1
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Chua GNL, Liu S. When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. Annu Rev Biophys 2024; 53:169-191. [PMID: 38237015 DOI: 10.1146/annurev-biophys-030822-032904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.
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Affiliation(s)
- Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
- Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
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2
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Chakraborty UK, Park Y, Sengupta K, Jung W, Joshi CP, Francis DH, Chen P. A 'through-DNA' mechanism for metal uptake-vs.-efflux regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570191. [PMID: 38105935 PMCID: PMC10723295 DOI: 10.1101/2023.12.05.570191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Transition metals like Zn are essential for all organisms including bacteria, but fluctuations of their concentrations in the cell can be lethal. Organisms have thus evolved complex mechanisms for cellular metal homeostasis. One mechanistic paradigm involves pairs of transcription regulators sensing intracellular metal concentrations to regulate metal uptake and efflux. Here we report that Zur and ZntR, a prototypical pair of regulators for Zn uptake and efflux in E. coli , respectively, can coordinate their regulation through DNA, besides sensing cellular Zn 2+ concentrations. Using a combination of live-cell single-molecule tracking and in vitro single-molecule FRET measurements, we show that unmetallated ZntR can enhance the unbinding kinetics of Zur from DNA by directly acting on Zur-DNA complexes, possibly through forming heteromeric ternary and quaternary complexes that involve both protein-DNA and protein-protein interactions. This 'through-DNA' mechanism may functionally facilitate the switching in Zn uptake regulation when bacteria encounter changing Zn environments; it could also be relevant for regulating the uptake-vs.-efflux of various metals across different bacterial species and yeast.
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3
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Guo AD, Yan KN, Hu H, Zhai L, Hu TF, Su H, Chi Y, Zha J, Xu Y, Zhao D, Lu X, Xu YJ, Zhang J, Tan M, Chen XH. Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors. Nat Chem 2023:10.1038/s41557-023-01196-z. [PMID: 37106095 DOI: 10.1038/s41557-023-01196-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Precise dissection of DNA-protein interactions is essential for elucidating the recognition basis, dynamics and gene regulation mechanism. However, global profiling of weak and dynamic DNA-protein interactions remains a long-standing challenge. Here, we establish the light-induced lysine (K) enabled crosslinking (LIKE-XL) strategy for spatiotemporal and global profiling of DNA-protein interactions. Harnessing unique abilities to capture weak and transient DNA-protein interactions, we demonstrate that LIKE-XL enables the discovery of low-affinity transcription-factor/DNA interactions via sequence-specific DNA baits, determining the binding sites for transcription factors that have been previously unknown. More importantly, we successfully decipher the dynamics of the transcription factor subproteome in response to drug treatment in a time-resolved manner, and find downstream target transcription factors from drug perturbations, providing insight into their dynamic transcriptional networks. The LIKE-XL strategy offers a complementary method to expand the DNA-protein profiling toolbox and map accurate DNA-protein interactomes that were previously inaccessible via non-covalent strategies, for better understanding of protein function in health and disease.
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Affiliation(s)
- An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke-Nian Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Teng-Fei Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yijia Chi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyin Zha
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dongxin Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Jiang Xu
- School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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4
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Fisunov GY, Zubov AI, Pobeguts OV, Varizhuk AM, Galyamina MA, Evsyutina DV, Semashko TA, Manuvera VA, Kovalchuk SI, Ziganshin RK, Barinov NA, Klinov DV, Govorun VM. The Dynamics of Mycoplasma gallisepticum Nucleoid Structure at the Exponential and Stationary Growth Phases. Front Microbiol 2021; 12:753760. [PMID: 34867875 PMCID: PMC8637272 DOI: 10.3389/fmicb.2021.753760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
The structure and dynamics of bacterial nucleoids play important roles in regulating gene expression. Bacteria of class Mollicutes and, in particular, mycoplasmas feature extremely reduced genomes. They lack multiple structural proteins of the nucleoid, as well as regulators of gene expression. We studied the organization of Mycoplasma gallisepticum nucleoids in the stationary and exponential growth phases at the structural and protein levels. The growth phase transition results in the structural reorganization of M. gallisepticum nucleoid. In particular, it undergoes condensation and changes in the protein content. The observed changes corroborate with the previously identified global rearrangement of the transcriptional landscape in this bacterium during the growth phase transition. In addition, we identified that the glycolytic enzyme enolase functions as a nucleoid structural protein in this bacterium. It is capable of non-specific DNA binding and can form fibril-like complexes with DNA.
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Affiliation(s)
- Gleb Y Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander I Zubov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Olga V Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Mariya A Galyamina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria V Evsyutina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valentin A Manuvera
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Sergey I Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Rustam K Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nicolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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5
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Liu M, Qiu JG, Ma F, Zhang CY. Advances in single-molecule fluorescent nanosensors. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1716. [PMID: 33779063 DOI: 10.1002/wnan.1716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022]
Abstract
Single-molecule detection represents the ultimate sensitivity in measurement science with the characteristics of simplicity, rapidity, low sample consumption, and high signal-to-noise ratio and has attracted considerable attentions in biosensor development. In recent years, a variety of functional nanomaterials with unique chemical, optical, mechanical, and electronic features have been synthesized. The integration of single-molecule detection with functional nanomaterials enables the construction of novel single-molecule fluorescent nanosensors with excellent performance. Herein, we review the advance in single-molecule fluorescent nanosensors constructed by novel nanomaterials including quantum dots, gold nanoparticles, upconversion nanoparticles, fluorescent conjugated polymer nanoparticles, nanosheets, and magnetic nanoparticles in the past decade (2011-2020), and discuss the strategies, features, and applications of single-molecule fluorescent nanosensors in the detection of microRNAs, DNAs, enzymes, proteins, viruses, and live cells. Moreover, we highlight the future direction and challenges in this area. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > In Vitro Nanoparticle-Based Sensing Diagnostic Tools > Diagnostic Nanodevices.
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Affiliation(s)
- Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
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6
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Kopu̅stas A, Ivanovaitė Š, Rakickas T, Pocevičiu̅tė E, Paksaitė J, Karvelis T, Zaremba M, Manakova E, Tutkus M. Oriented Soft DNA Curtains for Single-Molecule Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3428-3437. [PMID: 33689355 PMCID: PMC8280724 DOI: 10.1021/acs.langmuir.1c00066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Over the past 20 years, single-molecule methods have become extremely important for biophysical studies. These methods, in combination with new nanotechnological platforms, can significantly facilitate experimental design and enable faster data acquisition. A nanotechnological platform, which utilizes a flow-stretch of immobilized DNA molecules, called DNA Curtains, is one of the best examples of such combinations. Here, we employed new strategies to fabricate a flow-stretch assay of stably immobilized and oriented DNA molecules using a protein template-directed assembly. In our assay, a protein template patterned on a glass coverslip served for directional assembly of biotinylated DNA molecules. In these arrays, DNA molecules were oriented to one another and maintained extended by either single- or both-end immobilization to the protein templates. For oriented both-end DNA immobilization, we employed heterologous DNA labeling and protein template coverage with the antidigoxigenin antibody. In contrast to single-end immobilization, both-end immobilization does not require constant buffer flow for keeping DNAs in an extended configuration, allowing us to study protein-DNA interactions at more controllable reaction conditions. Additionally, we increased the immobilization stability of the biotinylated DNA molecules using protein templates fabricated from traptavidin. Finally, we demonstrated that double-tethered Soft DNA Curtains can be used in nucleic acid-interacting protein (e.g., CRISPR-Cas9) binding assay that monitors the binding location and position of individual fluorescently labeled proteins on DNA.
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Affiliation(s)
- Aurimas Kopu̅stas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Šaru̅nė Ivanovaitė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Tomas Rakickas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Ernesta Pocevičiu̅tė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Justė Paksaitė
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Tautvydas Karvelis
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Marijonas Tutkus
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
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7
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Takahashi S, Oshige M, Katsura S. DNA Manipulation and Single-Molecule Imaging. Molecules 2021; 26:1050. [PMID: 33671359 PMCID: PMC7922115 DOI: 10.3390/molecules26041050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan;
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
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8
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Ainsworth HC, Howard TD, Langefeld CD. Intrinsic DNA topology as a prioritization metric in genomic fine-mapping studies. Nucleic Acids Res 2020; 48:11304-11321. [PMID: 33084892 PMCID: PMC7672465 DOI: 10.1093/nar/gkaa877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/23/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
In genomic fine-mapping studies, some approaches leverage annotation data to prioritize likely functional polymorphisms. However, existing annotation resources can present challenges as many lack information for novel variants and/or may be uninformative for non-coding regions. We propose a novel annotation source, sequence-dependent DNA topology, as a prioritization metric for fine-mapping. DNA topology and function are well-intertwined, and as an intrinsic DNA property, it is readily applicable to any genomic region. Here, we constructed and applied Minor Groove Width (MGW) as a prioritization metric. Using an established MGW-prediction method, we generated a MGW census for 199 038 197 SNPs across the human genome. Summarizing a SNP's change in MGW (ΔMGW) as a Euclidean distance, ΔMGW exhibited a strongly right-skewed distribution, highlighting the infrequency of SNPs that generate dissimilar shape profiles. We hypothesized that phenotypically-associated SNPs can be prioritized by ΔMGW. We tested this hypothesis in 116 regions analyzed by a Massively Parallel Reporter Assay and observed enrichment of large ΔMGW for functional polymorphisms (P = 0.0007). To illustrate application in fine-mapping studies, we applied our MGW-prioritization approach to three non-coding regions associated with systemic lupus erythematosus. Together, this study presents the first usage of sequence-dependent DNA topology as a prioritization metric in genomic association studies.
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Affiliation(s)
- Hannah C Ainsworth
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Timothy D Howard
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA
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9
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Krogh TJ, Franke A, Møller-Jensen J, Kaleta C. Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation. Front Microbiol 2020; 11:2002. [PMID: 32983020 PMCID: PMC7491251 DOI: 10.3389/fmicb.2020.02002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Both intrinsic and extrinsic mechanisms regulating bacterial expression have been elucidated and described, however, such studies have mainly focused on local effects on the two-dimensional structure of the prokaryote genome while long-range as well as spatial interactions influencing gene expression are still only poorly understood. In this paper, we investigate the association between co-expression and distance between genes, using RNA-seq data at multiple growth phases in order to illuminate whether such conserved patterns are an indication of a gene regulatory mechanism relevant for prokaryotic cell proliferation, adaption, and evolution. We observe recurrent sinusoidal patterns in correlation of pairwise expression as function of genomic distance and rule out that these are caused by transcription-induced supercoiling gradients, gene clustering in operons, or association with regulatory transcription factors (TFs). By comparing spatial proximity for pairs of genomic bins with their correlation of pairwise expression, we further observe a high co-expression proportional with the spatial proximity. Based on these observations, we propose that the observed patterns are related to nucleoid structure as a product of transcriptional spilling, where genes actively influence transcription of spatially proximal genes through increases within shared local pools of RNA polymerases (RNAP), and actively spilling transcription onto neighboring genes.
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Affiliation(s)
- Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University Kiel, Kiel, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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10
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Calabrese C, Uriarte I, Insausti A, Vallejo-López M, Basterretxea FJ, Cochrane SA, Davis BG, Corzana F, Cocinero EJ. Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars. ACS CENTRAL SCIENCE 2020; 6:293-303. [PMID: 32123748 PMCID: PMC7047431 DOI: 10.1021/acscentsci.9b01277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 06/10/2023]
Abstract
The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, "naked" conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5' and OH-3' are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3' is "born free" in the "naked" lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for "life's code" and suggest a mechanism by which the resulting freedom of OH-3' (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5'-to-3'.
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Affiliation(s)
- Camilla Calabrese
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Iciar Uriarte
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Aran Insausti
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
| | - Montserrat Vallejo-López
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Francisco J. Basterretxea
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
| | - Stephen A. Cochrane
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
- The
Rosalind Franklin Institute, Oxfordshire, OX11 0FA, United Kingdom
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La
Rioja, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento
de Química Física, Facultad de Ciencia y
Tecnología, Universidad del
País Vasco (UPV/EHU), Campus de Leioa, Ap. 644, 48080 Bilbao, Spain
- Instituto
Biofisika (CSIC, UPV/EHU), 48080 Bilbao, Spain
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11
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Li Y, Zhao L, Yao Y, Guo X. Single-Molecule Nanotechnologies: An Evolution in Biological Dynamics Detection. ACS APPLIED BIO MATERIALS 2019; 3:68-85. [DOI: 10.1021/acsabm.9b00840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Lihua Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yuan Yao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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12
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Murugan E, J NJ, Ariraman M, Rajendran S, Kathirvel J, Akshata CR, Kumar K. Core-Shell Nanostructured Fe 3O 4-Poly(styrene- co-vinylbenzyl chloride) Grafted PPI Dendrimers Stabilized with AuNPs/PdNPs for Efficient Nuclease Activity. ACS OMEGA 2018; 3:13685-13693. [PMID: 30411048 PMCID: PMC6217652 DOI: 10.1021/acsomega.8b01326] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/17/2018] [Indexed: 06/08/2023]
Abstract
Four different novel magnetic core-shell nanocomposites stabilized with Au/Pd nanoparticles (NPs) were prepared by a simple procedure and demonstrated their catalytic activity for effective cleavage of pBR322 DNA. Initially, the Fe3O4-poly(styrene-divinylbenzene-vinylbenzyl chloride) (ST-DVB-VBC) matrix functionalized with 3-aminobenzoic acid was prepared and grafted with PPI-G(2) and PPI-G(3) dendrimers. Each core-shell matrix was immobilized with AuNPs and PdNPs separately. The resulting composites were characterized by FT-IR, UV-vis, SEM, TEM, XRD, VSM, XPS, Raman, and TGA. The magnetic core-shell nanocomposites at concentrations from 30 to 50 μM were employed separately to study DNA cleavage by agarose gel electrophoresis. Among the four magnetic core-shell nanocomposites, Fe3O4-poly(ST-DVB-VBC)-PPI-G(3)-AuNPs showed higher activity than others for DNA cleavage, and formed Form-II and -III DNA. When the concentration of Fe3O4-poly(ST-DVB-VBC)-PPI-G(3)-AuNPs was increased from 40 to 45 and 45 to 50 μM, Form-III (linear) DNA was observed with 10 and 22%, respectively, in addition to Form-II. This observation suggests formation of linear DNA from the supercoiled DNA via nicked DNA-intermediated consecutive cleaving process. The magnetic core-shell nanocomposites were stable and monodispersed, and exhibited rapid magnetic response. These properties are crucial for their application in biomolecular separations and targeted drug-delivery in the future.
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Affiliation(s)
- Eagambaram Murugan
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
| | - Nimita Jebaranjitham J
- PG
Department of Chemistry, Women’s
Christian College (An Autonomous Institution Affiliated to University
of Madras), College Road, Chennai 600 006, India
| | - Mathivathanan Ariraman
- Department
of Chemical Engineering, National Chung
Hsing University, Taichung
City 402, Taiwan
| | - Saravanan Rajendran
- Escuela
Universitaria de Ingeniería Mecánica (EUDIM), Universidad de Tarapacá, Avda. General Velásquez, 1775 Arica, Chile
| | - Janankiraman Kathirvel
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
| | - C. R. Akshata
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
| | - Kalpana Kumar
- Department
of Physical Chemistry, School of Chemical Sciences, University of Madras, Maraimalai Campus, Chennai 600025, Tamil Nadu, India
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13
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Krogh TJ, Møller-Jensen J, Kaleta C. Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. Front Microbiol 2018; 9:2019. [PMID: 30210483 PMCID: PMC6119826 DOI: 10.3389/fmicb.2018.02019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.
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Affiliation(s)
- Thøger J Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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14
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Mechanisms of Protein Search for Targets on DNA: Theoretical Insights. Molecules 2018; 23:molecules23092106. [PMID: 30131459 PMCID: PMC6225296 DOI: 10.3390/molecules23092106] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 11/17/2022] Open
Abstract
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years, only recently microscopic aspects of these processes became more clear. In this work, we present a review on current theoretical understanding of the molecular mechanisms of the protein target search. A comprehensive discrete-state stochastic method to explain the dynamics of the protein search phenomena is introduced and explained. Our theoretical approach utilizes a first-passage analysis and it takes into account the most relevant physical-chemical processes. It is able to describe many fascinating features of the protein search, including unusually high effective association rates, high selectivity and specificity, and the robustness in the presence of crowders and sequence heterogeneity.
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15
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Loescher S, Groeer S, Walther A. 3D DNA Origami Nanoparticles: From Basic Design Principles to Emerging Applications in Soft Matter and (Bio‐)Nanosciences. Angew Chem Int Ed Engl 2018; 57:10436-10448. [DOI: 10.1002/anie.201801700] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/11/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Sebastian Loescher
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
| | - Saskia Groeer
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
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16
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Loescher S, Groeer S, Walther A. 3D‐DNA‐Origami‐Nanopartikel: von grundlegenden Designprinzipien hin zu neuartigen Anwendungen in der weichen Materie und den (Bio‐)Nanowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sebastian Loescher
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
| | - Saskia Groeer
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
| | - Andreas Walther
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
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17
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Chakraborty D, Wales DJ. Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA. J Phys Chem Lett 2018; 9:229-241. [PMID: 29240425 DOI: 10.1021/acs.jpclett.7b01933] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Chemistry, The University of Texas at Austin , 24th Street Stop A5300, Austin, Texas 78712, United States
| | - David J Wales
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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18
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Nagao M, Fujiwara Y, Matsubara T, Hoshino Y, Sato T, Miura Y. Design of Glycopolymers Carrying Sialyl Oligosaccharides for Controlling the Interaction with the Influenza Virus. Biomacromolecules 2017; 18:4385-4392. [DOI: 10.1021/acs.biomac.7b01426] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masanori Nagao
- Department
of Engineering, Graduate School of Chemical Engineering, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Yurina Fujiwara
- Department
of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Teruhiko Matsubara
- Department
of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yu Hoshino
- Department
of Engineering, Graduate School of Chemical Engineering, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Toshinori Sato
- Department
of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yoshiko Miura
- Department
of Engineering, Graduate School of Chemical Engineering, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
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19
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20
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21
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Chen C, Pettitt BM. DNA Shape versus Sequence Variations in the Protein Binding Process. Biophys J 2017; 110:534-544. [PMID: 26840719 DOI: 10.1016/j.bpj.2015.11.3527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/15/2015] [Accepted: 11/02/2015] [Indexed: 01/02/2023] Open
Abstract
The binding process of a protein with a DNA involves three stages: approach, encounter, and association. It has been known that the complexation of protein and DNA involves mutual conformational changes, especially for a specific sequence association. However, it is still unclear how the conformation and the information in the DNA sequences affects the binding process. What is the extent to which the DNA structure adopted in the complex is induced by protein binding, or is instead intrinsic to the DNA sequence? In this study, we used the multiscale simulation method to explore the binding process of a protein with DNA in terms of DNA sequence, conformation, and interactions. We found that in the approach stage the protein can bind both the major and minor groove of the DNA, but uses different features to locate the binding site. The intrinsic conformational properties of the DNA play a significant role in this binding stage. By comparing the specific DNA with the nonspecific in unbound, intermediate, and associated states, we found that for a specific DNA sequence, ∼40% of the bending in the association forms is intrinsic and that ∼60% is induced by the protein. The protein does not induce appreciable bending of nonspecific DNA. In addition, we proposed that the DNA shape variations induced by protein binding are required in the early stage of the binding process, so that the protein is able to approach, encounter, and form an intermediate at the correct site on DNA.
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Affiliation(s)
- Chuanying Chen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas.
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22
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Ordu O, Lusser A, Dekker NH. Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics. Biophys Rev 2016; 8:33-49. [PMID: 28058066 PMCID: PMC5167136 DOI: 10.1007/s12551-016-0212-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a short piece of DNA wrapped around a core of eight histone proteins. In addition to their role in packaging DNA, nucleosomes impact the regulation of essential nuclear processes such as replication, transcription, and repair by controlling the accessibility of DNA. Thus, knowledge of this fundamental DNA-protein complex is crucial for understanding the mechanisms of gene control. While structural and biochemical studies over the past few decades have provided key insights into both the molecular composition and functional aspects of nucleosomes, these approaches necessarily average over large populations and times. In contrast, single-molecule methods are capable of revealing features of subpopulations and dynamic changes in the structure or function of biomolecules, rendering them a powerful complementary tool for probing mechanistic aspects of DNA-protein interactions. In this review, we highlight how these single-molecule approaches have recently yielded new insights into nucleosomal and subnucleosomal structures and dynamics.
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Affiliation(s)
- Orkide Ordu
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H. Dekker
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
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23
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Zhen CY, Tatavosian R, Huynh TN, Duc HN, Das R, Kokotovic M, Grimm JB, Lavis LD, Lee J, Mejia FJ, Li Y, Yao T, Ren X. Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin. eLife 2016; 5. [PMID: 27723458 PMCID: PMC5056789 DOI: 10.7554/elife.17667] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022] Open
Abstract
The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes. DOI:http://dx.doi.org/10.7554/eLife.17667.001
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Affiliation(s)
- Chao Yu Zhen
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Roubina Tatavosian
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Thao Ngoc Huynh
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Raibatak Das
- Department of Integrative Biology, University of Colorado Denver, Denver, United States
| | - Marko Kokotovic
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jun Lee
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Frances J Mejia
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Yang Li
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, United States
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24
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Single molecule fluorescence spectroscopy for quantitative biological applications. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0083-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Abstract
The repair of DNA by homologous recombination is an essential, efficient, and high-fidelity process that mends DNA lesions formed during cellular metabolism; these lesions include double-stranded DNA breaks, daughter-strand gaps, and DNA cross-links. Genetic defects in the homologous recombination pathway undermine genomic integrity and cause the accumulation of gross chromosomal abnormalities-including rearrangements, deletions, and aneuploidy-that contribute to cancer formation. Recombination proceeds through the formation of joint DNA molecules-homologously paired but metastable DNA intermediates that are processed by several alternative subpathways-making recombination a versatile and robust mechanism to repair damaged chromosomes. Modern biophysical methods make it possible to visualize, probe, and manipulate the individual molecules participating in the intermediate steps of recombination, revealing new details about the mechanics of genetic recombination. We review and discuss the individual stages of homologous recombination, focusing on common pathways in bacteria, yeast, and humans, and place particular emphasis on the molecular mechanisms illuminated by single-molecule methods.
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Affiliation(s)
- Jason C Bell
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
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26
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Juette MF, Terry DS, Wasserman MR, Altman RB, Zhou Z, Zhao H, Blanchard SC. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale. Nat Methods 2016; 13:341-4. [PMID: 26878382 PMCID: PMC4814340 DOI: 10.1038/nmeth.3769] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/17/2015] [Indexed: 02/07/2023]
Abstract
Single-molecule fluorescence microscopy is uniquely suited for detecting transient molecular recognition events, yet achieving the time resolution and statistics needed to realize this potential has proven challenging. Here we present a single-molecule imaging and analysis platform using scientific complementary metal-oxide semiconductor (sCMOS) detectors that enables imaging of 15,000 individual molecules simultaneously at millisecond rates. This system enabled the detection of previously obscured processes relevant to the fidelity mechanism in protein synthesis.
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Affiliation(s)
- Manuel F. Juette
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Daniel S. Terry
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Michael R. Wasserman
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Roger B. Altman
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Hong Zhao
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill-Cornell Medical College, New York, NY, USA
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27
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Ravarani CNJ, Chalancon G, Breker M, de Groot NS, Babu MM. Affinity and competition for TBP are molecular determinants of gene expression noise. Nat Commun 2016; 7:10417. [PMID: 26832815 PMCID: PMC4740812 DOI: 10.1038/ncomms10417] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
Cell-to-cell variation in gene expression levels (noise) generates phenotypic diversity and is an important phenomenon in evolution, development and disease. TATA-box binding protein (TBP) is an essential factor that is required at virtually every eukaryotic promoter to initiate transcription. While the presence of a TATA-box motif in the promoter has been strongly linked with noise, the molecular mechanism driving this relationship is less well understood. Through an integrated analysis of multiple large-scale data sets, computer simulation and experimental validation in yeast, we provide molecular insights into how noise arises as an emergent property of variable binding affinity of TBP for different promoter sequences, competition between interaction partners to bind the same surface on TBP (to either promote or disrupt transcription initiation) and variable residence times of TBP complexes at a promoter. These determinants may be fine-tuned under different conditions and during evolution to modulate eukaryotic gene expression noise.
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Affiliation(s)
- Charles N J Ravarani
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guilhem Chalancon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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28
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Rahbani JF, Hariri AA, Cosa G, Sleiman HF. Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions. ACS NANO 2015; 9:11898-11908. [PMID: 26556531 DOI: 10.1021/acsnano.5b04387] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.
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Affiliation(s)
- Janane F Rahbani
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Amani A Hariri
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
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29
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Gasiorek M, Schneider HJ. Unwinding DNA and RNA with Synthetic Complexes: On the Way to Artificial Helicases. Chemistry 2015; 21:18328-32. [PMID: 26503404 DOI: 10.1002/chem.201502738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Indexed: 01/04/2023]
Abstract
Synthetic helicases can be designed on the basis of ligands that bind more strongly to single-stranded nucleic acids than to double-stranded nucleic acids. This can be achieved with ligands containing phenyl groups, which intercalate into single strands, but due to their small size not into double strands. Moreover, two phenyl rings are combined with a distance that allows bis-intercalation with only single strands and not double strands. In this respect, such ligands also mimic single-strand binding (SSB) proteins. Exploration with more than 23 ligands, mostly newly synthesised, shows that the distance between the phenyl rings and between those and the linker influence the DNA unwinding efficiency, which can reach a melting point decrease of almost ΔTm =50 °C at much lower concentrations than that with any other known artificial helicases. Conformational pre-organisation of the ligand plays a decisive role in optimal efficiency. Substituents at the phenyl rings have a large effect, and increase, for example, in the order of H<F<Cl<Br, which illustrates the strong role of dispersive interactions in intercalation. Studies with homopolymers revealed significant selectivity: for example, with a ligand concentration of 40 μM at 35 °C, only GC double strands melt (ΔTm =48 °C), whereas the AT strand remains untouched, and with poly(rA)-poly(rU) as an RNA model one observes unfolding at 29 °C with a concentration of only 30 μM.
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Affiliation(s)
- Martin Gasiorek
- FR Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken (Germany)
| | - Hans-Jörg Schneider
- FR Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken (Germany).
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30
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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31
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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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