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McCauley MJ, Joshi J, Becker N, Hu Q, Botuyan MV, Rouzina I, Mer G, James Maher L, Williams MC. Quantifying ATP-Independent Nucleosome Chaperone Activity with Single-Molecule Methods. Methods Mol Biol 2024; 2694:29-55. [PMID: 37823998 DOI: 10.1007/978-1-0716-3377-9_2] [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] [Indexed: 10/13/2023]
Abstract
The dynamics of histone-DNA interactions govern chromosome organization and regulates the processes of transcription, replication, and repair. Accurate measurements of the energies and the kinetics of DNA binding to component histones of the nucleosome under a variety of conditions are essential to understand these processes at the molecular level. To accomplish this, we employ three specific single-molecule techniques: force disruption (FD) with optical tweezers, confocal imaging (CI) in a combined fluorescence plus optical trap, and survival probability (SP) measurements of disrupted and reformed nucleosomes. Short arrays of positioned nucleosomes serve as a template for study, facilitating rapid quantification of kinetic parameters. These arrays are then exposed to FACT (FAcilitates Chromatin Transcription), a non-ATP-driven heterodimeric nuclear chaperone known to both disrupt and tether histones during transcription. FACT binding drives off the outer wrap of DNA and destabilizes the histone-DNA interactions of the inner wrap as well. This reorganization is driven by two key domains with distinct function. FD experiments show the SPT16 MD domain stabilizes DNA-histone contacts, while the HMGB box of SSRP1 binds DNA, destabilizing the nucleosome. Surprisingly, CI experiments do not show tethering of disrupted histones, but increased rates of histone release from the DNA. SI experiments resolve this, showing that the two active domains of FACT combine to chaperone nucleosome reassembly after the timely release of force. These combinations of single-molecule approaches show FACT is a true nucleosome catalyst, lowering the barrier to both disruption and reformation.
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Affiliation(s)
| | - Joha Joshi
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nicole Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA, USA.
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2
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Guo M, Lin Z, Zhai C, Chen Y, Zhou X, Chai Z, Guo T, Hu C. Deep learning for precise axial localization of trapped microspheres in reflective optical systems. OPTICS EXPRESS 2023; 31:12397-12409. [PMID: 37157400 DOI: 10.1364/oe.487866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
High-precision axial localization measurement is an important part of micro-nanometer optical measurement, but there have been issues such as low calibration efficiency, poor accuracy, and cumbersome measurement, especially in reflected light illumination systems, where the lack of clarity of imaging details leads to the low accuracy of commonly used methods. Herein, we develop a trained residual neural network coupled with a convenient data acquisition strategy to address this challenge. Our method improves the axial localization precision of microspheres in both reflective illumination systems and transmission illumination systems. Using this new localization method, the reference position of the trapped microsphere can be extracted from the identification results, namely the "positioning point" among the experimental groups. This point relies on the unique signal characteristics of each sample measurement, eliminates systematic repeatability errors when performing identification across samples, and improves the localization precision of different samples. This method has been verified on both transmission and reflected illumination optical tweezers platforms. We will bring greater convenience to measurements in solution environments and will provide higher-order guarantees for force spectroscopy measurements in scenarios such as microsphere-based super-resolution microscopy and the surface mechanical properties of adherent flexible materials and cells.
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3
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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4
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From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers. Essays Biochem 2021; 65:129-142. [PMID: 33438724 DOI: 10.1042/ebc20200024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
Single-molecule manipulation with optical tweezers has uncovered macromolecular behaviour hidden to other experimental techniques. Recent instrumental improvements have made it possible to expand the range of systems accessible to optical tweezers. Beyond focusing on the folding and structural changes of isolated single molecules, optical tweezers studies have evolved into unraveling the basic principles of complex molecular processes such as co-translational folding on the ribosome, kinase activation dynamics, ligand-receptor binding, chaperone-assisted protein folding, and even dynamics of intrinsically disordered proteins (IDPs). In this mini-review, we illustrate the methodological principles of optical tweezers before highlighting recent advances in studying complex protein conformational dynamics - from protein synthesis to physiological function - as well as emerging future issues that are beginning to be addressed with novel approaches.
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Bustamante CJ, Chemla YR, Liu S, Wang MD. Optical tweezers in single-molecule biophysics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:25. [PMID: 34849486 PMCID: PMC8629167 DOI: 10.1038/s43586-021-00021-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.
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Affiliation(s)
- Carlos J. Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy NanoScience Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
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Inukai R, Takao H, Shimokawa F, Terao K. Capture and elongation of single chromosomal DNA molecules using optically driven microchopsticks. BIOMICROFLUIDICS 2020; 14:044114. [PMID: 32831987 PMCID: PMC7428348 DOI: 10.1063/5.0017727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/05/2020] [Indexed: 05/11/2023]
Abstract
DNA analysis based on the observation of single DNA molecules has been a key technology in molecular biology. Several techniques for manipulating single DNA molecules have been proposed for this purpose; however, these techniques have limits on the manipulatable DNA. To overcome this, we demonstrate a method of DNA manipulation using microstructures captured by optical tweezers that allow the manipulation of a chromosomal DNA molecule. For proper DNA handling, we developed microstructures analogous to chopsticks to capture and elongate single DNA molecules under an optical microscope. Two microstructures (i.e., microchopsticks) were captured by two focused laser beams to pinch a single yeast chromosomal DNA molecule between them and thereby manipulate it. The experiments demonstrated successful DNA manipulation and revealed that the size and geometry of the microchopsticks are important factors for effective DNA handling. This technique allows a high degree of freedom in handling single DNA molecules, potentially leading to applications in the study of chromosomal DNA.
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Affiliation(s)
- Ryo Inukai
- Department of Intelligent Mechanical Systems Engineering, Kagawa University, Takamatsu 761-0396, Japan
| | | | | | - Kyohei Terao
- Author to whom correspondence should be addressed:. Tel.: +81 (87) 864-2346
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7
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Choudhary D, Mossa A, Jadhav M, Cecconi C. Bio-Molecular Applications of Recent Developments in Optical Tweezers. Biomolecules 2019; 9:E23. [PMID: 30641944 PMCID: PMC6359149 DOI: 10.3390/biom9010023] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 12/17/2022] Open
Abstract
In the past three decades, the ability to optically manipulate biomolecules has spurred a new era of medical and biophysical research. Optical tweezers (OT) have enabled experimenters to trap, sort, and probe cells, as well as discern the structural dynamics of proteins and nucleic acids at single molecule level. The steady improvement in OT's resolving power has progressively pushed the envelope of their applications; there are, however, some inherent limitations that are prompting researchers to look for alternatives to the conventional techniques. To begin with, OT are restricted by their one-dimensional approach, which makes it difficult to conjure an exhaustive three-dimensional picture of biological systems. The high-intensity trapping laser can damage biological samples, a fact that restricts the feasibility of in vivo applications. Finally, direct manipulation of biological matter at nanometer scale remains a significant challenge for conventional OT. A significant amount of literature has been dedicated in the last 10 years to address the aforementioned shortcomings. Innovations in laser technology and advances in various other spheres of applied physics have been capitalized upon to evolve the next generation OT systems. In this review, we elucidate a few of these developments, with particular focus on their biological applications. The manipulation of nanoscopic objects has been achieved by means of plasmonic optical tweezers (POT), which utilize localized surface plasmons to generate optical traps with enhanced trapping potential, and photonic crystal optical tweezers (PhC OT), which attain the same goal by employing different photonic crystal geometries. Femtosecond optical tweezers (fs OT), constructed by replacing the continuous wave (cw) laser source with a femtosecond laser, promise to greatly reduce the damage to living samples. Finally, one way to transcend the one-dimensional nature of the data gained by OT is to couple them to the other large family of single molecule tools, i.e., fluorescence-based imaging techniques. We discuss the distinct advantages of the aforementioned techniques as well as the alternative experimental perspective they provide in comparison to conventional OT.
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Affiliation(s)
- Dhawal Choudhary
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy.
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.
| | - Alessandro Mossa
- Istituto Statale di Istruzione Superiore "Leonardo da Vinci", Via del Terzolle 91, 50127 Firenze, Italy.
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, Via Giovanni Sansone 1, 50019 Sesto Fiorentino, Italy.
| | - Milind Jadhav
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy.
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy.
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.
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8
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Ray S, Chauvier A, Walter NG. Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics. RNA Biol 2018; 16:1077-1085. [PMID: 30328748 DOI: 10.1080/15476286.2018.1536594] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Riboswitches are dynamic RNA motifs that are mostly embedded in the 5'-untranslated regions of bacterial mRNAs, where they regulate gene expression transcriptionally or translationally by undergoing conformational changes upon binding of a small metabolite or ion. Due to the small size of typical ligands, relatively little free energy is available from ligand binding to overcome the often high energetic barrier of reshaping RNA structure. Instead, most riboswitches appear to take advantage of the directional and hierarchical folding of RNA by employing the ligand as a structural 'linchpin' to adjust the kinetic partitioning between alternate folds. In this model, even small, local structural and kinetic effects of ligand binding can cascade into global RNA conformational changes affecting gene expression. Single-molecule (SM) microscopy tools are uniquely suited to study such kinetically controlled RNA folding since they avoid the ensemble averaging of bulk techniques that loses sight of unsynchronized, transient, and/or multi-state kinetic behavior. This review summarizes how SM methods have begun to unravel riboswitch-mediated gene regulation.
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Affiliation(s)
- Sujay Ray
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Adrien Chauvier
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Nils G Walter
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
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9
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Chen J, Li K, Li X. Influence of permittivity on gradient force exerted on Mie spheres. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2018; 35:553-560. [PMID: 29603937 DOI: 10.1364/josaa.35.000553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
In optical trapping, whether a particle could be stably trapped into the focus region greatly depends on the strength of the gradient force. Individual theoretical study on gradient force exerted on a Mie particle is rare because the mathematical separation of the gradient force and the scattering force in the Mie regime is difficult. Based on the recent forces separation work by Du et al. [Sci. Rep.7, 18042 (2017)SRCEC32045-232210.1038/s41598-017-17874-1], we investigate the influence of permittivity (an important macroscopic physical quantity) on the gradient force exerted on a Mie particle by cooperating numerical calculation using fast Fourier transform and analytical analysis using multipole expansion. It is revealed that gradient forces exerted on small spheres are mainly determined by the electric dipole moment except for certain permittivity with which the real part of polarizability of the electric dipole approaches zero, and gradient forces exerted on larger spheres are complex because of the superposition of the multipole moments. The classification of permittivity corresponding to different varying tendencies of gradient forces exerted on small spheres or larger Mie particles are illustrated. Absorption of particles favors the trapping of small spheres by gradient force, while it is bad for the trapping of larger particles. Moreover, the absolute values of the maximal gradient forces exerted on larger Mie particles decline greatly versus the varied imaginary part of permittivity. This work provides elaborate investigation on the different varying tendencies of gradient forces versus permittivity, which favors more accurate and free optical trapping.
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10
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Zhao D, Liu S, Gao Y. Single-molecule manipulation and detection. Acta Biochim Biophys Sin (Shanghai) 2018; 50:231-237. [PMID: 29377975 DOI: 10.1093/abbs/gmx146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/23/2017] [Indexed: 11/13/2022] Open
Abstract
Compared to conventional ensemble methods, studying macromolecules at single-molecule level can reveal extraordinary clear and even surprising views for a biological reaction. In the past 20 years, single-molecule techniques have been undergoing a very rapid development, and these cutting edge technologies have revolutionized the biological research by facilitating single-molecule manipulation and detection. Here we give a brief review about these advanced techniques, including optical tweezers, magnetic tweezers, atomic force microscopy (AFM), hydrodynamic flow-stretching assay, and single-molecule fluorescence resonance energy transfer (smFRET). We are trying to describe their basic principles and provide a few examples of applications for each technique. This review aims to give a rather introductory survey of single-molecule techniques for audiences with biological or biophysical background.
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Affiliation(s)
- Deyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Siyun Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Gao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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11
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Chung HS. Transition Path Times Measured by Single-Molecule Spectroscopy. J Mol Biol 2017; 430:409-423. [PMID: 28551335 DOI: 10.1016/j.jmb.2017.05.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/18/2017] [Indexed: 11/28/2022]
Abstract
The transition path is a tiny fraction of a molecular trajectory during which the free-energy barrier is crossed. It is a single-molecule property and contains all mechanistic information of folding processes of biomolecules such as proteins and nucleic acids. However, the transition path has been difficult to probe because it is short and rarely visited when transitions actually occur. Recent technical advances in single-molecule spectroscopy have made it possible to directly probe transition paths, which has opened up new theoretical and experimental approaches to investigating folding mechanisms. This article reviews recent single-molecule fluorescence and force spectroscopic measurements of transition path times and their connection to both theory and simulations.
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Affiliation(s)
- Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Dr., Bethesda, MD 20892-0520, USA.
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12
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Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of λ-DNA substrates for single-molecule studies. Sci Rep 2017; 7:2071. [PMID: 28522818 PMCID: PMC5437064 DOI: 10.1038/s41598-017-01984-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA. A set of PCR cassettes facilitates the introduction of recombinant DNA sequences into the λ-phage genome with 90-100% yield. Extrahelical structures and chemical modifications can be inserted at user-defined sites via an improved nicking enzyme-based strategy. As a proof-of-principle, we explore the interactions of S. cerevisiae Proliferating Cell Nuclear Antigen (yPCNA) with modified DNA sequences and structures incorporated within λ-DNA. Our results demonstrate that S. cerevisiae Replication Factor C (yRFC) can load yPCNA onto 5'-ssDNA flaps, (CAG)13 triplet repeats, and homoduplex DNA. However, yPCNA remains trapped on the (CAG)13 structure, confirming a proposed mechanism for triplet repeat expansion. We anticipate that this molecular toolbox will be broadly useful for other studies that require site-specific modification of long DNA substrates.
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Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Armando de la Torre
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Andrew A Leal
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
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13
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Whitley K, Comstock M, Chemla Y. High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy. Methods Enzymol 2017; 582:137-169. [PMID: 28062033 PMCID: PMC5540136 DOI: 10.1016/bs.mie.2016.10.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We describe the design, construction, and application of an instrument combining dual-trap, high-resolution optical tweezers and a confocal microscope. This hybrid instrument allows nanomechanical manipulation and measurement simultaneously with single-molecule fluorescence detection. We present the general design principles that overcome the challenges of maximizing optical trap resolution while maintaining single-molecule fluorescence sensitivity, and provide details on the construction and alignment of the instrument. This powerful new tool is just beginning to be applied to biological problems. We present step-by-step instructions on an application of this technique that highlights the instrument's capabilities, detecting conformational dynamics in a nucleic acid-processing enzyme.
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Affiliation(s)
- K.D. Whitley
- University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - M.J. Comstock
- Michigan State University, East Lansing, MI, United States
| | - Y.R. Chemla
- University of Illinois at Urbana–Champaign, Urbana, IL, United States,Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Urbana, IL, United States,Corresponding author:
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14
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Rodríguez-Sevilla P, Labrador-Páez L, Jaque D, Haro-González P. Optical trapping for biosensing: materials and applications. J Mater Chem B 2017; 5:9085-9101. [DOI: 10.1039/c7tb01921a] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optical trapping has been evidence as a very powerful tool for the manipulation and study of biological entities. This review explains the main concepts regarding the use of optical trapping for biosensing, focusing its attention to those applications involving the manipulation of particles which are used as handles, force transducers and sensors.
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Affiliation(s)
- P. Rodríguez-Sevilla
- Fluorescence Imaging Group
- Departamento de Física de Materiales
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - L. Labrador-Páez
- Fluorescence Imaging Group
- Departamento de Física de Materiales
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - D. Jaque
- Fluorescence Imaging Group
- Departamento de Física de Materiales
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - P. Haro-González
- Fluorescence Imaging Group
- Departamento de Física de Materiales
- Universidad Autónoma de Madrid
- Madrid
- Spain
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