurements Using Magnetic Tweezers. J Am Chem Soc 2020; 142:9203-9209. [DOI: 10.1021/jacs.9b11957] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Hai-Long Dong
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Wei Qiang
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Lei Yin
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xue-Feng Chen
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Fu-Chao Jia
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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32
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Shepherd JW, Greenall RJ, Probert M, Noy A, Leake M. The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA. Nucleic Acids Res 2020; 48:1748-1763. [PMID: 31930331 PMCID: PMC7038985 DOI: 10.1093/nar/gkz1227] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/26/2022] Open
Abstract
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20-30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.
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Affiliation(s)
- Jack W Shepherd
- Department of Physics, University of York, York YO10 5DD, UK
| | | | | | - Agnes Noy
- Department of Physics, University of York, York YO10 5DD, UK
| | - Mark C Leake
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York,YO10 5NG, UK
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33
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Fu H, Zhang C, Qiang XW, Yang YJ, Dai L, Tan ZJ, Zhang XH. Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers. PHYSICAL REVIEW LETTERS 2020; 124:058101. [PMID: 32083903 DOI: 10.1103/physrevlett.124.058101] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
We report that trivalent cobalt hexammine cations decrease the persistence length, stretching modulus, helical density, and size of plectonemes formed under torque of DNA but increase those of RNA. Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of plectonemes while increasing the helical densities of both DNA and RNA. The experimental results are explained by different binding modes of the cations on DNA and RNA in our all-atom molecular dynamics simulations. The significant variations of the helical densities and structures of DNA and RNA duplexes induced by high-valent cations may affect interactions of the duplexes with proteins.
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Affiliation(s)
- Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xiao-Wei Qiang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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34
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Meyer AC, Öz Y, Gundlach N, Karbach M, Lu P, Müller G. Molecular chains under tension: Thermal and mechanical activation of statistically interacting extension and contraction particles. Phys Rev E 2020; 101:022504. [PMID: 32168618 DOI: 10.1103/physreve.101.022504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/23/2020] [Indexed: 11/07/2022]
Abstract
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds between monomers or of entire groups of monomers to tension is governed by the activation of statistically interacting particles representing quanta of extension or contraction. This method of analysis is capable of describing thermal unbending of the freely jointed or wormlike chain kind, linear or nonlinear contour elasticity, and structural transformations including effects of cooperativity. The versatility of this approach is demonstrated in an application to double-stranded DNA undergoing torsionally unconstrained stretching across three regimes of mechanical response including an overstretching transition. The three-regime force-extension characteristic, derived from a single free-energy expression, accurately matches empirical evidence.
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Affiliation(s)
- Aaron C Meyer
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Yahya Öz
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Norman Gundlach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Michael Karbach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Ping Lu
- Department of Applied Science and Mathematics, Bluefield State College, Bluefield, West Virginia 24701, USA
| | - Gerhard Müller
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
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35
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Sun C, Purohit PK. Stick-slip kinetics in a bistable bar immersed in a heat bath. INTERNATIONAL JOURNAL OF SOLIDS AND STRUCTURES 2019; 180-181:205-220. [PMID: 32831392 PMCID: PMC7442296 DOI: 10.1016/j.ijsolstr.2019.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Structural transitions in some rod-like biological macromolecules under tension are known to proceed by the propagation through the length of the molecule of an interface separating two phases. A continuum mechanical description of the motion of this interface, or phase boundary, takes the form of a kinetic law which relates the thermodynamic driving force across it with its velocity in the reference configuration. For biological macromolecules immersed in a heat bath, thermally activated kinetics described by the Arrhenius law is often a good choice. Here we show that 'stick-slip' kinetics, characteristic of friction, can also arise in an overdamped bistable bar immersed in a heat bath. To mimic a rod-like biomolecule we model the bar as a chain of masses and bistable springs moving in a viscous fluid. We conduct Langevin dynamics calculations on the chain and extract a temperature dependent kinetic relation by observing that the dissipation at a phase boundary can be estimated by performing an energy balance. Using this kinetic relation we solve boundary value problems for a bistable bar immersed in a constant temperature bath and show that the resultant force-extension relation matches very well with the Langevin dynamics results. We estimate the force fluctuations at the pulled end of the bar due to thermal kicks from the bath by using a partition function. We also show rate dependence of hysteresis in cyclic loading of the bar arising from the stick-slip kinetics. Our kinetic relation could be applied to rod-like biomolecules, such as, DNA and coiled-coil proteins which exhibit structural transitions that depend on both temperature and loading rate.
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Affiliation(s)
- Chuanpeng Sun
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
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36
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Abstract
Torsional stress plays a vital role in many genomic transactions, including replication and transcription, and often results in underwound (negatively supercoiled) DNA. Here, we present a single-molecule method, termed Optical DNA Supercoiling (ODS), that advances our ability to study negatively supercoiled DNA. Since ODS is based on dual-trap optical tweezers, it is compatible with a wide range of functionalities that are difficult to combine with traditional methods of DNA twist control. This includes the ability to image supercoiled DNA with fluorescence microscopy and move the supercoiled substrate rapidly between different buffer/protein solutions. We demonstrate that ODS yields unique and important insights into both the biomechanical properties of negatively supercoiled DNA and the dynamics of DNA–protein interactions on underwound DNA. Cellular DNA is regularly subject to torsional stress during genomic processes, such as transcription and replication, resulting in a range of supercoiled DNA structures. For this reason, methods to prepare and study supercoiled DNA at the single-molecule level are widely used, including magnetic, angular-optical, micropipette, and magneto-optical tweezers. However, it is currently challenging to combine DNA supercoiling control with spatial manipulation and fluorescence microscopy. This limits the ability to study complex and dynamic interactions of supercoiled DNA. Here we present a single-molecule assay that can rapidly and controllably generate negatively supercoiled DNA using a standard dual-trap optical tweezers instrument. This method, termed Optical DNA Supercoiling (ODS), uniquely combines the ability to study supercoiled DNA using force spectroscopy, fluorescence imaging of the whole DNA, and rapid buffer exchange. The technique can be used to generate a wide range of supercoiled states, with between <5 and 70% lower helical twist than nonsupercoiled DNA. Highlighting the versatility of ODS, we reveal previously unobserved effects of ionic strength and sequence on the structural state of underwound DNA. Next, we demonstrate that ODS can be used to directly visualize and quantify protein dynamics on supercoiled DNA. We show that the diffusion of the mitochondrial transcription factor TFAM can be significantly hindered by local regions of underwound DNA. This finding suggests a mechanism by which supercoiling could regulate mitochondrial transcription in vivo. Taken together, we propose that ODS represents a powerful method to study both the biophysical properties and biological interactions of negatively supercoiled DNA.
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37
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Zhao X, Guo S, Lu C, Chen J, Le S, Fu H, Yan J. Single-molecule manipulation quantification of site-specific DNA binding. Curr Opin Chem Biol 2019; 53:106-117. [DOI: 10.1016/j.cbpa.2019.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/24/2019] [Accepted: 08/24/2019] [Indexed: 10/25/2022]
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38
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Sahoo AK, Bagchi B, Maiti PK. Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes. J Chem Phys 2019; 151:164902. [PMID: 31675856 DOI: 10.1063/1.5117163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here, we probe, via all-atom molecular dynamics (MD) simulations, the change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, the stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.
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Affiliation(s)
- Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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39
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Statistical physics and mesoscopic modeling to interpret tethered particle motion experiments. Methods 2019; 169:57-68. [PMID: 31302177 DOI: 10.1016/j.ymeth.2019.07.006] [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: 03/01/2019] [Revised: 06/11/2019] [Accepted: 07/07/2019] [Indexed: 11/22/2022] Open
Abstract
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques provide raw data such as the tracked particle amplitude of movement, from which relevant information about DNA conformations or states must be recovered. Solving this inverse problem appeals to specific theoretical tools that have been designed in the two last decades, together with the data pre-processing procedures that ought to be implemented to avoid biases inherent to these experimental techniques. These statistical tools and models are reviewed in this paper.
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40
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Melkonyan L, Bercy M, Bizebard T, Bockelmann U. Overstretching Double-Stranded RNA, Double-Stranded DNA, and RNA-DNA Duplexes. Biophys J 2019; 117:509-519. [PMID: 31337545 PMCID: PMC6697464 DOI: 10.1016/j.bpj.2019.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 06/17/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022] Open
Abstract
Using single-molecule force measurements, we compare the overstretching transition of the four types of duplexes composed of DNA or RNA strands. Three of the four extremities of each double helix are attached to two microscopic beads, and a stretching force is applied with a dual-beam optical trapping interferometer. We find that overstretching occurs for all four duplexes with small differences between the plateau forces. Double-stranded RNA (dsRNA) exhibits a smooth transition in contrast to the other three duplexes that show sawtooth patterns, the latter being a characteristic signature of peeling. This difference is observed for a wide range of experimental conditions. We present a theoretical description that explains the difference and predicts that peeling and bubble formation do not occur in overstretching double-stranded RNA. Formation of S-RNA is proposed, an overstretching mechanism that contrary to the other two does not generate single strands. We suggest that this singular RNA property helps RNA structures to assemble and play their essential roles in the biological cell.
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Affiliation(s)
- Lena Melkonyan
- Nanobiophysique, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Paris, France
| | - Mathilde Bercy
- Nanobiophysique, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Paris, France
| | - Thierry Bizebard
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris, France.
| | - Ulrich Bockelmann
- Nanobiophysique, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Paris, France.
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41
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Yang YJ, Song L, Zhao XC, Zhang C, Wu WQ, You HJ, Fu H, Zhou EC, Zhang XH. A Universal Assay for Making DNA, RNA, and RNA-DNA Hybrid Configurations for Single-Molecule Manipulation in Two or Three Steps without Ligation. ACS Synth Biol 2019; 8:1663-1672. [PMID: 31264849 DOI: 10.1021/acssynbio.9b00241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite having a great variety of topologies, most DNA, RNA, and RNA-DNA hybrid (RDH) configurations for single-molecule manipulation are composed of several single-stranded (ss) DNA and ssRNA strands, with functional labels at the two ends for surface tethering. On this basis, we developed a simple, robust, and universal amplification-annealing (AA) assay for making all these configurations in two or three steps without inefficient digestion and ligation reactions. As examples, we made ssDNA, short ssDNA with double-stranded (ds) DNA handles, dsDNA with ssDNA handles, replication-fork shaped DNA/RDH/RNA, DNA holiday junction, three-site multiple-labeled and nicked DNA, torsion-constrained RNA/RDH, and short ssRNA with RDH handles. In addition to single-molecule manipulation techniques including optical tweezers, magnetic tweezers, and atomic force microscopy, these configurations can be applied in other surface-tethering techniques as well.
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Affiliation(s)
- Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Lun Song
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xiao-Cong Zhao
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Wen-Qiang Wu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Hui-Juan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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42
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Liu JH, Xi K, Zhang X, Bao L, Zhang X, Tan ZJ. Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling. Biophys J 2019; 117:74-86. [PMID: 31164196 PMCID: PMC6626833 DOI: 10.1016/j.bpj.2019.05.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/25/2019] [Accepted: 05/17/2019] [Indexed: 12/21/2022] Open
Abstract
DNA-RNA hybrid (DRH) duplexes play essential roles during the replication of DNA and the reverse transcription of RNA viruses, and their flexibility is important for their biological functions. Recent experiments indicated that A-form RNA and B-form DNA have a strikingly different flexibility in stretching and twist-stretch coupling, and the structural flexibility of DRH duplex is of great interest, especially in stretching and twist-stretch coupling. In this work, we performed microsecond all-atom molecular dynamics simulations with new AMBER force fields to characterize the structural flexibility of DRH duplex in stretching and twist-stretch coupling. We have calculated all the helical parameters, stretch modulus, and twist-stretch coupling parameters for the DRH duplex. First, our analyses on structure suggest that the DRH duplex exhibits an intermediate conformation between A- and B-forms and closer to A-form, which can be attributed to the stronger rigidity of the RNA strand than the DNA strand. Second, our calculations show that the DRH duplex has the stretch modulus of 834 ± 34 pN and a very weak twist-stretch coupling. Our quantitative analyses indicate that, compared with DNA and RNA duplexes, the different flexibility of the DRH duplex in stretching and twist-stretch coupling is mainly attributed to its apparently different basepair inclination in the helical structure.
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Affiliation(s)
- Ju-Hui Liu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xinghua Zhang
- College of Life Science, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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43
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Wasserman MR, Liu S. A Tour de Force on the Double Helix: Exploiting DNA Mechanics To Study DNA-Based Molecular Machines. Biochemistry 2019; 58:4667-4676. [PMID: 31251042 DOI: 10.1021/acs.biochem.9b00346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA is both a fundamental building block of life and a fascinating natural polymer. The advent of single-molecule manipulation tools made it possible to exert controlled force on individual DNA molecules and measure their mechanical response. Such investigations elucidated the elastic properties of DNA and revealed its distinctive structural configurations across force regimes. In the meantime, a detailed understanding of DNA mechanics laid the groundwork for single-molecule studies of DNA-binding proteins and DNA-processing enzymes that bend, stretch, and twist DNA. These studies shed new light on the metabolism and transactions of nucleic acids, which constitute a major part of the cell's operating system. Furthermore, the marriage of single-molecule fluorescence visualization and force manipulation has enabled researchers to directly correlate the applied tension to changes in the DNA structure and the behavior of DNA-templated complexes. Overall, experimental exploitation of DNA mechanics has been and will continue to be a unique and powerful strategy for understanding how molecular machineries recognize and modify the physical state of DNA to accomplish their biological functions.
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Affiliation(s)
- Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry , The Rockefeller University , New York , New York 10065 , United States
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44
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Zhao XC, Fu H, Song L, Yang YJ, Zhou EC, Liu GX, Chen XF, Li Z, Wu WQ, Zhang XH. S-DNA and RecA/RAD51-Mediated Strand Exchange in Vitro. Biochemistry 2019; 58:2009-2016. [PMID: 30900876 DOI: 10.1021/acs.biochem.8b01125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
S-DNA (stretched DNA) is an elongated base-paired DNA conformation under high tension. Because the RecA/Rad51 family DNA recombinases form helical filaments on DNA and mediate the formation of the DNA triplex (D-loop), in which the DNA is stretched, and because the extension of these nucleoprotein filaments is similar to the extension of S-DNA, S-DNA has long been hypothesized as a possible state of DNA that participants in RecA/Rad51-mediated DNA strand exchange in homologous recombination. Such a hypothesis, however, is still lacking direct experimental studies. In this work, we have studied the polymerization and strand exchange on S-DNA mediated by Escherichia coli RecA, human Rad51, and Saccharomyces cerevisiae Rad51 by single-molecule magnetic tweezers. We report that RecA/Rad51 polymerizes faster on S-DNA than on B-DNA with the same buffer conditions. Furthermore, the RecA/Rad51-mediated DNA triplex forms faster from S-DNA than from B-DNA together with the homologous single-stranded DNA. These results provide evidence that S-DNA can interact with RecA and Rad51 and shed light on the possible functions of S-DNA.
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Affiliation(s)
- Xiao-Cong Zhao
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Hang Fu
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Lun Song
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Ya-Jun Yang
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Er-Chi Zhou
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Guang-Xue Liu
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Xue-Feng Chen
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Zhuo Li
- Third Institute of Oceanography , State Oceanic Administration , Xiamen 361005 , China
| | - Wen-Qiang Wu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology , Henan University , Kaifeng 475001 , China
| | - Xing-Hua Zhang
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
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45
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Backer AS, Biebricher AS, King GA, Wuite GJL, Heller I, Peterman EJG. Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA. SCIENCE ADVANCES 2019; 5:eaav1083. [PMID: 30915395 PMCID: PMC6430628 DOI: 10.1126/sciadv.aav1083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/04/2019] [Indexed: 05/22/2023]
Abstract
DNA structural transitions facilitate genomic processes, mediate drug-DNA interactions, and inform the development of emerging DNA-based biotechnology such as programmable materials and DNA origami. While some features of DNA conformational changes are well characterized, fundamental information such as the orientations of the DNA base pairs is unknown. Here, we use concurrent fluorescence polarization imaging and DNA manipulation experiments to probe the structure of S-DNA, an elusive, elongated conformation that can be accessed by mechanical overstretching. To this end, we directly quantify the orientations and rotational dynamics of fluorescent DNA-intercalated dyes. At extensions beyond the DNA overstretching transition, intercalators adopt a tilted (θ ~ 54°) orientation relative to the DNA axis, distinct from the nearly perpendicular orientation (θ ~ 90°) normally assumed at lower extensions. These results provide the first experimental evidence that S-DNA has substantially inclined base pairs relative to those of the standard (Watson-Crick) B-DNA conformation.
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Affiliation(s)
- Adam S. Backer
- Sandia National Laboratories, New Mexico, P.O. Box 5800, Albuquerque, NM 87185-1413, USA
- Corresponding author. (A.S.Ba.); (E.J.G.P.)
| | - Andreas S. Biebricher
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
| | - Graeme A. King
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
| | - Gijs J. L. Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
| | - Erwin J. G. Peterman
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, Netherlands
- Corresponding author. (A.S.Ba.); (E.J.G.P.)
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46
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Newton MD, Taylor BJ, Driessen RPC, Roos L, Cvetesic N, Allyjaun S, Lenhard B, Cuomo ME, Rueda DS. DNA stretching induces Cas9 off-target activity. Nat Struct Mol Biol 2019; 26:185-192. [PMID: 30804513 PMCID: PMC7613072 DOI: 10.1038/s41594-019-0188-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 12/24/2022]
Abstract
CRISPR/Cas9 is a powerful genome-editing tool, but spurious off-target edits present a barrier to therapeutic applications. To understand how CRISPR/Cas9 discriminates between on-targets and off-targets, we have developed a single-molecule assay combining optical tweezers with fluorescence to monitor binding to λ-DNA. At low forces, the Streptococcus pyogenes Cas9 complex binds and cleaves DNA specifically. At higher forces, numerous off-target binding events appear repeatedly at the same off-target sites in a guide-RNA-sequence-dependent manner, driven by the mechanical distortion of the DNA. Using single-molecule Förster resonance energy transfer (smFRET) and cleavage assays, we show that DNA bubbles induce off-target binding and cleavage at these sites, even with ten mismatches, as well as at previously identified in vivo off-targets. We propose that duplex DNA destabilization during cellular processes (for example, transcription, replication, etc.) can expose these cryptic off-target sites to Cas9 activity, highlighting the need for improved off-target prediction algorithms.
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Affiliation(s)
- Matthew D Newton
- Molecular Virology, Department of Medicine, Imperial College London, London, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK
| | | | | | - Leonie Roos
- Computational Regulatory Genomics, MRC-London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Nevena Cvetesic
- Computational Regulatory Genomics, MRC-London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Shenaz Allyjaun
- Molecular Virology, Department of Medicine, Imperial College London, London, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC-London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - David S Rueda
- Molecular Virology, Department of Medicine, Imperial College London, London, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK.
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47
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Cristofalo M, Kovari D, Corti R, Salerno D, Cassina V, Dunlap D, Mantegazza F. Nanomechanics of Diaminopurine-Substituted DNA. Biophys J 2019; 116:760-771. [PMID: 30795872 DOI: 10.1016/j.bpj.2019.01.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 10/27/2022] Open
Abstract
2,6-diaminopurine (DAP) is a nucleobase analog of adenine. When incorporated into double-stranded DNA (dsDNA), it forms three hydrogen bonds with thymine. Rare in nature, DAP substitution alters the physical characteristics of a DNA molecule without sacrificing sequence specificity. Here, we show that in addition to stabilizing double-strand hybridization, DAP substitution also changes the mechanical and conformational properties of dsDNA. Thermal melting experiments reveal that DAP substitution raises melting temperatures without diminishing sequence-dependent effects. Using a combination of atomic force microscopy (AFM), magnetic tweezer (MT) nanomechanical assays, and circular dichroism spectroscopy, we demonstrate that DAP substitution increases the flexural rigidity of dsDNA yet also facilitates conformational shifts, which manifest as changes in molecule length. DAP substitution increases both the static and dynamic persistence length of DNA (measured by AFM and MT, respectively). In the static case (AFM), in which tension is not applied to the molecule, the contour length of DAP-DNA appears shorter than wild-type (WT)-DNA; under tension (MT), they have similar dynamic contour lengths. At tensions above 60 pN, WT-DNA undergoes characteristic overstretching because of strand separation (tension-induced melting) and spontaneous adoption of a conformation termed S-DNA. Cyclic overstretching and relaxation of WT-DNA at near-zero loading rates typically yields hysteresis, indicative of tension-induced melting; conversely, cyclic stretching of DAP-DNA showed little or no hysteresis, consistent with the adoption of the S-form, similar to what has been reported for GC-rich sequences. However, DAP-DNA overstretching is distinct from GC-rich overstretching in that it happens at a significantly lower tension. In physiological salt conditions, evenly mixed AT/GC DNA typically overstretches around 60 pN. GC-rich sequences overstretch at similar if not slightly higher tensions. Here, we show that DAP-DNA overstretches at 52 pN. In summary, DAP substitution decreases the overall stability of the B-form double helix, biasing toward non-B-form DNA helix conformations at zero tension and facilitating the B-to-S transition at high tension.
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Affiliation(s)
- Matteo Cristofalo
- School of Medicine and Surgery, Università di Milano-Bicocca, Monza (MB), Italy
| | - Daniel Kovari
- Department of Physics, Emory University, Atlanta, Georgia
| | - Roberta Corti
- School of Medicine and Surgery, Università di Milano-Bicocca, Monza (MB), Italy
| | - Domenico Salerno
- School of Medicine and Surgery, Università di Milano-Bicocca, Monza (MB), Italy.
| | - Valeria Cassina
- School of Medicine and Surgery, Università di Milano-Bicocca, Monza (MB), Italy
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, Georgia.
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48
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Transcription factor regulation of RNA polymerase's torque generation capacity. Proc Natl Acad Sci U S A 2019; 116:2583-2588. [PMID: 30635423 DOI: 10.1073/pnas.1807031116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During transcription, RNA polymerase (RNAP) supercoils DNA as it translocates. The resulting torsional stress in DNA can accumulate and, in the absence of regulatory mechanisms, becomes a barrier to RNAP elongation, causing RNAP stalling, backtracking, and transcriptional arrest. Here we investigate whether and how a transcription factor may regulate both torque-induced Escherichia coli RNAP stalling and the torque generation capacity of RNAP. Using a unique real-time angular optical trapping assay, we found that RNAP working against a resisting torque was highly prone to extensive backtracking. We then investigated transcription in the presence of GreB, a transcription factor known to rescue RNAP from the backtracked state. We found that GreB greatly suppressed RNAP backtracking and remarkably increased the torque that RNAP was able to generate by 65%, from 11.2 pN⋅nm to 18.5 pN·nm. Variance analysis of the real-time positional trajectories of RNAP after a stall revealed the kinetic parameters of backtracking and GreB rescue. These results demonstrate that backtracking is the primary mechanism by which torsional stress limits transcription and that the transcription factor GreB effectively enhances the torsional capacity of RNAP. These findings suggest a broader role for transcription factors in regulating RNAP functionality and elongation.
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49
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Zhang C, Fu H, Yang Y, Zhou E, Tan Z, You H, Zhang X. The Mechanical Properties of RNA-DNA Hybrid Duplex Stretched by Magnetic Tweezers. Biophys J 2018; 116:196-204. [PMID: 30635125 DOI: 10.1016/j.bpj.2018.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/25/2022] Open
Abstract
RNA can anneal to its DNA template to generate an RNA-DNA hybrid (RDH) duplex and a displaced DNA strand, termed R-loop. RDH duplex occupies up to 5% of the mammalian genome and plays important roles in many biological processes. The functions of RDH duplex are affected by its mechanical properties, including the elasticity and the conformation transitions. The mechanical properties of RDH duplex, however, are still unclear. In this work, we studied the mechanical properties of RDH duplex using magnetic tweezers in comparison with those of DNA and RNA duplexes with the same sequences. We report that the contour length of RDH duplex is ∼0.30 nm/bp, and the stretching modulus of RDH duplex is ∼660 pN, neither of which is sensitive to NaCl concentration. The persistence length of RDH duplex depends on NaCl concentration, decreasing from ∼63 nm at 1 mM NaCl to ∼49 nm at 500 mM NaCl. Under high tension of ∼60 pN, the end-opened RDH duplex undergoes two distinct overstretching transitions; at high salt in which the basepairs are stable, it undergoes the nonhysteretic transition, leading to a basepaired elongated structure, whereas at low salt, it undergoes a hysteretic peeling transition, leading to the single-stranded DNA strand under force and the single-stranded RNA strand coils. The peeled RDH is difficult to reanneal back to the duplex conformation, which may be due to the secondary structures formed in the coiled single-stranded RNA strand. These results help us understand the full picture of the structures and mechanical properties of nucleic acid duplexes in solution and provide a baseline for studying the interaction of RDH with proteins at the single-molecule level.
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Affiliation(s)
- Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Yajun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Erchi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
| | - Zhijie Tan
- School of Physics and Technology, Wuhan University, Wuhan, China
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinghua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China.
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50
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Yu M, Le S, Efremov AK, Zeng X, Bershadsky A, Yan J. Effects of Mechanical Stimuli on Profilin- and Formin-Mediated Actin Polymerization. NANO LETTERS 2018; 18:5239-5247. [PMID: 29976069 DOI: 10.1021/acs.nanolett.8b02211] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Self-assembling actin filaments not only form the basis of the cytoskeleton network in cells but also are utilized as nanosized building blocks to make novel active matter in which the dynamic polymerization and depolymerization of actin filaments play a key role. Formins belong to a main family of actin nucleation factors that bind to the barbed end of actin filaments and regulate actin polymerization through an interaction with profilin. Due to actomyosin contractility and relative rotation between formin and actin filaments, formin-dependent actin polymerization is subject to force and rotation constraints. However, it remains unclear how force and rotation constraints affect formin-dependent actin polymerization in the presence of profilin. Here, we show that for rotation-unconstrained actin filaments, elongation is accelerated by both force and profilin. The combined effect leads to surprisingly fast actin elongation that can approach the diffusion-limited rate at forces of a few piconewtons. The elongation of rotation-constrained filaments is also accelerated by profilin but is insensitive to applied force. We show that FH2, the main actin binding domain, plays the primary mechanosensing role. Together, the findings not only significantly advance our understanding of the mechanochemical regulation of formin-mediated actin polymerization in cells but also can potentially be utilized to make novel actin-based active matter.
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Affiliation(s)
- Miao Yu
- Mechanobiology Institute, National University of Singapore , Singapore 117411
- Department of Physics , National University of Singapore , Singapore 117542
| | - Shimin Le
- Mechanobiology Institute, National University of Singapore , Singapore 117411
- Department of Physics , National University of Singapore , Singapore 117542
| | - Artem K Efremov
- Mechanobiology Institute, National University of Singapore , Singapore 117411
- Centre for Bioimaging Sciences , National University of Singapore , Singapore 117546
| | - Xiangjun Zeng
- Department of Physics , National University of Singapore , Singapore 117542
| | - Alexander Bershadsky
- Mechanobiology Institute, National University of Singapore , Singapore 117411
- Department of Molecular Cell Biology , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore , Singapore 117411
- Department of Physics , National University of Singapore , Singapore 117542
- Centre for Bioimaging Sciences , National University of Singapore , Singapore 117546
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