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Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
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Characterization of structures and molecular interactions of RNA and lipid carriers using atomic force microscopy. Adv Colloid Interface Sci 2023; 313:102855. [PMID: 36774766 DOI: 10.1016/j.cis.2023.102855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Ribonucleic acid (RNA) and lipid are essential biomolecules in many biological processes, and hold a great prospect for biomedical applications, such as gene therapy, vaccines and therapeutic drug delivery. The characterization of morphology and intra-/inter-molecular interactions of RNA and lipid molecules is critical for understanding their functioning mechanisms. Atomic force microscopy (AFM) is a sophisticated technique for characterizing biomolecules featured by its piconewton force sensitivity, sub-nanometer spatial resolution, and flexible operation conditions in both air and liquid. The goal of this review is to highlight the representative and outstanding discoveries of the characterization of RNA and lipid molecules through morphology identification, physicochemical property determination and intermolecular force measurements by AFM. The first section introduces the AFM imaging of RNA molecules to obtain high-resolution morphologies and nanostructures in air and liquid, followed by the discussion of employing AFM force spectroscopy in understanding the nanomechanical properties and intra-/inter-molecular interactions of RNA molecules, including RNA-RNA and RNA-biomolecule interactions. The second section focuses on the studies of lipid and RNA encapsulated in lipid carrier (RNA-lipid) by AFM as well as the sample preparation and factors influencing the morphology and structure of lipid/RNA-lipid complexes. Particularly, the nanomechanical properties of lipid and RNA-lipid characterized by nanomechanical imaging and force measurements are discussed. The future perspectives and remaining challenges on the characterization of RNA and lipid offered by the versatile AFM techniques are also discussed. This review provides useful insights on the characterization of RNA and lipids nanostructures along with their molecular interactions, and also enlightens the application of AFM techniques in investigating a broad variety of biomolecules.
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Kinetics of DNA strand transfer between polymerase and proofreading exonuclease active sites regulates error correction during high-fidelity replication. J Biol Chem 2022; 299:102744. [PMID: 36436560 PMCID: PMC9800556 DOI: 10.1016/j.jbc.2022.102744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
We show that T7 DNA polymerase (pol) and exonuclease (exo) domains contribute to selective error correction during DNA replication by regulating bidirectional strand transfer between the two active sites. To explore the kinetic basis for selective removal of mismatches, we used a fluorescent cytosine analog (1,3-diaza-2-oxophenoxazine) to monitor the kinetics of DNA transfer between the exo and pol sites. We globally fit stopped-flow fluorescence and base excision kinetic data and compared results obtained with ssDNA versus duplex DNA to resolve how DNA transfer governs exo specificity. We performed parallel studies using hydrolysis-resistant phosphorothioate oligonucleotides to monitor DNA transfer to the exo site without hydrolysis. ssDNA binds to the exo site at the diffusion limit (109 M-1 s-1, Kd = 40 nM) followed by fast hydrolysis of the 3'-terminal nucleotide (>5000 s-1). Analysis using duplex DNA with a 3'-terminal mismatch or a buried mismatch exposed a unique intermediate state between pol and exo active sites and revealed that transfer via the intermediate to the exo site is stimulated by free nucleoside triphosphates. Transfer from the exo site back to the pol site after cleavage is fast and efficient. We propose a model to explain why buried mismatches are removed faster than single 3'-terminal mismatches and thereby provide an additional opportunity for error correction. Our data provide the first comprehensive model to explain how DNA transfer from pol to exo active sites and back again after base excision allow efficient selective mismatch removal during DNA replication to improve fidelity by more than 1000-fold.
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Fu Y, Wang J, Wang Y, Sun H. Investigating the Effect of Tyrosine Kinase Inhibitors on the Interaction between Human Serum Albumin by Atomic Force Microscopy. Biomolecules 2022; 12:biom12060819. [PMID: 35740944 PMCID: PMC9221072 DOI: 10.3390/biom12060819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
It is important for elucidating the regulation mechanism of life activities, as well as for the prevention, diagnosis, and drug design of diseases, to study protein–protein interactions (PPIs). Here, we investigated the interactions of human serum albumin (HSA) in the presence of tyrosine kinase inhibitors (TKIs: imatinib, nilotinib, dasatinib, bosutinib, and ponatinib) using atomic force microscopy (AFM). The distribution of rupture events including the specific interaction force Fi and the non-specific interaction force F0 between HSA pairs was analyzed. Based on the force measurements, Fi and F0 between HSA pairs in the control experiment were calculated to be 47 ± 1.5 and 116.1 ± 1.3 pN. However, Fi was significantly decreased in TKIs, while F0 was slightly decreased. By measuring the rupture forces at various loading rates and according to the Bell equation, the kinetic parameters of the complexes were investigated in greater detail. Molecular docking was used as a complementary means by which to explore the force of this effect. The whole measurements indicated that TKIs influenced PPIs in a variety of ways, among which hydrogen bonding and hydrophobic interactions were the most important. In conclusion, these outcomes give us a better insight into the mechanisms of PPIs when there are exogenous compounds present as well as in different liquid environments.
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Affiliation(s)
- Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (Y.F.); (H.S.)
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (Y.F.); (H.S.)
- Correspondence:
| | - Yan Wang
- Key Laboratory of Drug Design, College of Chemistry and Chemical Engineering, Huangshan University, Huangshan 245041, China;
| | - Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China; (Y.F.); (H.S.)
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Yin H, Gavriliuc M, Lin R, Xu S, Wang Y. Modulation and Visualization of EF-G Power Stroke During Ribosomal Translocation. Chembiochem 2019; 20:2927-2935. [PMID: 31194278 PMCID: PMC6888950 DOI: 10.1002/cbic.201900276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 11/30/2022]
Abstract
During ribosome translocation, the elongation factor EF‐G undergoes large conformational change while maintaining its contact with the moving tRNA. We previously measured a power stroke accompanying EF‐G catalysis, which was consistent with structural studies. However, the role of power stroke in translocation fidelity remains unclear. Here, we report quantitative measurements of the power strokes of structurally modified EF‐Gs by using two different techniques and reveal the correlation between power stroke and translocation efficiency and fidelity. We discovered that the reduced power stroke only lowered the percentage of translocation but did not introduce translocation error. The established force ‐structure–function correlation for EF‐G indicates that power stroke drives ribosomal translocation, but the mRNA reading frame is probably maintained by ribosome itself. Furthermore, the microscope detection method reported here can be simply implemented for other biochemical applications.
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Affiliation(s)
- Heng Yin
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Miriam Gavriliuc
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Ran Lin
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
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Schön P. Atomic force microscopy of RNA: State of the art and recent advancements. Semin Cell Dev Biol 2017; 73:209-219. [PMID: 28843977 DOI: 10.1016/j.semcdb.2017.08.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022]
Abstract
The atomic force microscope (AFM) has become a powerful tool for the visualization, probing and manipulation of RNA at the single molecule level. AFM measurements can be carried out in buffer solution in a physiological medium, which is crucial to study the structure and function of biomolecules, also allowing studying them at work. Imaging the specimen in its native state is a great advantage compared to other high resolution methods such as electron microscopy and X-ray diffraction. There is no need to stain, freeze or crystallize biological samples. Moreover, compared to NMR spectroscopy for instance, for AFM studies the size of the biomolecules is not limiting. Consequently the AFM allows one also to investigate larger RNA molecules. In particular, structural studies of nucleic acids and assemblies thereof, have been carried out by AFM routinely including ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. These are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In particular by AFM unique information can be obtained on these RNA based assemblies. Moreover, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. Important applications include the detection and quantification of RNA in biological samples. A selection of recent highlights and breakthroughs will be provided related to structural and functional studies by AFM. The main intention of this short review to provide the reader with a flavor of what AFM is able to contribute to RNA research and engineering.
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Affiliation(s)
- Peter Schön
- NanoBioInterface Research Group, Research Center Design and Technology, Saxion University of Applied Sciences, 7500 KB Enschede, The Netherlands; Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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Nick TA, de Oliveira TE, Pilat DW, Spenkuch F, Butt HJ, Helm M, Netz PA, Berger R. Stability of a Split Streptomycin Binding Aptamer. J Phys Chem B 2016; 120:6479-89. [PMID: 27281393 DOI: 10.1021/acs.jpcb.6b02440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Thomas A Nick
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
| | - Tiago E de Oliveira
- Instituto de Química, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Dominik W Pilat
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
| | - Felix Spenkuch
- Johannes Gutenberg Universität Mainz , Institute of Pharmacy and Biochemistry, 55128 Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
| | - Mark Helm
- Johannes Gutenberg Universität Mainz , Institute of Pharmacy and Biochemistry, 55128 Mainz, Germany
| | - Paulo A Netz
- Instituto de Química, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research , 55128 Mainz, Germany
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8
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Schön P. Imaging and force probing RNA by atomic force microscopy. Methods 2016; 103:25-33. [PMID: 27222101 DOI: 10.1016/j.ymeth.2016.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 12/12/2022] Open
Abstract
In the past 30years, the atomic force microscope (AFM) has become a true enabling platform in the life sciences opening entire novel avenues for structural and dynamic studies of biological systems. It enables visualization, probing and manipulation across the length scales, from single molecules to living cells in buffer solution under physiological conditions without the need for labeling or staining of the specimen. In particular, for structural studies of nucleic acids and assemblies thereof, the AFM has matured into a routinely used tool providing nanometer spatial resolution. This includes ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. By AFM unique information can be obtained on RNA based assemblies which are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In addition, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review first the basic functioning principles of commonly used AFM modes including AFM based force spectroscopy will be briefly described. Next a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. The main intention of this short review to give the reader a flavor of what AFM contributes to RNA research and engineering.
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Affiliation(s)
- Peter Schön
- NanoBioInterface Chair, Research Center Design and Technology, Saxion University of Applied Sciences, 7500 KB Enschede, The Netherlands; Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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9
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Yao L, Li Y, Tsai TW, Xu S, Wang Y. Noninvasive Measurement of the Mechanical Force Generated by Motor Protein EF-G during Ribosome Translocation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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10
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Yao L, Li Y, Tsai TW, Xu S, Wang Y. Noninvasive Measurement of the Mechanical Force Generated by Motor Protein EF-G during Ribosome Translocation. Angew Chem Int Ed Engl 2013; 52:14041-4. [DOI: 10.1002/anie.201307419] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 09/23/2013] [Indexed: 01/13/2023]
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11
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Jung YJ, Albrecht JA, Kwak JW, Park JW. Direct quantitative analysis of HCV RNA by atomic force microscopy without labeling or amplification. Nucleic Acids Res 2012; 40:11728-36. [PMID: 23074195 PMCID: PMC3526272 DOI: 10.1093/nar/gks953] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Force-based atomic force microscopy (AFM) was used to detect HCV (hepatitis C virus) RNA directly and to quantitatively analyse it without the need for reverse transcription or amplification. Capture and detection DNA probes were designed. The former was spotted onto a substrate with a conventional microarrayer, and the latter was immobilized on an AFM probe. To control the spacing between the immobilized DNAs on the surface, dendron self-assembly was employed. Force-distance curves showed that the mean force of the specific unbinding events was 32 ± 5 pN, and the hydrodynamic distance of the captured RNA was 30-60 nm. Adhesion force maps were generated with criteria including the mean force value, probability of obtaining the specific curves and hydrodynamic distance. The maps for the samples whose concentrations ranged from 0.76 fM to 6.0 fM showed that cluster number has a linear relationship with RNA concentration, while the difference between the observed number and the calculated one increased at low concentrations. Because the detection limit is expected to be enhanced by a factor of 10 000 when a spot of 1 micron diameter is employed, it is believed that HCV RNA of a few copy numbers can be detected by the use of AFM.
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Affiliation(s)
- Yu Jin Jung
- Nanogea Corporation, 6162 Bristol Parkway, Culver City, CA 90230, USA.
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12
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Force spectroscopy 101: how to design, perform, and analyze an AFM-based single molecule force spectroscopy experiment. Curr Opin Chem Biol 2011; 15:710-8. [DOI: 10.1016/j.cbpa.2011.07.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/17/2022]
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13
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Heus HA, Puchner EM, van Vugt-Jonker AJ, Zimmermann JL, Gaub HE. Atomic force microscope-based single-molecule force spectroscopy of RNA unfolding. Anal Biochem 2011; 414:1-6. [DOI: 10.1016/j.ab.2011.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 01/28/2023]
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Brampton C, Wahab O, Batchelor MR, Allen S, Williams PM. Biomembrane force probe investigation of RNA dissociation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:247-57. [DOI: 10.1007/s00249-010-0642-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/13/2010] [Accepted: 11/10/2010] [Indexed: 01/26/2023]
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Abstract
Understanding how RNA folds and what causes it to unfold has become more important as knowledge of the diverse functions of RNA has increased. Here we review the contributions of single-molecule experiments to providing answers to questions such as: How much energy is required to unfold a secondary or tertiary structure? How fast is the process? How do helicases unwind double helices? Are the unwinding activities of RNA-dependent RNA polymerases and of ribosomes different from other helicases? We discuss the use of optical tweezers to monitor the unfolding activities of helicases, polymerases, and ribosomes, and to apply force to unfold RNAs directly. We also review the applications of fluorescence and fluorescence resonance energy transfer to measure RNA dynamics.
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Affiliation(s)
- Pan T X Li
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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16
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Noy A. Strength in numbers: probing and understanding intermolecular bonding with chemical force microscopy. SCANNING 2008; 30:96-105. [PMID: 18220259 DOI: 10.1002/sca.20082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Scanning probe microscopy (SPM) provided researchers with a simple, intuitive, and versatile tool for probing intermolecular interactions using SPM probes functionalized with distinct chemical species. Chemical force microscopy (CFM) was developed as a way to probe and map these interactions in a rational and systematic way. But does the rupture strength of a bond measured in these experiments provide the definitive and useful information about the interaction? The answer to this question is closely linked to understanding the fundamental physics of bond rupture under an external loading force. Even a simple model shows that bond rupture can proceed in a variety of different regimes. I discuss the approaches for extracting quantitative information about the interaction from these experiments and show that even though the measured rupture force is almost never unique for a given bond, force spectroscopy measurements can still determine the essential interaction parameters.
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Affiliation(s)
- Aleksandr Noy
- Chemistry, Materials, Energy, and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
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17
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Functionalization of Probe Tips and Supports for Single-Molecule Recognition Force Microscopy. Top Curr Chem (Cham) 2008; 285:29-76. [DOI: 10.1007/128_2007_24] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Vilfan ID, Kamping W, van den Hout M, Candelli A, Hage S, Dekker NH. An RNA toolbox for single-molecule force spectroscopy studies. Nucleic Acids Res 2007; 35:6625-39. [PMID: 17905817 PMCID: PMC2095808 DOI: 10.1093/nar/gkm585] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/15/2007] [Accepted: 07/17/2007] [Indexed: 01/29/2023] Open
Abstract
Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNA-enzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk biochemical studies. Next, the incorporation of modified nucleotides into the RNA construct is required for its surface immobilization. In addition, RNA constructs for single-molecule studies are commonly assembled from different single-stranded RNA molecules, demanding good control of hybridization or ligation. Finally, precautions to prevent RNase- and divalent cation-dependent RNA digestion must be taken. The rather limited selection of molecular biology tools adapted to the manipulation of RNA molecules, as well as the sensitivity of RNA to degradation, make RNA construct preparation a challenging task. We briefly illustrate the types of single-molecule force spectroscopy experiments that can be performed on RNA, and then present an overview of the toolkit of molecular biology techniques at one's disposal for the assembly of such RNA constructs. Within this context, we evaluate the molecular biology protocols in terms of their effectiveness in producing long and stable RNA constructs.
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Affiliation(s)
| | | | | | | | | | - Nynke H. Dekker
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, The Netherlands
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Jung YJ, Hong BJ, Zhang W, Tendler SJB, Williams PM, Allen S, Park JW. Dendron arrays for the force-based detection of DNA hybridization events. J Am Chem Soc 2007; 129:9349-55. [PMID: 17625845 DOI: 10.1021/ja0676105] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule force measurement methods have attracted increasing interest over recent years for the development of novel approaches for biomolecular screening. However, many of these developments are currently hindered by the available biomolecule surface attachment methods, in that it is still not trivial to create surfaces and devices with highly defined surface functionality and/or uniformity. Here we offer a new approach to address such issues based on the formation of dendron arrays. Through the measurement of forces between dendron surfaces functionalized with complementary DNA oligonucleotides, we observed several unique properties of the surfaces modified via this approach. The capability to record attractive or "jump-in" forces associated with molecular binding events is one of them. Additionally, these events occur in greater than 80% of measurements, and the forces are dependent on the number of complementary DNA bases of the associating strands while being insensitive to the measurement rate. Combined with a narrow distribution of both attractive forces and unbinding forces we suggest such functionalized surfaces offer a significant advance for fast and accurate force-based studies of oligonucleotide hybridization.
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Affiliation(s)
- Yu Jin Jung
- Center for Integrated Molecular Systems, Department of Chemistry, Pohang University of Science and Technology, San 31 Hyoja-Dong, Pohang, Korea
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20
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Tinoco I, Li PTX, Bustamante C. Determination of thermodynamics and kinetics of RNA reactions by force. Q Rev Biophys 2006; 39:325-60. [PMID: 17040613 PMCID: PMC2542947 DOI: 10.1017/s0033583506004446] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA.
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Ritort F. Single-molecule experiments in biological physics: methods and applications. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2006; 18:R531-R583. [PMID: 21690856 DOI: 10.1088/0953-8984/18/32/r01] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.
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Affiliation(s)
- F Ritort
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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