1
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Singh RK, Burov S. Universal to nonuniversal transition of the statistics of rare events during the spread of random walks. Phys Rev E 2023; 108:L052102. [PMID: 38115504 DOI: 10.1103/physreve.108.l052102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 09/11/2023] [Indexed: 12/21/2023]
Abstract
Through numerous experiments that analyzed rare event statistics in heterogeneous media, it was discovered that in many cases the probability density function for particle position, P(X,t), exhibits a slower decay rate than the Gaussian function. Typically, the decay behavior is exponential, referred to as Laplace tails. However, many systems exhibit an even slower decay rate, such as power-law, log-normal, or stretched exponential. In this study, we utilize the continuous-time random walk method to investigate the rare events in particle hopping dynamics and find that the properties of the hop size distribution induce a critical transition between the Laplace universality of rare events and a more specific, slower decay of P(X,t). Specifically, when the hop size distribution decays slower than exponential, such as e^{-|x|^{β}} (β>1), the Laplace universality no longer applies, and the decay is specific, influenced by a few large events, rather than by the accumulation of many smaller events that give rise to Laplace tails.
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Affiliation(s)
- R K Singh
- Department of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Stanislav Burov
- Department of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
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2
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Sakai I, Akimoto T. Sample-to-sample fluctuations of transport coefficients in the totally asymmetric simple exclusion process with quenched disorder. Phys Rev E 2023; 107:054131. [PMID: 37328985 DOI: 10.1103/physreve.107.054131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
We consider the totally asymmetric simple exclusion processes on quenched random energy landscapes. We show that the current and the diffusion coefficient differ from those for homogeneous environments. Using the mean-field approximation, we analytically obtain the site density when the particle density is low or high. As a result, the current and the diffusion coefficient are described by the dilute limit of particles or holes, respectively. However, in the intermediate regime, due to the many-body effect, the current and the diffusion coefficient differ from those for single-particle dynamics. The current is almost constant and becomes the maximal value in the intermediate regime. Moreover, the diffusion coefficient decreases with the particle density in the intermediate regime. We obtain analytical expressions for the maximal current and the diffusion coefficient based on the renewal theory. The deepest energy depth plays a central role in determining the maximal current and the diffusion coefficient. As a result, the maximal current and the diffusion coefficient depend crucially on the disorder, i.e., non-self-averaging. Based on the extreme value theory, we find that sample-to-sample fluctuations of the maximal current and diffusion coefficient are characterized by the Weibull distribution. We show that the disorder averages of the maximal current and the diffusion coefficient converge to zero as the system size is increased and quantify the degree of the non-self-averaging effect for the maximal current and the diffusion coefficient.
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Affiliation(s)
- Issei Sakai
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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3
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Sakai I, Akimoto T. Non-self-averaging of current in a totally asymmetric simple exclusion process with quenched disorder. Phys Rev E 2023; 107:L052103. [PMID: 37329050 DOI: 10.1103/physreve.107.l052103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/01/2023] [Indexed: 06/18/2023]
Abstract
We investigate the current properties in the totally asymmetric simple exclusion process (TASEP) on a quenched random energy landscape. In low- and high-density regimes, the properties are characterized by single-particle dynamics. In the intermediate one, the current becomes constant and is maximized. Based on the renewal theory, we derive accurate results for the maximum current. The maximum current significantly depends on a disorder realization, i.e., non-self-averaging (SA). We demonstrate that the disorder average of the maximum current decreases with the system size, and the sample-to-sample fluctuations of the maximum current exceed those of current in the low- and high-density regimes. We find a significant difference between single-particle dynamics and the TASEP. In particular, the non-SA behavior of the maximum current is always observed, whereas the transition from non-SA to SA for current in single-particle dynamics exists.
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Affiliation(s)
- Issei Sakai
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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4
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Jin Y, Bae J, Kim TY, Hwang H, Kim T, Yu M, Oh H, Hashiya K, Bando T, Sugiyama H, Jo K. Twelve Colors of Streptavidin–Fluorescent Proteins (SA-FPs): A Versatile Tool to Visualize Genetic Information in Single-Molecule DNA. Anal Chem 2022; 94:16927-16935. [DOI: 10.1021/acs.analchem.2c04344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yu Jin
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Tehee Yurie Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Hyeseung Hwang
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Taesoo Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Myungheon Yu
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Hyesoo Oh
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
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5
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Kaczmarczyk AP, Déclais AC, Newton MD, Boulton SJ, Lilley DMJ, Rueda DS. Search and processing of Holliday junctions within long DNA by junction-resolving enzymes. Nat Commun 2022; 13:5921. [PMID: 36207294 PMCID: PMC9547003 DOI: 10.1038/s41467-022-33503-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2022] Open
Abstract
Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.
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Affiliation(s)
- Artur P Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
| | | | - Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David M J Lilley
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK.
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6
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Kim YT, Oh H, Seo MJ, Lee DH, Shin J, Bong S, Heo S, Hapsari ND, Jo K. 21 Fluorescent Protein-Based DNA Staining Dyes. Molecules 2022; 27:5248. [PMID: 36014487 PMCID: PMC9412447 DOI: 10.3390/molecules27165248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Fluorescent protein-DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope. Here, we constructed 21 kinds of FP-DBPs using various colors of fluorescent proteins and two DNA-binding motifs. From the database of fluorescent proteins (FPbase.org), we chose bright FPs, such as RRvT, tdTomato, mNeonGreen, mClover3, YPet, and mScarlet, which are four to eight times brighter than original wild-type GFP. Additionally, we chose other FPs, such as mOrange2, Emerald, mTurquoise2, mStrawberry, and mCherry, for variations in emitting wavelengths. For DNA-binding motifs, we used HMG (high mobility group) as an 11-mer peptide or a 36 kDa tTALE (truncated transcription activator-like effector). Using 21 FP-DBPs, we attempted to stain DNA molecules and then analyzed fluorescence intensities. Most FP-DBPs successfully visualized DNA molecules. Even with the same DNA-binding motif, the order of FP and DBP affected DNA staining in terms of brightness and DNA stretching. The DNA staining pattern by FP-DBPs was also affected by the FP types. The data from 21 FP-DBPs provided a guideline to develop novel DNA-binding fluorescent proteins.
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Affiliation(s)
- Yurie Tehee Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Hyesoo Oh
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Myung Jun Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Dong Hyeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Jieun Shin
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Serang Bong
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Sujeong Heo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
- Chemistry Education Program, Department of Mathematics and Science Education, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Kyubong Jo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
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7
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Tan CJ, Basak R, Yadav I, van Kan JA, Arluison V, van der Maarel JRC. Mobility of Bacterial Protein Hfq on dsDNA: Role of C-Terminus-Mediated Transient Binding. J Phys Chem B 2022; 126:1477-1482. [PMID: 35166115 DOI: 10.1021/acs.jpcb.1c10234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mobility of protein is fundamental in the machinery of life. Here, we have investigated the effect of DNA binding in conjunction with DNA segmental fluctuation (internal motion) of the bacterial Hfq master regulator devoid of its amyloid C-terminus domain. Hfq is one of the most abundant nucleoid associated proteins that shape the bacterial chromosome and is involved in several aspects of nucleic acid metabolism. Fluorescence microscopy has been used to track a C-terminus domain lacking mutant form of Hfq on double-stranded DNA, which is stretched by confinement to a rectangular nanofluidic channel. The mobility of the mutant is strongly accelerated with respect to the wild-type variant. Furthermore, it shows a reverse dependence on the internal motion of DNA, in that slower motion results in slower protein diffusion. The results demonstrate the subtle role of DNA internal motion in controlling the mobility of a nucleoid associated protein, and, in particular, the importance of transient binding and moving DNA strands out of the way.
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Affiliation(s)
- Chuan Jie Tan
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Rajib Basak
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Indresh Yadav
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Véronique Arluison
- Université de Paris, UFR SDV, Paris 75006, France.,Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette 91191, France
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8
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Basak R, Yadav I, Arluison V, van Kan JA, van der Maarel JRC. Probing Amyloid-DNA Interaction with Nanofluidics. Methods Mol Biol 2022; 2538:305-317. [PMID: 35951308 DOI: 10.1007/978-1-0716-2529-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanofluidics is an emerging methodology to investigate single biomacromolecules without functionalization and/or attachment of the molecules to a substrate. In conjunction with fluorescence microscopy, it can be used to investigate structural and dynamical aspects of amyloid-DNA interaction. Here, we summarize the methodology for fabricating lab-on-chip devices in relatively cheap polymer resins and featuring quasi one-dimensional nanochannels with a cross-sectional diameter of tens to a few hundred nanometers. Site-specific staining of amyloid-forming protein Hfq with a fluorescence dye is also described. The methodology is illustrated with two application studies. The first study involves assembling bacterial amyloid proteins such as Hfq on double-stranded DNA and monitoring the folding and compaction of DNA in a condensed state. The second study is about the concerted motion of Hfq on DNA and how this is related to DNA's internal motion. Explicit details of procedures and workflows are given throughout.
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Affiliation(s)
- Rajib Basak
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Indresh Yadav
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France
- Université de Paris, Paris, France
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore, Singapore
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9
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Belan O, Moore G, Kaczmarczyk A, Newton MD, Anand R, Boulton SJ, Rueda DS. Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis. STAR Protoc 2021; 2:100588. [PMID: 34169285 PMCID: PMC8209646 DOI: 10.1016/j.xpro.2021.100588] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Here, we describe a rapid and versatile protocol to generate gapped DNA substrates for single-molecule (SM) analysis using optical tweezers via site-specific Cas9 nicking and force-induced melting. We provide examples of single-stranded (ss) DNA gaps of different length and position. We outline protocols to visualize these substrates by replication protein A-enhanced Green Fluorescent Protein (RPA-eGFP) and SYTOX Orange staining using commercially available optical tweezers (C-TRAP). Finally, we demonstrate the utility of these substrates for SM analysis of bidirectional growth of RAD-51-ssDNA filaments. For complete details on the use and execution of this protocol, please refer to Belan et al. (2021).
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Affiliation(s)
- Ondrej Belan
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - George Moore
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London W12 0NN, UK
| | - Artur Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London W12 0NN, UK
| | - Matthew D. Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London W12 0NN, UK
| | - Roopesh Anand
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Simon J. Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - David S. Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London W12 0NN, UK
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10
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Goswami K, Sebastian KL. Exact solution to the first-passage problem for a particle with a dichotomous diffusion coefficient. Phys Rev E 2020; 102:042103. [PMID: 33212715 DOI: 10.1103/physreve.102.042103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/17/2020] [Indexed: 11/07/2022]
Abstract
We consider the problem of first-passage time for reaching a boundary of a particle which diffuses in one dimension and is confined to the region x∈(0,L), with a diffusion coefficient that switches randomly between two states, having diffusivities that are different. Exact analytical expressions are found for the survival probability of the particle as a function of time. The survival probability has a multiexponential decay, and to characterize it, we use the average rate constant k, as well as the instantaneous rate r(t). Our approach can easily be extended to the case where the diffusion coefficient takes n different values. The model should be of interest to biological processes, in which a reactant searches for a target in a heterogeneous environment, making the diffusion coefficient a random function of time. The best example for this is a protein searching for a target site on the DNA.
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Affiliation(s)
- Koushik Goswami
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - K L Sebastian
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India.,Indian Institute of Technology, Kozhippara P.O., Palakkad 678557, Kerala, India
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11
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Yadav I, Basak R, Yan P, van Kan JA, Arluison V, van der Maarel JRC. Role of Internal DNA Motion on the Mobility of a Nucleoid-Associated Protein. J Phys Chem Lett 2020; 11:8424-8429. [PMID: 32930601 DOI: 10.1021/acs.jpclett.0c02251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein transport on DNA is at the core of the machinery of life. Here we investigated the influence of DNA internal motion on the mobility of Hfq, which is involved in several aspects of nucleic acid metabolism and is one of the nucleoid-associated proteins that shape the bacterial chromosome. Fluorescence microscopy was used to follow Hfq on double-stranded DNA that was stretched by confinement to a channel with a diameter of 125 nm. The protein mobility shows a strong dependence on the internal motion of DNA in that slower motion results in faster protein diffusion. A model of released diffusion is proposed that is based on three-dimensional diffusion through the interior of the DNA coil interspersed by periods in which the protein is immobilized in a bound state. We surmise that the coupling between DNA internal motion and protein mobility has important implications for DNA metabolism and protein-binding-related regulation of gene expression.
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Affiliation(s)
- Indresh Yadav
- Department of Physics, National University of Singapore, Singapore 117542
| | - Rajib Basak
- Department of Physics, National University of Singapore, Singapore 117542
| | - Peiyan Yan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Véronique Arluison
- Université de Paris, UFR SDV, 75006 Paris, France
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France
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12
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Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models. Proc Natl Acad Sci U S A 2020; 117:21889-21895. [PMID: 32820079 PMCID: PMC7486748 DOI: 10.1073/pnas.2002971117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA glycosylase repairs DNA damage to maintain the genome integrity, and thus it is essential for the survival of all organisms. However, it remains a long-standing puzzle how glycosylase diffuses along the genomic DNA to locate the sparse and aberrant lesion sites efficiently and accurately in the genome containing numerous base pairs. Previously, only the high-speed–low-accuracy search mode has been characterized experimentally, while the low-speed–high-accuracy mode is undetectable. Here, we observed the low-speed mode of glycosylase AlkD translocating, and further dissected its molecular mechanisms. To achieve this, we developed an integrated platform by combining scanning FRET-FCS with Markov state model. We expect that this platform can be widely applied to investigate other glycosylases and DNA-binding proteins. DNA glycosylase is responsible for repairing DNA damage to maintain the genome stability and integrity. However, how glycosylase can efficiently and accurately recognize DNA lesions across the enormous DNA genome remains elusive. It has been hypothesized that glycosylase translocates along the DNA by alternating between a fast but low-accuracy diffusion mode and a slow but high-accuracy mode when searching for DNA lesions. However, the slow mode has not been successfully characterized due to the limitation in the spatial and temporal resolutions of current experimental techniques. Using a newly developed scanning fluorescence resonance energy transfer (FRET)–fluorescence correlation spectroscopy (FCS) platform, we were able to observe both slow and fast modes of glycosylase AlkD translocating on double-stranded DNA (dsDNA), reaching the temporal resolution of microsecond and spatial resolution of subnanometer. The underlying molecular mechanism of the slow mode was further elucidated by Markov state model built from extensive all-atom molecular dynamics simulations. We found that in the slow mode, AlkD follows an asymmetric diffusion pathway, i.e., rotation followed by translation. Furthermore, the essential role of Y27 in AlkD diffusion dynamics was identified both experimentally and computationally. Our results provided mechanistic insights on how conformational dynamics of AlkD–dsDNA complex coordinate different diffusion modes to accomplish the search for DNA lesions with high efficiency and accuracy. We anticipate that the mechanism adopted by AlkD to search for DNA lesions could be a general one utilized by other glycosylases and DNA binding proteins.
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13
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Abstract
Accurate DNA repair and replication are critical for genomic stability and cancer prevention. RAD51 and its gene family are key regulators of DNA fidelity through diverse roles in double-strand break repair, replication stress, and meiosis. RAD51 is an ATPase that forms a nucleoprotein filament on single-stranded DNA. RAD51 has the function of finding and invading homologous DNA sequences to enable accurate and timely DNA repair. Its paralogs, which arose from ancient gene duplications of RAD51, have evolved to regulate and promote RAD51 function. Underscoring its importance, misregulation of RAD51, and its paralogs, is associated with diseases such as cancer and Fanconi anemia. In this review, we focus on the mammalian RAD51 structure and function and highlight the use of model systems to enable mechanistic understanding of RAD51 cellular roles. We also discuss how misregulation of the RAD51 gene family members contributes to disease and consider new approaches to pharmacologically inhibit RAD51.
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Affiliation(s)
- Braulio Bonilla
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - Sarah R Hengel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - McKenzie K Grundy
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
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14
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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15
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Vestergaard CL, Blainey PC, Flyvbjerg H. Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA. Nucleic Acids Res 2019; 46:2446-2458. [PMID: 29361033 PMCID: PMC5861423 DOI: 10.1093/nar/gky004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/05/2018] [Indexed: 12/28/2022] Open
Abstract
We reanalyze trajectories of hOGG1 repair proteins diffusing on DNA. A previous analysis of these trajectories with the popular mean-squared-displacement approach revealed only simple diffusion. Here, a new optimal estimator of diffusion coefficients reveals two-state kinetics of the protein. A simple, solvable model, in which the protein randomly switches between a loosely bound, highly mobile state and a tightly bound, less mobile state is the simplest possible dynamic model consistent with the data. It yields accurate estimates of hOGG1’s (i) diffusivity in each state, uncorrupted by experimental errors arising from shot noise, motion blur and thermal fluctuations of the DNA; (ii) rates of switching between states and (iii) rate of detachment from the DNA. The protein spends roughly equal time in each state. It detaches only from the loosely bound state, with a rate that depends on pH and the salt concentration in solution, while its rates for switching between states are insensitive to both. The diffusivity in the loosely bound state depends primarily on pH and is three to ten times higher than in the tightly bound state. We propose and discuss some new experiments that take full advantage of the new tools of analysis presented here.
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Affiliation(s)
- Christian L Vestergaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.,Decision and Bayesian Computation, Pasteur Institute, CNRS UMR 3571, 25-28 rue du Dr Roux, 75015 Paris, France.,Bioinformatics and Biostatistics Hub, C3BI, Pasteur Institute, CNRS USR 3756, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Paul C Blainey
- MIT Department of Biological Engineering and Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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16
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Akimoto T, Saito K. Exact results for first-passage-time statistics in biased quenched trap models. Phys Rev E 2019; 99:052127. [PMID: 31212478 DOI: 10.1103/physreve.99.052127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Indexed: 11/07/2022]
Abstract
We provide exact results for the mean and variance of first-passage times (FPTs) of making a directed revolution in the presence of a bias in heterogeneous quenched environments where the disorder is expressed by random traps on a ring with period L. FPT statistics are crucially affected by the disorder realization. In the large-L limit, we obtain exact formulas for the FPT statistics, which are described by the sample mean and variance for waiting times of periodically arranged traps. Furthermore, we find that these formulas are still useful for nonperiodic heterogeneous environments; i.e., the results are valid for almost all disorder realizations. Our findings are fundamentally important for the application of FPT to estimate diffusivity of a heterogeneous environment under a bias.
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Affiliation(s)
- Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Keiji Saito
- Department of Physics, Keio University, Yokohama 223-8522, Japan
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17
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Piatt SC, Loparo JJ, Price AC. The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI. Biophys J 2019; 116:2367-2377. [PMID: 31113551 PMCID: PMC6588823 DOI: 10.1016/j.bpj.2019.04.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 02/02/2023] Open
Abstract
A one-dimensional (1D) search is an essential step in DNA target recognition. Theoretical studies have suggested that the sequence dependence of 1D diffusion can help resolve the competing demands of a fast search and high target affinity, a conflict known as the speed-selectivity paradox. The resolution requires that the diffusion energy landscape is correlated with the underlying specific binding energies. In this work, we report observations of a 1D search by quantum dot-labeled EcoRI. Our data supports the view that proteins search DNA via rotation-coupled sliding over a corrugated energy landscape. We observed that whereas EcoRI primarily slides along DNA at low salt concentrations, at higher concentrations, its diffusion is a combination of sliding and hopping. We also observed long-lived pauses at genomic star sites, which differ by a single nucleotide from the target sequence. To reconcile these observations with prior biochemical and structural data, we propose a model of search in which the protein slides over a sequence-independent energy landscape during fast search but rapidly interconverts with a "hemispecific" binding mode in which a half site is probed. This half site interaction stabilizes the transition to a fully specific mode of binding, which can then lead to target recognition.
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Affiliation(s)
- Sadie C Piatt
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.
| | - Allen C Price
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts.
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18
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Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. MICROBIAL CELL 2019; 6:65-101. [PMID: 30652106 PMCID: PMC6334232 DOI: 10.15698/mic2019.01.665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Kenny K H Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Michael J Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - João P Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Julie S Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
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19
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Akimoto T, Barkai E, Saito K. Non-self-averaging behaviors and ergodicity in quenched trap models with finite system sizes. Phys Rev E 2018; 97:052143. [PMID: 29906876 DOI: 10.1103/physreve.97.052143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Tracking tracer particles in heterogeneous environments plays an important role in unraveling material properties. These heterogeneous structures are often static and depend on the sample realizations. Sample-to-sample fluctuations of such disorder realizations sometimes become considerably large. When we investigate the sample-to-sample fluctuations, fundamental averaging procedures are a thermal average for a single disorder realization and the disorder average for different disorder realizations. Here we report on non-self-averaging phenomena in quenched trap models with finite system sizes, where we consider the periodic and the reflecting boundary conditions. Sample-to-sample fluctuations of diffusivity greatly exceed trajectory-to-trajectory fluctuations of diffusivity in the corresponding annealed model. For a single disorder realization, the time-averaged mean square displacement and position-dependent observables converge to constants because of the existence of the equilibrium distribution. This is a manifestation of ergodicity. As a result, the time-averaged quantities depend neither on the initial condition nor on the thermal histories but depend crucially on the disorder realization.
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Affiliation(s)
- Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Eli Barkai
- Department of Physics, Bar Ilan University, Ramat-Gan 52900, Israel
| | - Keiji Saito
- Department of Physics, Keio University, Yokohama 223-8522, Japan
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20
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Chu X, Muñoz V. Roles of conformational disorder and downhill folding in modulating protein-DNA recognition. Phys Chem Chem Phys 2018; 19:28527-28539. [PMID: 29044255 DOI: 10.1039/c7cp04380e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Transcription factors are thought to efficiently search for their target DNA site via a combination of conventional 3D diffusion and 1D diffusion along the DNA molecule mediated by non-specific electrostatic interactions. This process requires the DNA-binding protein to quickly exchange between a search competent and a target recognition mode, but little is known as to how these two binding modes are encoded in the conformational properties of the protein. Here, we investigate this issue on the engrailed homeodomain (EngHD), a DNA-binding domain that folds ultrafast and exhibits a complex conformational behavior consistent with the downhill folding scenario. We explore the interplay between folding and DNA recognition using a coarse-grained computational model that allows us to manipulate the folding properties of the protein and monitor its non-specific and specific binding to DNA. We find that conformational disorder increases the search efficiency of EngHD by promoting a fast gliding search mode in addition to sliding. When gliding, EngHD remains loosely bound to DNA moving linearly along its length. A partially disordered EngHD also binds more dynamically to the target site, reducing the half-life of the specific complex via a spring-loaded mechanism. These findings apply to all conditions leading to partial disorder. However, we also find that at physiologically relevant temperatures EngHD is well folded and can only obtain the conformational flexibility required to accelerate 1D diffusion when it folds/unfolds within the downhill scenario (crossing a marginal free energy barrier). In addition, the conformational flexibility of native downhill EngHD enables its fast reconfiguration to lock into the specific binding site upon arrival, thereby affording finer control of the on- and off-rates of the specific complex. Our results provide key mechanistic insights into how DNA-binding domains optimize specific DNA recognition through the control of their conformational dynamics and folding mechanism.
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Affiliation(s)
- Xiakun Chu
- IMDEA Nanosciences, Faraday 9, Campus de Cantoblanco, Madrid, 28049, Spain
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21
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Akimoto T, Yamamoto E. Detection of transition times from single-particle-tracking trajectories. Phys Rev E 2017; 96:052138. [PMID: 29347678 DOI: 10.1103/physreve.96.052138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 06/07/2023]
Abstract
In heterogeneous environments, the diffusivity is not constant but changes with time. It is important to detect changes in the diffusivity from single-particle-tracking trajectories in experiments. Here, we devise a novel method for detecting the transition times of the diffusivity from trajectory data. A key idea of this method is the introduction of a characteristic time scale of the diffusive states, which is obtained by a fluctuation analysis of the time-averaged mean square displacements. We test our method in silico by using the Langevin equation with a fluctuating diffusivity. We show that our method can successfully detect the transition times of diffusive states and obtain the diffusion coefficient as a function of time. This method will provide a quantitative description of the fluctuating diffusivity in heterogeneous environments and can be applied to time series with transitions of states.
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Affiliation(s)
- Takuma Akimoto
- Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Eiji Yamamoto
- Graduate School of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
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22
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Wieczór M, Czub J. How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1. Nucleic Acids Res 2017. [PMID: 28633355 PMCID: PMC5737604 DOI: 10.1093/nar/gkx534] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein-DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation.
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Affiliation(s)
- Milosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
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23
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Kostiuk G, Dikic J, Schwarz FW, Sasnauskas G, Seidel R, Siksnys V. The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA. Nucleic Acids Res 2017; 45:5968-5979. [PMID: 28453854 PMCID: PMC5449598 DOI: 10.1093/nar/gkx294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
Endonucleases that generate DNA double strand breaks often employ two independent subunits such that the active site from each subunit cuts either DNA strand. Restriction enzyme BcnI is a remarkable exception. It binds to the 5΄-CC/SGG-3΄ (where S = C or G, ‘/’ designates the cleavage position) target as a monomer forming an asymmetric complex, where a single catalytic center approaches the scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements have previously shown that the same BcnI molecule cuts both DNA strands at the target site without dissociation from the DNA. Here, we analyse the BcnI DNA binding and target recognition steps at the single molecule level. We find, using FRET, that BcnI adopts either ‘open’ or ‘closed’ conformation in solution. Next, we directly demonstrate that BcnI slides over long distances on DNA using 1D diffusion and show that sliding is accompanied by occasional jumping events, where the enzyme leaves the DNA and rebinds immediately at a distant site. Furthermore, we quantify the dynamics of the BcnI interactions with cognate and non-cognate DNA, and determine the preferred binding orientation of BcnI to the target site. These results provide new insights into the intricate dynamics of BcnI–DNA interactions.
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Affiliation(s)
- Georgij Kostiuk
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Jasmina Dikic
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Friedrich W Schwarz
- BCUBE, Technische Universitaet Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Ralf Seidel
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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24
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Chow E, Skolnick J. DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid. Biophys J 2017; 112:2261-2270. [PMID: 28591599 DOI: 10.1016/j.bpj.2017.04.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/17/2017] [Accepted: 04/28/2017] [Indexed: 12/18/2022] Open
Abstract
Transcription factors must diffuse through densely packed and coiled DNA to find their binding sites. Using a coarse-grained model of DNA and lac repressor (LacI) in the Escherichia coli nucleoid, simulations were performed to examine how LacI diffuses in such a space. Despite the canonical picture of LacI diffusing rather freely, in reality the DNA is densely packed, is not rigid but highly mobile, and the dynamics of DNA dictates to a great extent the LacI motion. A possibly better picture of unbound LacI motion is that of gated diffusion, where DNA confines LacI in a cage, but LacI can move between cages when hindering DNA strands move out of the way. Three-dimensional diffusion constants for unbound LacI computed from simulations closely match those for unbound LacI in vivo reported in the literature. The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid. A consequence of the DNA internal motion is that protein target search may be accelerated.
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Affiliation(s)
- Edmond Chow
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia.
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biosciences, Georgia Institute of Technology, Atlanta, Georgia
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25
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Structural Foundations of RNA Silencing by Argonaute. J Mol Biol 2017; 429:2619-2639. [PMID: 28757069 DOI: 10.1016/j.jmb.2017.07.018] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
Nearly every cell in the human body contains a set of programmable gene-silencing proteins named Argonaute. Argonaute proteins mediate gene regulation by small RNAs and thereby contribute to cellular homeostasis during diverse physiological process, such as stem cell maintenance, fertilization, and heart development. Over the last decade, remarkable progress has been made toward understanding Argonaute proteins, small RNAs, and their roles in eukaryotic biology. Here, we review current understanding of Argonaute proteins from a structural prospective and discuss unanswered questions surrounding this fascinating class of enzymes.
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26
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Kong M, Beckwitt EC, Springall L, Kad NM, Van Houten B. Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time. Methods Enzymol 2017; 592:213-257. [PMID: 28668122 DOI: 10.1016/bs.mie.2017.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair.
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Affiliation(s)
- Muwen Kong
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Emily C Beckwitt
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Luke Springall
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Bennett Van Houten
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States.
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27
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Kanke M, Tahara E, Huis In't Veld PJ, Nishiyama T. Cohesin acetylation and Wapl-Pds5 oppositely regulate translocation of cohesin along DNA. EMBO J 2016; 35:2686-2698. [PMID: 27872142 PMCID: PMC5167340 DOI: 10.15252/embj.201695756] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 01/17/2023] Open
Abstract
Cohesin is a ring-shaped protein complex that plays a crucial role in sister chromatid cohesion and gene expression. The dynamic association of cohesin with chromatin is essential for these functions. However, the exact nature of cohesin dynamics, particularly cohesin translocation, remains unclear. We evaluated the dynamics of individual cohesin molecules on DNA and found that the cohesin core complex possesses an intrinsic ability to traverse DNA in an adenosine triphosphatase (ATPase)-dependent manner. Translocation ability is suppressed in the presence of Wapl-Pds5 and Sororin; this suppression is alleviated by the acetylation of cohesin and the action of mitotic kinases. In Xenopus laevis egg extracts, cohesin is translocated on unreplicated DNA in an ATPase- and Smc3 acetylation-dependent manner. Cohesin movement changes from bidirectional to unidirectional when cohesin faces DNA replication; otherwise, it is incorporated into replicating DNA without being translocated or is dissociated from replicating DNA This study provides insight into the nature of individual cohesin dynamics and the mechanisms by which cohesin achieves cohesion in different chromatin contexts.
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Affiliation(s)
- Mai Kanke
- Division of Biological Science, Graduate School of Science Nagoya University, Nagoya, Japan
| | - Eri Tahara
- Division of Biological Science, Graduate School of Science Nagoya University, Nagoya, Japan
| | | | - Tomoko Nishiyama
- Division of Biological Science, Graduate School of Science Nagoya University, Nagoya, Japan
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28
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Akimoto T, Barkai E, Saito K. Universal Fluctuations of Single-Particle Diffusivity in a Quenched Environment. PHYSICAL REVIEW LETTERS 2016; 117:180602. [PMID: 27835019 DOI: 10.1103/physrevlett.117.180602] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Indexed: 06/06/2023]
Abstract
Local diffusion coefficients in disordered materials such as living cells are highly heterogeneous. We consider finite systems with quenched disorder in order to investigate the effects of sample disorder fluctuations and confinement on single-particle diffusivity. While the system is ergodic in a single disorder realization, the time-averaged mean square displacement depends crucially on the disorder; i.e., the system is ergodic but non-self-averaging. Moreover, we show that the disorder average of the time-averaged mean square displacement decreases with the system size. We find a universal distribution for diffusivity in the sense that the shape of the distribution does not depend on the dimension. Quantifying the degree of the non-self-averaging effect, we show that fluctuations of single-particle diffusivity far exceed the corresponding annealed theory and also find confinement effects. The relevance for experimental situations is also discussed.
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Affiliation(s)
- Takuma Akimoto
- Graduate School of Science and Technology, Keio University, Yokohama 223-8522, Japan
| | - Eli Barkai
- Department of Physics, Bar Ilan University, Ramat-Gan 52900, Israel
| | - Keiji Saito
- Department of Physics, Keio University, Yokohama 223-8522, Japan
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29
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Greene EC. On the influence of protein-DNA register during homologous recombination. Cell Cycle 2016; 15:172-5. [PMID: 26652653 DOI: 10.1080/15384101.2015.1121352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Homologous recombination enables the exchange of genetic information between related DNA molecules and is a driving force in evolution. Using single-molecule optical microscopy we have recently shown that members of the Rad51/RecA family of recombinases stabilize paired homologous strand of DNA in precise 3-nt increments. Here we discuss an interesting conceptual implication of these results, which is that the recombinases may actively sense and reorganize their alignment register relative to the bound DNA sequences to ensure optimal base triplet pairing interactions during the early stages of recombination.
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Affiliation(s)
- Eric C Greene
- a Department of Biochemistry & Molecular Biophysics , Columbia University , New York , NY , USA
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30
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Gunnarsson A, Simonsson Nyström L, Burazerovic S, Gunnarsson J, Snijder A, Geschwindner S, Höök F. Affinity Capturing and Surface Enrichment of a Membrane Protein Embedded in a Continuous Supported Lipid Bilayer. ChemistryOpen 2016; 5:445-449. [PMID: 27777836 PMCID: PMC5062009 DOI: 10.1002/open.201600070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 11/26/2022] Open
Abstract
Investigations of ligand-binding kinetics to membrane proteins are hampered by their poor stability and low expression levels, which often translates into sensitivity-related limitations impaired by low signal-to-noise ratios. Inspired by affinity capturing of water-soluble proteins, which utilizes water as the mobile phase, we demonstrate affinity capturing and local enrichment of membrane proteins by using a fluid lipid bilayer as the mobile phase. Specific membrane-protein capturing and enrichment in a microfluidic channel was accomplished by immobilizing a synthesized trivalent nitrilotriacetic acid (tris-NTA)-biotin conjugate. A polymer-supported lipid bilayer containing His6-tagged β-secretase (BACE) was subsequently laterally moved over the capture region by using a hydrodynamic flow. Specific enrichment of His6-BACE in the Ni2+-NTA-modified region of the substrate resulted in a stationary three-fold increase in surface coverage, and an accompanied increase in ligand-binding response.
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Affiliation(s)
| | | | - Sabina Burazerovic
- Department of Applied PhysicsChalmers University of Technology412 96GöteborgSweden
| | | | - Arjan Snijder
- Discovery SciencesAstraZeneca R&D Mölndal43183MölndalSweden
| | | | - Fredrik Höök
- Department of Applied PhysicsChalmers University of Technology412 96GöteborgSweden
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31
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Klein M, Chandradoss SD, Depken M, Joo C. Why Argonaute is needed to make microRNA target search fast and reliable. Semin Cell Dev Biol 2016; 65:20-28. [PMID: 27235676 DOI: 10.1016/j.semcdb.2016.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/19/2016] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
MicroRNA (miRNA) interferes with the translation of cognate messenger RNA (mRNA) by finding, preferentially binding, and marking it for degradation. To facilitate the search process, Argonaute (Ago) proteins come together with miRNA, forming a dynamic search complex. In this review we use the language of free-energy landscapes to discuss recent single-molecule and high-resolution structural data in the light of theoretical work appropriated from the study of transcription-factor search. We suggest that experimentally observed internal states of the Ago-miRNA search complex may have the explicit biological function of speeding up search while maintaining specificity.
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Affiliation(s)
- Misha Klein
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Stanley D Chandradoss
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Martin Depken
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft, 2629HZ, The Netherlands.
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft, 2629HZ, The Netherlands.
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32
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Dror I, Rohs R, Mandel-Gutfreund Y. How motif environment influences transcription factor search dynamics: Finding a needle in a haystack. Bioessays 2016; 38:605-12. [PMID: 27192961 PMCID: PMC5023137 DOI: 10.1002/bies.201600005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transcription factors (TFs) have to find their binding sites, which are distributed throughout the genome. Facilitated diffusion is currently the most widely accepted model for this search process. Based on this model the TF alternates between one-dimensional sliding along the DNA, and three-dimensional bulk diffusion. In this view, the non-specific associations between the proteins and the DNA play a major role in the search dynamics. However, little is known about how the DNA properties around the motif contribute to the search. Accumulating evidence showing that TF binding sites are embedded within a unique environment, specific to each TF, leads to the hypothesis that the search process is facilitated by favorable DNA features that help to improve the search efficiency. Here, we review the field and present the hypothesis that TF-DNA recognition is dictated not only by the motif, but is also influenced by the environment in which the motif resides.
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Affiliation(s)
- Iris Dror
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa, Israel.,Departments of Biological Sciences, Chemistry, Physics, and Computer Science, Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA
| | - Remo Rohs
- Departments of Biological Sciences, Chemistry, Physics, and Computer Science, Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA
| | - Yael Mandel-Gutfreund
- Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa, Israel
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33
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Coarse-grained models for studying protein diffusion along DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1262] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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34
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Lee S, Oh Y, Lee J, Choe S, Lim S, Lee HS, Jo K, Schwartz DC. DNA binding fluorescent proteins for the direct visualization of large DNA molecules. Nucleic Acids Res 2016; 44:e6. [PMID: 26264666 PMCID: PMC4705684 DOI: 10.1093/nar/gkv834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/03/2015] [Accepted: 08/06/2015] [Indexed: 12/14/2022] Open
Abstract
Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Yeeun Oh
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Jungyoon Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Sojeong Choe
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Korea
| | - Hyun Soo Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
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35
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Chandradoss SD, Schirle NT, Szczepaniak M, MacRae IJ, Joo C. A Dynamic Search Process Underlies MicroRNA Targeting. Cell 2015; 162:96-107. [PMID: 26140593 DOI: 10.1016/j.cell.2015.06.032] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 12/31/2022]
Abstract
Argonaute proteins play a central role in mediating post-transcriptional gene regulation by microRNAs (miRNAs). Argonautes use the nucleotide sequences in miRNAs as guides for identifying target messenger RNAs for repression. Here, we used single-molecule FRET to directly visualize how human Argonaute-2 (Ago2) searches for and identifies target sites in RNAs complementary to its miRNA guide. Our results suggest that Ago2 initially scans for target sites with complementarity to nucleotides 2-4 of the miRNA. This initial transient interaction propagates into a stable association when target complementarity extends to nucleotides 2-8. This stepwise recognition process is coupled to lateral diffusion of Ago2 along the target RNA, which promotes the target search by enhancing the retention of Ago2 on the RNA. The combined results reveal the mechanisms that Argonaute likely uses to efficiently identify miRNA target sites within the vast and dynamic agglomeration of RNA molecules in the living cell.
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Affiliation(s)
- Stanley D Chandradoss
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Lorentzweg 1, 2628 CJ, Delft, The Netherlands
| | - Nicole T Schirle
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Malwina Szczepaniak
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Lorentzweg 1, 2628 CJ, Delft, The Netherlands
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Lorentzweg 1, 2628 CJ, Delft, The Netherlands
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36
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Fish J, Scrimgeour J. Fast weighted centroid algorithm for single particle localization near the information limit. APPLIED OPTICS 2015; 54:6360-6366. [PMID: 26193415 DOI: 10.1364/ao.54.006360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A simple weighting scheme that enhances the localization precision of center of mass calculations for radially symmetric intensity distributions is presented. The algorithm effectively removes the biasing that is common in such center of mass calculations. Localization precision compares favorably with other localization algorithms used in super-resolution microscopy and particle tracking, while significantly reducing the processing time and memory usage. We expect that the algorithm presented will be of significant utility when fast computationally lightweight particle localization or tracking is desired.
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37
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Mechetin GV, Zharkov DO. Mechanisms of diffusional search for specific targets by DNA-dependent proteins. BIOCHEMISTRY (MOSCOW) 2015; 79:496-505. [PMID: 25100007 DOI: 10.1134/s0006297914060029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To perform their functions, many DNA-dependent proteins have to quickly locate specific targets against the vast excess of nonspecific DNA. Although this problem was first formulated over 40 years ago, the mechanism of such search remains one of the unsolved fundamental problems in the field of protein-DNA interactions. Several complementary mechanisms have been suggested: sliding, based on one-dimensional random diffusion along the DNA contour; hopping, in which the protein "jumps" between the closely located DNA fragments; macroscopic association-dissociation of the protein-DNA complex; and intersegmental transfer. This review covers the modern state of the problem of target DNA search, theoretical descriptions, and methods of research at the macroscopic (molecule ensembles) and microscopic (individual molecules) levels. Almost all studied DNA-dependent proteins search for specific targets by combined three-dimensional diffusion and one-dimensional diffusion along the DNA contour.
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Affiliation(s)
- G V Mechetin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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38
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Colomb W, Sarkar SK. Extracting physics of life at the molecular level: A review of single-molecule data analyses. Phys Life Rev 2015; 13:107-37. [PMID: 25660417 DOI: 10.1016/j.plrev.2015.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
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Affiliation(s)
- Warren Colomb
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States.
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39
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Ando T, Skolnick J. Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models. PLoS Comput Biol 2014; 10:e1003990. [PMID: 25504215 PMCID: PMC4263358 DOI: 10.1371/journal.pcbi.1003990] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 10/16/2014] [Indexed: 11/19/2022] Open
Abstract
DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA. Recent experimental results and theoretical analyses revealed that the proteins show a rotation-coupled sliding along DNA helical pitch. Here, we performed Brownian dynamics simulations using newly developed coarse-grained protein and DNA models for evaluating how hydrodynamic interactions between the protein and DNA molecules, binding affinity of the protein to DNA, and DNA fluctuations affect the one dimensional diffusion of the protein on the DNA. Our results indicate that intermolecular hydrodynamic interactions reduce 1D diffusivity by 30%. On the other hand, structural fluctuations of DNA give rise to steric collisions between the CG-proteins and DNA, resulting in faster 1D sliding of the protein. Proteins with low binding affinities consistent with experimental estimates of non-specific DNA binding show hopping along the CG-DNA. This hopping significantly increases sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome.
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Affiliation(s)
- Tadashi Ando
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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40
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Cravens SL, Hobson M, Stivers JT. Electrostatic properties of complexes along a DNA glycosylase damage search pathway. Biochemistry 2014; 53:7680-92. [PMID: 25408964 PMCID: PMC4263432 DOI: 10.1021/bi501011m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human uracil DNA glycosylase (hUNG) follows an extended reaction coordinate for locating rare uracil bases in genomic DNA. This process begins with diffusion-controlled engagement of undamaged DNA, followed by a damage search step in which the enzyme remains loosely associated with the DNA chain (translocation), and finally, a recognition step that allows the enzyme to efficiently bind and excise uracil when it is encountered. At each step along this coordinate, the enzyme must form DNA interactions that are highly specialized for either rapid damage searching or catalysis. Here we make extensive measurements of hUNG activity as a function of salt concentration to dissect the thermodynamic, kinetic, and electrostatic properties of key enzyme states along this reaction coordinate. We find that the interaction of hUNG with undamaged DNA is electrostatically driven at a physiological concentration of potassium ions (ΔGelect = -3.5 ± 0.5 kcal mol(-1)), with only a small nonelectrostatic contribution (ΔGnon = -2.0 ± 0.2 kcal mol(-1)). In contrast, the interaction with damaged DNA is dominated by the nonelectrostatic free energy term (ΔGnon = -7.2 ± 0.1 kcal mol(-1)), yet retains the nonspecific electrostatic contribution (ΔGelect = -2.3 ± 0.2 kcal mol(-1)). Stopped-flow kinetic experiments established that the salt sensitivity of damaged DNA binding originates from a reduction of kon, while koff is weakly dependent on salt. Similar findings were obtained from the salt dependences of the steady-state kinetic parameters, where the diffusion-controlled kcat/Km showed a salt dependence similar to kon, while kcat (limited by product release) was weakly dependent on salt. Finally, the salt dependence of translocation between two uracil sites separated by 20 bp in the same DNA chain was indistinguishable from that of kon. This result suggests that the transition-state for translocation over this spacing resembles that for DNA association from bulk solution and that hUNG escapes the DNA ion cloud during translocation. These findings provide key insights into how the ionic environment in cells influences the DNA damage search pathway.
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Affiliation(s)
- Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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41
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Bhattacherjee A, Levy Y. Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding. Nucleic Acids Res 2014; 42:12404-14. [PMID: 25324308 PMCID: PMC4227778 DOI: 10.1093/nar/gku932] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The recognition of DNA-binding proteins (DBPs) to their specific site often precedes by a search technique in which proteins slide, hop along the DNA contour or perform inter-segment transfer and 3D diffusion to dissociate and re-associate to distant DNA sites. In this study, we demonstrated that the strength and nature of the non-specific electrostatic interactions, which govern the search dynamics of DBPs, are strongly correlated with the conformation of the DNA. We tuned two structural parameters, namely curvature and the extent of helical twisting in circular DNA. These two factors are mutually independent of each other and can modulate the electrostatic potential through changing the geometry of the circular DNA conformation. The search dynamics for DBPs on circular DNA is therefore markedly different compared with linear B-DNA. Our results suggest that, for a given DBP, the rotation-coupled sliding dynamics is precluded in highly curved DNA (as well as for over-twisted DNA) because of the large electrostatic energy barrier between the inside and outside of the DNA molecule. Under such circumstances, proteins prefer to hop in order to explore interior DNA sites. The change in the balance between sliding and hopping propensities as a function of DNA curvature or twisting may result in different search efficiency and speed.
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Affiliation(s)
- Arnab Bhattacherjee
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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42
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Ryu KS, Tugarinov V, Clore GM. Probing the rate-limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by (15)Nz-exchange NMR spectroscopy. J Am Chem Soc 2014; 136:14369-72. [PMID: 25253516 PMCID: PMC4210153 DOI: 10.1021/ja5081585] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Indexed: 11/30/2022]
Abstract
The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by (15)Nz-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mechanisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that predominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer between specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that transfer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by z-exchange spectroscopy. Intramolecular transfer with comparable rate constants occurs between sites of the same and opposing polarity, indicating that both rotation-coupled sliding and hopping/flipping (analogous to geminate recombination) occur. The half-life for intramolecular transfer (0.5-1 s) is many orders of magnitude larger than the calculated transfer time (1-100 μs) by sliding, leading us to conclude that the intramolecular transfer rates measured by z-exchange spectroscopy represent the rate-limiting step for a one-base-pair shift from the specific site to the immediately adjacent nonspecific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may become rate-limiting at very low salt concentrations.
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Affiliation(s)
- Kyoung-Seok Ryu
- Laboratory
of Chemical Physics, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
- Korean
Basic Science Institute, Ochang-Eup, Chunbuk-Do 363-883, South Korea
| | - Vitali Tugarinov
- Laboratory
of Chemical Physics, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
| | - G. Marius Clore
- Laboratory
of Chemical Physics, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
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43
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Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics. Biophys J 2014; 106:220-31. [PMID: 24411254 DOI: 10.1016/j.bpj.2013.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/19/2013] [Accepted: 11/04/2013] [Indexed: 01/10/2023] Open
Abstract
Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10(-11) liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20-100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation.
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44
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Vuzman D, Levy Y. The “Monkey-Bar” Mechanism for Searching for the DNA Target Site: The Molecular Determinants. Isr J Chem 2014. [DOI: 10.1002/ijch.201400107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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45
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Lee JB, Cho WK, Park J, Jeon Y, Kim D, Lee SH, Fishel R. Single-molecule views of MutS on mismatched DNA. DNA Repair (Amst) 2014; 20:82-93. [PMID: 24629484 PMCID: PMC4245035 DOI: 10.1016/j.dnarep.2014.02.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 02/11/2014] [Accepted: 02/14/2014] [Indexed: 01/09/2023]
Abstract
Base-pair mismatches that occur during DNA replication or recombination can reduce genetic stability or conversely increase genetic diversity. The genetics and biophysical mechanism of mismatch repair (MMR) has been extensively studied since its discovery nearly 50 years ago. MMR is a strand-specific excision-resynthesis reaction that is initiated by MutS homolog (MSH) binding to the mismatched nucleotides. The MSH mismatch-binding signal is then transmitted to the immediate downstream MutL homolog (MLH/PMS) MMR components and ultimately to a distant strand scission site where excision begins. The mechanism of signal transmission has been controversial for decades. We have utilized single molecule Forster Resonance Energy Transfer (smFRET), Fluorescence Tracking (smFT) and Polarization Total Internal Reflection Fluorescence (smP-TIRF) to examine the interactions and dynamic behaviors of single Thermus aquaticus MutS (TaqMutS) particles on mismatched DNA. We determined that TaqMutS forms an incipient clamp to search for a mismatch in ~1 s intervals by 1-dimensional (1D) thermal fluctuation-driven rotational diffusion while in continuous contact with the helical duplex DNA. When MutS encounters a mismatch it lingers for ~3 s to exchange bound ADP for ATP (ADP→ATP exchange). ATP binding by TaqMutS induces an extremely stable clamp conformation (~10 min) that slides off the mismatch and moves along the adjacent duplex DNA driven simply by 1D thermal diffusion. The ATP-bound sliding clamps rotate freely while in discontinuous contact with the DNA. The visualization of a train of MSH proteins suggests that dissociation of ATP-bound sliding clamps from the mismatch permits multiple mismatch-dependent loading events. These direct observations have provided critical clues into understanding the molecular mechanism of MSH proteins during MMR.
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Affiliation(s)
- Jong-Bong Lee
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea; School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 790-784, Republic of Korea.
| | - Won-Ki Cho
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Jonghyun Park
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Yongmoon Jeon
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Daehyung Kim
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Seung Hwan Lee
- School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang 790-784, Republic of Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, United States; Physics Department, The Ohio State University, Columbus, OH 43210, United States.
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46
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Hughes CD, Simons M, Mackenzie CE, Van Houten B, Kad NM. Single molecule techniques in DNA repair: a primer. DNA Repair (Amst) 2014; 20:2-13. [PMID: 24819596 DOI: 10.1016/j.dnarep.2014.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.
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Affiliation(s)
- Craig D Hughes
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Cassidy E Mackenzie
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil M Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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47
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Mackay J. Transcription factor seeks DNA-cognate site preferred. J Mol Biol 2014; 426:1370-2. [PMID: 24333952 DOI: 10.1016/j.jmb.2013.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel Mackay
- School of Molecular Bioscience, University of Sydney, NSW 2006, Australia
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48
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Guardiani C, Cencini M, Cecconi F. Coarse-grained modeling of protein unspecifically bound to DNA. Phys Biol 2014; 11:026003. [PMID: 24685517 DOI: 10.1088/1478-3975/11/2/026003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
There is now a certain consensus that transcription factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D diffusion in solution (jumps), 1D diffusion along DNA (sliding), and small jumps (hopping), achieving association rates higher than for 3D diffusion alone. We investigate the FD phenomenology through molecular dynamics simulations in the framework of coarse-grained modeling. We show that, despite the crude approximations, the model generates, upon varying the equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix, leading to a coupling of translation along the DNA axis with rotation around it. The 1D diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument that can be used to quantitatively reproduce the measured values.
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Affiliation(s)
- Carlo Guardiani
- Dipartimento di Fisica, University 'Sapienza', Piazzale A. Moro 2, 00185 Rome, Italy
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Affiliation(s)
- Daniel Duzdevich
- Department of Biological Sciences, Department of Chemistry, and Department of
Biochemistry and Molecular
Biophysics and the Howard Hughes Medical Institute, Columbia University, 650 West 168th Street, New York, New York 10032, United
States
| | - Sy Redding
- Department of Biological Sciences, Department of Chemistry, and Department of
Biochemistry and Molecular
Biophysics and the Howard Hughes Medical Institute, Columbia University, 650 West 168th Street, New York, New York 10032, United
States
| | - Eric C. Greene
- Department of Biological Sciences, Department of Chemistry, and Department of
Biochemistry and Molecular
Biophysics and the Howard Hughes Medical Institute, Columbia University, 650 West 168th Street, New York, New York 10032, United
States
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50
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Silverstein TD, Gibb B, Greene EC. Visualizing protein movement on DNA at the single-molecule level using DNA curtains. DNA Repair (Amst) 2014; 20:94-109. [PMID: 24598576 DOI: 10.1016/j.dnarep.2014.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 11/18/2022]
Abstract
A fundamental feature of many nucleic-acid binding proteins is their ability to move along DNA either by diffusion-based mechanisms or by ATP-hydrolysis driven translocation. For example, most site-specific DNA-binding proteins must diffuse to some extent along DNA to either find their target sites, or to otherwise fulfill their biological roles. Similarly, nucleic-acid translocases such as helicases and polymerases must move along DNA to fulfill their functions. In both instances, the proteins must also be capable of moving in crowded environments while navigating through DNA-bound obstacles. These types of behaviors can be challenging to analyze by bulk biochemical methods because of the transient nature of the interactions, and/or heterogeneity of the reaction intermediates. The advent of single-molecule methodologies has overcome some of these problems, and has led to many new insights into the mechanisms that contribute to protein motion along DNA. We have developed DNA curtains as a tool to facilitate single molecule observations of protein-nucleic acid interactions, and we have applied these new research tools to systems involving both diffusive-based motion as well as ATP directed translocation. Here we highlight these studies by first discussing how diffusion contributes to target searches by proteins involved in post-replicative mismatch repair. We then discuss DNA curtain assays of two different DNA translocases, RecBCD and FtsK, which participate in homologous DNA recombination and site-specific DNA recombination, respectively.
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Affiliation(s)
- Timothy D Silverstein
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bryan Gibb
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, USA.
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