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Henneman B, Erkelens AM, Heinsman J, Battjes J, Dame RT. Quantitation of DNA Binding Affinity Using Tethered Particle Motion. Methods Mol Biol 2024; 2819:497-518. [PMID: 39028521 DOI: 10.1007/978-1-0716-3930-6_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered particle motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to measure binding constants of proteins binding to DNA reliably, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This change in bead motion makes it possible to measure the DNA-binding properties of proteins. We use the bacterial protein integration host factor (IHF) and the archaeal histone HMfA as examples to show how specific binding to DNA can be measured. Moreover, we show how the end-to-end distance can provide structural insights into protein-DNA binding.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Joost Heinsman
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Julius Battjes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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Tan T, Tan Y, Wang Y, Yang X, Zhai B, Zhang S, Yang X, Nie H, Gao J, Zhou J, Zhang L, Wang S. Negative supercoils regulate meiotic crossover patterns in budding yeast. Nucleic Acids Res 2022; 50:10418-10435. [PMID: 36107772 PMCID: PMC9561271 DOI: 10.1093/nar/gkac786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/21/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
Interference exists ubiquitously in many biological processes. Crossover interference patterns meiotic crossovers, which are required for faithful chromosome segregation and evolutionary adaption. However, what the interference signal is and how it is generated and regulated is unknown. We show that yeast top2 alleles which cannot bind or cleave DNA accumulate a higher level of negative supercoils and show weaker interference. However, top2 alleles which cannot religate the cleaved DNA or release the religated DNA accumulate less negative supercoils and show stronger interference. Moreover, the level of negative supercoils is negatively correlated with crossover interference strength. Furthermore, negative supercoils preferentially enrich at crossover-associated Zip3 regions before the formation of meiotic DNA double-strand breaks, and regions with more negative supercoils tend to have more Zip3. Additionally, the strength of crossover interference and homeostasis change coordinately in mutants. These findings suggest that the accumulation and relief of negative supercoils pattern meiotic crossovers.
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Affiliation(s)
- Taicong Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Yingjin Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Ying Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Xiao Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University , Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education , Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health , Jinan, Shandong 250012, China
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
| | - Binyuan Zhai
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University , Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education , Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health , Jinan, Shandong 250012, China
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
| | - Shuxian Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- Advanced Medical Research Institute, Shandong University , Jinan, Shandong 250012, China
| | - Xuan Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Hui Nie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Jinmin Gao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Liangran Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- Advanced Medical Research Institute, Shandong University , Jinan, Shandong 250012, China
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University , Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education , Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health , Jinan, Shandong 250012, China
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
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Martinez-Garcia M, White CI, Franklin FCH, Sanchez-Moran E. The Role of Topoisomerase II in DNA Repair and Recombination in Arabidopsis thaliana. Int J Mol Sci 2021; 22:13115. [PMID: 34884922 PMCID: PMC8658145 DOI: 10.3390/ijms222313115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
DNA entanglements and supercoiling arise frequently during normal DNA metabolism. DNA topoisomerases are highly conserved enzymes that resolve the topological problems that these structures create. Topoisomerase II (TOPII) releases topological stress in DNA by removing DNA supercoils through breaking the two DNA strands, passing a DNA duplex through the break and religating the broken strands. TOPII performs key DNA metabolic roles essential for DNA replication, chromosome condensation, heterochromatin metabolism, telomere disentanglement, centromere decatenation, transmission of crossover (CO) interference, interlock resolution and chromosome segregation in several model organisms. In this study, we reveal the endogenous role of Arabidopsis thaliana TOPII in normal root growth and cell cycle, and mitotic DNA repair via homologous recombination. Additionally, we show that the protein is required for meiotic DSB repair progression, but not for CO formation. We propose that TOPII might promote mitotic HR DNA repair by relieving stress needed for HR strand invasion and D-loop formation.
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Affiliation(s)
| | - Charles I. White
- Génétique, Reproduction et Développement, Faculté de Médecine, UMR CNRS 6293—INSERM U1103—Université Clermont Auvergne, 28 Place Henri Dunant, 63001 Clermont-Ferrand, France;
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Tirtom NE, Hsu Y, Li HW. Polyamines stimulate RecA-mediated recombination by condensing duplex DNA and stabilizing intermediates. Phys Chem Chem Phys 2020; 22:11928-11935. [PMID: 32432615 DOI: 10.1039/d0cp01061h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Polyamines are naturally occurring cationic molecules in cells. In addition to their roles in modulating gene expression and cell proliferation, they have been shown to stimulate DNA recombination. The molecular mechanism for stimulation is not clear. We utilized single-molecule tethered particle motion (TPM) experiments to investigate how polyamines stimulate RecA-mediated recombination. We showed that natural polyamines, spermine and spermidine, condense duplex DNA, but with different efficiencies. While ∼300 μM of spermine condenses 50% of duplex DNA, 2.0 mM of spermidine is required to achieve the same level of condensation. The condensation takes place in a stepwise manner, and is reversible upon removal of polyamines. We also showed that addition of polyamines stimulates the duplex capture activity of RecA filament and stabilizes the intermediates with longer dwell time. Through condensing duplex DNA and stabilizing the complex of RecA filaments and duplex DNA, polyamines stimulate the formation of functional intermediates by ∼20-fold, and promote recombination progression.
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Affiliation(s)
| | - Yang Hsu
- Department of Chemistry, National Taiwan Normal University, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taiwan.
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Lin YH, Chu CC, Fan HF, Wang PY, Cox MM, Li HW. A 5'-to-3' strand exchange polarity is intrinsic to RecA nucleoprotein filaments in the absence of ATP hydrolysis. Nucleic Acids Res 2019; 47:5126-5140. [PMID: 30916331 PMCID: PMC6547424 DOI: 10.1093/nar/gkz189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
RecA is essential to recombinational DNA repair in which RecA filaments mediate the homologous DNA pairing and strand exchange. Both RecA filament assembly and the subsequent DNA strand exchange are directional. Here, we demonstrate that the polarity of DNA strand exchange is embedded within RecA filaments even in the absence of ATP hydrolysis, at least over short DNA segments. Using single-molecule tethered particle motion, we show that successful strand exchange in the presence of ATP proceeds with a 5′-to-3′ polarity, as demonstrated previously. RecA filaments prepared with ATPγS also exhibit a 5′-to-3′ progress of strand exchange, suggesting that the polarity is not determined by RecA disassembly and/or ATP hydrolysis. RecAΔC17 mutants, lacking a C-terminal autoregulatory flap, also promote strand exchange in a 5′-to-3′ polarity in ATPγS, a polarity that is largely lost with this RecA variant when ATP is hydrolyzed. We propose that there is an inherent strand exchange polarity mediated by the structure of the RecA filament groove, associated by conformation changes propagated in a polar manner as DNA is progressively exchanged. ATP hydrolysis is coupled to polar strand exchange over longer distances, and its contribution to the polarity requires an intact RecA C-terminus.
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Affiliation(s)
- Yu-Hsuan Lin
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Chia-Chieh Chu
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 11221 Taiwan
| | - Pang-Yen Wang
- Department of Chemistry, National Taiwan University, 10617, Taiwan
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin, Madison, 53706, USA
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, 10617, Taiwan
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Henneman B, Heinsman J, Battjes J, Dame RT. Quantitation of DNA-Binding Affinity Using Tethered Particle Motion. Methods Mol Biol 2019; 1837:257-275. [PMID: 30109615 DOI: 10.1007/978-1-4939-8675-0_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered Particle Motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to reliably measure binding constants of proteins binding to DNA, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This makes it possible to measure binding properties. We use the bacterial protein Integration Host Factor (IHF) as an example to show how specific binding to DNA can be measured. Moreover, we show a new intuitive quantitative approach to displaying data obtained via TPM.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Joost Heinsman
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Julius Battjes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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