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Bianco PR. Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays. Methods 2021; 204:348-360. [PMID: 34896247 PMCID: PMC9534331 DOI: 10.1016/j.ymeth.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022] Open
Abstract
There are multiple assays available that can provide insight into the biochemical mechanism of DNA helicases. For the first 22 years since their discovery, bulk-phase assays were used. These include gel-based, spectrophotometric, and spectrofluorometric assays that revealed many facets of these enzymes. From 2001, single-molecule studies have contributed additional insight into these DNA nanomachines to reveal details on energy coupling, step size, processivity as well as unique aspects of individual enzyme behavior that were masked in the averaging inherent in ensemble studies. In this review, important aspects of the study of helicases are discussed including beginning with active, nuclease-free enzyme, followed by several bulk-phase approaches that have been developed and still find widespread use today. Finally, two single-molecule approaches are discussed, and the resulting findings are related to the results obtained in bulk-phase studies.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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2
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Brosh RM, Matson SW. History of DNA Helicases. Genes (Basel) 2020; 11:genes11030255. [PMID: 32120966 PMCID: PMC7140857 DOI: 10.3390/genes11030255] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Since the discovery of the DNA double helix, there has been a fascination in understanding the molecular mechanisms and cellular processes that account for: (i) the transmission of genetic information from one generation to the next and (ii) the remarkable stability of the genome. Nucleic acid biologists have endeavored to unravel the mysteries of DNA not only to understand the processes of DNA replication, repair, recombination, and transcription but to also characterize the underlying basis of genetic diseases characterized by chromosomal instability. Perhaps unexpectedly at first, DNA helicases have arisen as a key class of enzymes to study in this latter capacity. From the first discovery of ATP-dependent DNA unwinding enzymes in the mid 1970's to the burgeoning of helicase-dependent pathways found to be prevalent in all kingdoms of life, the story of scientific discovery in helicase research is rich and informative. Over four decades after their discovery, we take this opportunity to provide a history of DNA helicases. No doubt, many chapters are left to be written. Nonetheless, at this juncture we are privileged to share our perspective on the DNA helicase field - where it has been, its current state, and where it is headed.
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Affiliation(s)
- Robert M. Brosh
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
| | - Steven W. Matson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
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3
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Schlierf M, Wang G, Chen XS, Ha T. Hexameric helicase G40P unwinds DNA in single base pair steps. eLife 2019; 8:42001. [PMID: 30688211 PMCID: PMC6370340 DOI: 10.7554/elife.42001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023] Open
Abstract
Most replicative helicases are hexameric, ring-shaped motor proteins that translocate on and unwind DNA. Despite extensive biochemical and structural investigations, how their translocation activity is utilized chemo-mechanically in DNA unwinding is poorly understood. We examined DNA unwinding by G40P, a DnaB-family helicase, using a single-molecule fluorescence assay with a single base pair resolution. The high-resolution assay revealed that G40P by itself is a very weak helicase that stalls at barriers as small as a single GC base pair and unwinds DNA with the step size of a single base pair. Binding of a single ATPγS could stall unwinding, demonstrating highly coordinated ATP hydrolysis between six identical subunits. We observed frequent slippage of the helicase, which is fully suppressed by the primase DnaG. We anticipate that these findings allow a better understanding on the fine balance of thermal fluctuation activation and energy derived from hydrolysis. Living cells store their genetic code written in molecules of DNA, with two strands of DNA twisted together to form the familiar double helix. When a cell prepares to divide, it must unwind its DNA so that the individual strands can be copied. Enzymes known as DNA helicases play a vital role in this unwinding process; yet, it is not completely clear how these enzymes move along the DNA. Schlierf et al. have now developed a new approach to see how an individual DNA helicase called G40P unwinds the DNA double helix. The experiments used a molecular ruler to measure the DNA unwinding and showed that the helicase opened the double helix one letter of genetic code at a time. Also, specific sequence of letters within the DNA molecules could slow down and stop G40P or even cause it to move backwards. DNA helicases work closely with other proteins inside cells to perform their task. DNA primases, for example, are enzymes that create the starting points for making new strands of DNA. Schlierf et al. found that the primase DnaG could also prevent G40P from moving backwards on the DNA, a new and unexpected function of DnaG. These findings contribute to an ongoing debate among researchers with partially contradictory models for how DNA helicases unwind the DNA double helix. Although originally from a virus, G40P is similar to a helicase enzyme found in bacteria. Therefore, a better understanding of this helicase may lead to new ways to stop bacteria copying their DNA, which might one day become new antibiotics to treat bacterial infections.
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Affiliation(s)
- Michael Schlierf
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Illinois, United States.,B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Ganggang Wang
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Taekjip Ha
- Physics Department and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Illinois, United States.,Howard Hughes Medical Institute, Baltimore, United States.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States.,Department of Biophysics, Johns Hopkins University, Baltimore, United States
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4
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Qian GS, Zhang TT, Zhao W, Xu JJ, Chen HY. Single-molecule imaging of telomerase activity via linear plasmon rulers. Chem Commun (Camb) 2017; 53:4710-4713. [DOI: 10.1039/c7cc00626h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A strategy for real-time monitoring of the extension of the telomerase primer based on plasmon rulers was demonstrated for the first time.
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Affiliation(s)
- Guang-Sheng Qian
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Ting-Ting Zhang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
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5
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Phelps C, Israels B, Marsh MC, von Hippel PH, Marcus AH. Using Multiorder Time-Correlation Functions (TCFs) To Elucidate Biomolecular Reaction Pathways from Microsecond Single-Molecule Fluorescence Experiments. J Phys Chem B 2016; 120:13003-13016. [PMID: 27992233 DOI: 10.1021/acs.jpcb.6b08449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in single-molecule fluorescence imaging have made it possible to perform measurements on microsecond time scales. Such experiments have the potential to reveal detailed information about the conformational changes in biological macromolecules, including the reaction pathways and dynamics of the rearrangements involved in processes, such as sequence-specific DNA "breathing" and the assembly of protein-nucleic acid complexes. Because microsecond-resolved single-molecule trajectories often involve "sparse" data, that is, they contain relatively few data points per unit time, they cannot be easily analyzed using the standard protocols that were developed for single-molecule experiments carried out with tens-of-millisecond time resolution and high "data density." Here, we describe a generalized approach, based on time-correlation functions, to obtain kinetic information from microsecond-resolved single-molecule fluorescence measurements. This approach can be used to identify short-lived intermediates that lie on reaction pathways connecting relatively long-lived reactant and product states. As a concrete illustration of the potential of this methodology for analyzing specific macromolecular systems, we accompany the theoretical presentation with the description of a specific biologically relevant example drawn from studies of reaction mechanisms of the assembly of the single-stranded DNA binding protein of the T4 bacteriophage replication complex onto a model DNA replication fork.
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Affiliation(s)
- Carey Phelps
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Brett Israels
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Morgan C Marsh
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Peter H von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
| | - Andrew H Marcus
- Institute of Molecular Biology and Department of Chemistry and Biochemistry and ‡Oregon Center for Optical, Molecular and Quantum Science and Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States
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6
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Structure and Mechanisms of SF1 DNA Helicases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 767:17-46. [PMID: 23161005 DOI: 10.1007/978-1-4614-5037-5_2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Superfamily I is a large and diverse group of monomeric and dimeric helicases defined by a set of conserved sequence motifs. Members of this class are involved in essential processes in both DNA and RNA metabolism in all organisms. In addition to conserved amino acid sequences, they also share a common structure containing two RecA-like motifs involved in ATP binding and hydrolysis and nucleic acid binding and unwinding. Unwinding is facilitated by a "pin" structure which serves to split the incoming duplex. This activity has been measured using both ensemble and single-molecule conditions. SF1 helicase activity is modulated through interactions with other proteins.
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7
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König SLB, Liyanage PS, Sigel RKO, Rueda D. Helicase-mediated changes in RNA structure at the single-molecule level. RNA Biol 2013; 10:133-48. [PMID: 23353571 DOI: 10.4161/rna.23507] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA helicases are a diverse group of RNA-dependent ATPases known to play a large number of biological roles inside the cell, such as RNA unwinding, remodeling, export and degradation. Understanding how helicases mediate changes in RNA structure is therefore of fundamental interest. The advent of single-molecule spectroscopic techniques has unveiled with unprecedented detail the interplay of RNA helicases with their substrates. In this review, we describe the characterization of helicase-RNA interactions by single-molecule approaches. State-of-the-art techniques are presented, followed by a discussion of recent advancements in this exciting field.
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8
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Insight into helicase mechanism and function revealed through single-molecule approaches. Q Rev Biophys 2010; 43:185-217. [PMID: 20682090 DOI: 10.1017/s0033583510000107] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Helicases are a class of nucleic acid (NA) motors that catalyze NTP-dependent unwinding of NA duplexes into single strands, a reaction essential to all areas of NA metabolism. In the last decade, single-molecule (sm) technology has proven to be highly useful in revealing mechanistic insight into helicase activity that is not always detectable via ensemble assays. A combination of methods based on fluorescence, optical and magnetic tweezers, and flow-induced DNA stretching has enabled the study of helicase conformational dynamics, force generation, step size, pausing, reversal and repetitive behaviors during translocation and unwinding by helicases working alone and as part of multiprotein complexes. The contributions of these sm investigations to our understanding of helicase mechanism and function will be discussed.
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9
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Jang H, Kim Y, Kwon H, Yeo W, Kim D, Min D. A Graphene-Based Platform for the Assay of Duplex-DNA Unwinding by Helicase. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 122:5839-5843. [PMID: 32313315 PMCID: PMC7159641 DOI: 10.1002/ange.201001332] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 04/19/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Hongje Jang
- Department of Chemistry, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 373‐1 Guseong‐dong, Yuseong‐gu, Daejeon 305‐701 (Korea), Fax: (+82)‐42‐350‐2810
| | - Young‐Kwan Kim
- Department of Chemistry, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 373‐1 Guseong‐dong, Yuseong‐gu, Daejeon 305‐701 (Korea), Fax: (+82)‐42‐350‐2810
| | - Hyun‐Mi Kwon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143‐701 (Korea)
| | - Woon‐Seok Yeo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143‐701 (Korea)
| | - Dong‐Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143‐701 (Korea)
| | - Dal‐Hee Min
- Department of Chemistry, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 373‐1 Guseong‐dong, Yuseong‐gu, Daejeon 305‐701 (Korea), Fax: (+82)‐42‐350‐2810
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10
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Jang H, Kim Y, Kwon H, Yeo W, Kim D, Min D. A graphene-based platform for the assay of duplex-DNA unwinding by helicase. Angew Chem Int Ed Engl 2010; 49:5703-7. [PMID: 20818755 PMCID: PMC7159720 DOI: 10.1002/anie.201001332] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 04/19/2010] [Indexed: 12/02/2022]
Affiliation(s)
- Hongje Jang
- Department of Chemistry, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 373‐1 Guseong‐dong, Yuseong‐gu, Daejeon 305‐701 (Korea), Fax: (+82)‐42‐350‐2810
| | - Young‐Kwan Kim
- Department of Chemistry, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 373‐1 Guseong‐dong, Yuseong‐gu, Daejeon 305‐701 (Korea), Fax: (+82)‐42‐350‐2810
| | - Hyun‐Mi Kwon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143‐701 (Korea)
| | - Woon‐Seok Yeo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143‐701 (Korea)
| | - Dong‐Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143‐701 (Korea)
| | - Dal‐Hee Min
- Department of Chemistry, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 373‐1 Guseong‐dong, Yuseong‐gu, Daejeon 305‐701 (Korea), Fax: (+82)‐42‐350‐2810
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11
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Abstract
Much of the dynamics information is lost in bulk measurements because of the population averaging. Single-molecule methods measure one molecule at a time; they provide knowledge not obtainable by other means. In this article, we review the application of the two most widely used single-molecule methods--fluorescence resonance energy transfer (FRET) and force versus extension measurements--to several RNA reactions. First, we discuss folding/unfolding studies on a hairpin ribozyme that revealed multiple conformations of the RNA with distinct kinetics, and on a series of RNA pseudoknots, whose mechanical stabilities were found to show a strong correlation with their frameshifting efficiency during translation. We also discuss several RNA-related molecular motors. Single-molecule experiments revealed detailed mechanisms for the interaction of HIV reverse transcriptase and nucleic acid helicases (NS3 and RIG-1) with their substrates. Optical tweezers studies showed that translation of a single messenger RNA by a ribosome occurs by successive translocation-and-pause cycles. Single-molecule FRET experiments yielded important information on ribosome conformational changes and tRNA dynamics during translation. Overall, single-molecule experiments have been very valuable for understanding RNA reactions.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.
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12
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Reinhard BM, Yassif JM, Vach P, Liphardt J. Plasmon rulers as dynamic molecular rulers in enzymology. Methods Enzymol 2010; 475:175-98. [PMID: 20627158 DOI: 10.1016/s0076-6879(10)75008-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This chapter provides an introduction to the concept of "plasmon rulers," pairs of biopolymer-linked tethered nanoparticles which act as nonblinking, nonbleaching rulers for dynamic molecular distance measurements. Plasmon rulers utilize the distance dependence of the plasmon coupling between individual noble metal particles to measure distances. Although the plasmon ruler approach is still an emerging technology, proof-of-principle experiments have demonstrated that plasmon rulers can already be used to investigate structural fluctuations in nucleoprotein complexes, monitor nuclease catalyzed DNA or RNA cleavage reactions, and detect DNA bending. The physical concepts underlying plasmon rulers are summarized, and effective assembly approaches as well as recent applications are discussed. Plasmon rulers are a useful addition to the single molecule biophysics toolbox, since they allow single biomolecules to be continuously monitored for days at high temporal resolutions.
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Affiliation(s)
- Björn M Reinhard
- Department of Chemistry, The Photonics Center, Boston University, Boston, Massachusetts, USA
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13
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Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules. Proc Natl Acad Sci U S A 2009; 106:361-8. [PMID: 19122145 DOI: 10.1073/pnas.0811965106] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Rad51 protein (Rad51) is central to recombinational repair of double-strand DNA breaks. It polymerizes onto DNA and promotes strand exchange between homologous chromosomes. We visualized the real-time assembly and disassembly of human Rad51 nucleoprotein filaments on double-stranded DNA by single-molecule fluorescence microscopy. Rad51 assembly extends the DNA by approximately 65%. Nucleoprotein filament formation occurs via rapid nucleation followed by growth from these nuclei. Growth does not continue indefinitely, however, and nucleoprotein filaments terminate when approximately 2 mum in length. The dependence of nascent filament formation on Rad51 concentration suggests that 2-3 Rad51 monomers are involved in nucleation. Rad51 nucleoprotein filaments are stable and remain extended when ATP hydrolysis is prevented; however, when permitted, filaments decrease in length as a result of conversion to ADP-bound nucleoprotein complexes and partial protein dissociation. Dissociation of Rad51 from dsDNA is slow and incomplete, thereby rationalizing the need for other proteins that facilitate disassembly.
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Abstract
Enzymes continue to be a major drug target class for the pharmaceutical industry with high-throughput screening the approach of choice for identifying initial active chemical compounds. The development of fluorescent- or absorbance-based readouts typically remains the formats of choice for enzyme screens and a wealth of experience from both industry and academia has led to a comprehensive set of standardized assay development and validation guidelines for enzyme assays. In this chapter, we generalize approaches to developing, validating, and troubleshooting assays that should be applicable in both industrial and academic settings. Real-life examples of various enzyme classes including kinases, proteases, transferases, and phosphatases are used to illustrate assay development approaches and solutions. Practical examples are given for how to deal with low-purity enzyme targets, compound interference, and identification of activators. Assay acceptance criteria and a number of assay notes on pitfalls to avoid should provide pointers on how to develop a suitable enzymatic assay applicable for HTS.
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Affiliation(s)
- Kevin P Williams
- Department of Pharmaceutical Sciences and BRITE, North Carolina Central University, Durham, NC, USA
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15
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Finkelstein IJ, Greene EC. Single molecule studies of homologous recombination. MOLECULAR BIOSYSTEMS 2008; 4:1094-104. [PMID: 18931785 DOI: 10.1039/b811681b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Single molecule methods offer an unprecedented opportunity to examine complex macromolecular reactions that are obfuscated by ensemble averaging. The application of single molecule techniques to study DNA processing enzymes has revealed new mechanistic details that are unobtainable from bulk biochemical studies. Homologous DNA recombination is a multi-step pathway that is facilitated by numerous enzymes that must precisely and rapidly manipulate diverse DNA substrates to repair potentially lethal breaks in the DNA duplex. In this review, we present an overview of single molecule assays that have been developed to study key aspects of homologous recombination and discuss the unique information gleaned from these experiments.
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Affiliation(s)
- Ilya J Finkelstein
- Departments of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA
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16
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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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17
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Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism. Proc Natl Acad Sci U S A 2007; 104:19790-5. [PMID: 18077411 DOI: 10.1073/pnas.0709793104] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Helicases are enzymes that couple ATP hydrolysis to the unwinding of double-stranded (ds) nucleic acids. The bacteriophage T4 helicase (gp41) is a hexameric helicase that promotes DNA replication within a highly coordinated protein complex termed the replisome. Despite recent progress, the gp41 unwinding mechanism and regulatory interactions within the replisome remain unclear. Here we use a single tethered DNA hairpin as a real-time reporter of gp41-mediated dsDNA unwinding and single-stranded (ss) DNA translocation with 3-base pair (bp) resolution. Although gp41 translocates on ssDNA as fast as the in vivo replication fork ( approximately 400 bp/s), its unwinding rate extrapolated to zero force is much slower ( approximately 30 bp/s). Together, our results have two implications: first, gp41 unwinds DNA through a passive mechanism; second, this weak helicase cannot efficiently unwind the T4 genome alone. Our results suggest that important regulations occur within the replisome to achieve rapid and processive replication.
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18
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Hopfner KP, Michaelis J. Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics. Curr Opin Struct Biol 2006; 17:87-95. [PMID: 17157498 DOI: 10.1016/j.sbi.2006.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 10/18/2006] [Accepted: 11/27/2006] [Indexed: 10/23/2022]
Abstract
Enzymes that translocate nucleic acids using ATP hydrolysis include DNA and RNA helicases, viral genome packaging motors and chromatin remodeling ATPases. Recent structural analysis, in conjunction with single-molecule studies, has revealed a wealth of new insights into how these enzymes use ATP-driven conformational changes to move on nucleic acids.
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19
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Lionnet T, Dawid A, Bigot S, Barre FX, Saleh OA, Heslot F, Allemand JF, Bensimon D, Croquette V. DNA mechanics as a tool to probe helicase and translocase activity. Nucleic Acids Res 2006; 34:4232-44. [PMID: 16935884 PMCID: PMC1616950 DOI: 10.1093/nar/gkl451] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Helicases and translocases are proteins that use the energy derived from ATP hydrolysis to move along or pump nucleic acid substrates. Single molecule manipulation has proved to be a powerful tool to investigate the mechanochemistry of these motors. Here we first describe the basic mechanical properties of DNA unraveled by single molecule manipulation techniques. Then we demonstrate how the knowledge of these properties has been used to design single molecule assays to address the enzymatic mechanisms of different translocases. We report on four single molecule manipulation systems addressing the mechanism of different helicases using specifically designed DNA substrates: UvrD enzyme activity detection on a stretched nicked DNA molecule, HCV NS3 helicase unwinding of a RNA hairpin under tension, the observation of RecBCD helicase/nuclease forward and backward motion, and T7 gp4 helicase mediated opening of a synthetic DNA replication fork. We then discuss experiments on two dsDNA translocases: the RuvAB motor studied on its natural substrate, the Holliday junction, and the chromosome-segregation motor FtsK, showing its unusual coupling to DNA supercoiling.
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Affiliation(s)
- Timothée Lionnet
- Laboratoire de Physique Statistique de l' Ecole Normale Supérieure, UMR 8550 CNRS24 rue Lhomond, 75231 Paris Cedex 05, France
- Département de Biologie, Ecole Normale Supérieure46 rue d'Ulm, 75231 Paris Cedex, 05, France
| | - Alexandre Dawid
- Département de Biologie, Ecole Normale Supérieure46 rue d'Ulm, 75231 Paris Cedex, 05, France
- Laboratoire Pierre Aigrain, Ecole Normale SupérieureUMR 8551 CNRS, 24 rue Lhomond, 75231 Paris Cedex 05, France
| | - Sarah Bigot
- Laboratoire de Microbiologie et de Génétique Moléculaire, CNRS UMR5100Toulouse, France
| | - François-Xavier Barre
- Laboratoire de Microbiologie et de Génétique Moléculaire, CNRS UMR5100Toulouse, France
- Centre de Génétique Moléculaire, CNRS UPR2167Gif-sur-Yvette, France
| | - Omar A. Saleh
- Laboratoire de Physique Statistique de l' Ecole Normale Supérieure, UMR 8550 CNRS24 rue Lhomond, 75231 Paris Cedex 05, France
- Département de Biologie, Ecole Normale Supérieure46 rue d'Ulm, 75231 Paris Cedex, 05, France
| | - François Heslot
- Département de Biologie, Ecole Normale Supérieure46 rue d'Ulm, 75231 Paris Cedex, 05, France
- Laboratoire Pierre Aigrain, Ecole Normale SupérieureUMR 8551 CNRS, 24 rue Lhomond, 75231 Paris Cedex 05, France
| | - Jean-François Allemand
- Laboratoire de Physique Statistique de l' Ecole Normale Supérieure, UMR 8550 CNRS24 rue Lhomond, 75231 Paris Cedex 05, France
- Département de Biologie, Ecole Normale Supérieure46 rue d'Ulm, 75231 Paris Cedex, 05, France
| | - David Bensimon
- Laboratoire de Physique Statistique de l' Ecole Normale Supérieure, UMR 8550 CNRS24 rue Lhomond, 75231 Paris Cedex 05, France
- Département de Biologie, Ecole Normale Supérieure46 rue d'Ulm, 75231 Paris Cedex, 05, France
| | - Vincent Croquette
- Laboratoire de Physique Statistique de l' Ecole Normale Supérieure, UMR 8550 CNRS24 rue Lhomond, 75231 Paris Cedex 05, France
- Département de Biologie, Ecole Normale Supérieure46 rue d'Ulm, 75231 Paris Cedex, 05, France
- To whom correspondence should be addressed at Laboratoire de Physique Statisque de l’ Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France. Tel: 33 1 44 32 34 92; Fax: 33 1 44 32 34 33;
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