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Abstract
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic modification of the 3D-genome organization. It is generally accepted that protein–protein and protein–DNA interactions form the basis of 3D-genome organization. However, the constant generation of mechanical forces, torques, and other stresses produced by various proteins translocating along DNA could be playing a larger role in genome organization than currently appreciated. Clearly, a thorough understanding of the mechanical determinants imposed by DNA transactions on the 3D organization of the genome is required. We provide here an overview of our current knowledge and highlight the importance of DNA and chromatin mechanics in gene expression.
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Affiliation(s)
- Rajiv Kumar Jha
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - Fedor Kouzine
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
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2
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Thibault T, Degrouard J, Baril P, Pichon C, Midoux P, Malinge JM. Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity. Nucleic Acids Res 2017; 45:e26. [PMID: 27899652 PMCID: PMC5389552 DOI: 10.1093/nar/gkw1034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022] Open
Abstract
Double-stranded DNA minicircles of less than 1000 bp in length have great interest in both fundamental research and therapeutic applications. Although minicircles have shown promising activity in gene therapy thanks to their good biostability and better intracellular trafficking, minicircles down to 250 bp in size have not yet been investigated from the test tube to the cell for lack of an efficient production method. Herein, we report a novel versatile plasmid-free method for the production of DNA minicircles comprising fewer than 250 bp. We designed a linear nicked DNA double-stranded oligonucleotide blunt-ended substrate for efficient minicircle production in a ligase-mediated and bending protein-assisted circularization reaction at high DNA concentration of 2 μM. This one pot multi-step reaction based-method yields hundreds of micrograms of minicircle with sequences of any base composition and position and containing or not a variety of site-specifically chemical modifications or physiological supercoiling. Biochemical and cellular studies were then conducted to design a 95 bp minicircle capable of binding in vitro two NF-κB transcription factors per minicircle and to efficiently inhibiting NF-κB-dependent transcriptional activity in human cells. Therefore, our production method could pave the way for the design of minicircles as new decoy nucleic acids.
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Affiliation(s)
- Thomas Thibault
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated to the University of Orléans and Inserm, 45071 Orléans Cedex 02 France
| | - Jeril Degrouard
- Laboratoire de Physique des Solides, Université Paris Sud, CNRS UMR 8502, 91405 Orsay Cedex, France
| | - Patrick Baril
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated to the University of Orléans and Inserm, 45071 Orléans Cedex 02 France
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated to the University of Orléans and Inserm, 45071 Orléans Cedex 02 France
| | - Patrick Midoux
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated to the University of Orléans and Inserm, 45071 Orléans Cedex 02 France
| | - Jean-Marc Malinge
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated to the University of Orléans and Inserm, 45071 Orléans Cedex 02 France
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3
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Seol Y, Neuman KC. The dynamic interplay between DNA topoisomerases and DNA topology. Biophys Rev 2016; 8:101-111. [PMID: 28510219 DOI: 10.1007/s12551-016-0240-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/07/2016] [Indexed: 01/03/2023] Open
Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA.
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4
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Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases, is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that established the fundamental mechanistic basis of topoisomerase activity, the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases have begun to be explored. In this review we survey established and emerging DNA topology dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
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DNA Topoisomerases Are Required for Preinitiation Complex Assembly during GAL Gene Activation. PLoS One 2015; 10:e0132739. [PMID: 26173127 PMCID: PMC4501763 DOI: 10.1371/journal.pone.0132739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/17/2015] [Indexed: 12/17/2022] Open
Abstract
To investigate the importance of topoisomerases for transcription of the galactose induced genes, we have studied the expression of GAL1, GAL2, GAL7 and GAL10 in Saccharomyces cerevisiae cells deficient for topoisomerases I and II. We find that topoisomerases are required for transcriptional activation of the GAL genes, but are dispensable for ongoing transcription, eliminating a role of the enzymes in transcriptional elongation. Furthermore, we demonstrate that promoter chromatin remodeling of the GAL genes is unaffected in the topoisomerase deficient strain. However, the cells fail to successfully recruit RNA polymerase II due to an inability of the TATA-binding protein (TBP) to bind to the TATA box in these promoters. We therefore argue that topoisomerases are required for accurate assembly of the preinitiation complex at the promoters of the GAL genes.
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6
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Abstract
The double helical structure of DNA lends itself to topological constraints. Many DNA-based processes alter the topological state of DNA, generating torsional stress, which is efficiently relieved by topoisomerases. Maintaining this topological balance is crucial to cell survival, as excessive torsional strain risks DNA damage. Here, we review the mechanisms that generate and modulate DNA torsion within the cell. In particular, we discuss how transcription-generated torsional stress affects Pol II kinetics and chromatin dynamics, highlighting an emerging role of DNA torsion as a feedback mediator of torsion-generating processes.
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Affiliation(s)
- Sheila S Teves
- Molecular and Cell Biology; University of California, Berkeley; Berkeley, CA USA
| | - Steven Henikoff
- Basic Sciences Division; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Howard Hughes Medical Institute; Seattle, WA USA
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7
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Abstract
Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions.
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Affiliation(s)
- Fedor Kouzine
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - David Levens
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - Laura Baranello
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
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Gowetski DB, Kodis EJ, Kahn JD. Rationally designed coiled-coil DNA looping peptides control DNA topology. Nucleic Acids Res 2013; 41:8253-65. [PMID: 23825092 PMCID: PMC3783159 DOI: 10.1093/nar/gkt553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein–DNA nanostructures.
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Affiliation(s)
- Daniel B Gowetski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
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9
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Bond LM, Peters JP, Becker NA, Kahn JD, Maher LJ. Gene repression by minimal lac loops in vivo. Nucleic Acids Res 2010; 38:8072-82. [PMID: 21149272 PMCID: PMC3001091 DOI: 10.1093/nar/gkq755] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 08/09/2010] [Accepted: 08/09/2010] [Indexed: 01/25/2023] Open
Abstract
The inflexibility of double-stranded DNA with respect to bending and twisting is well established in vitro. Understanding apparent DNA physical properties in vivo is a greater challenge. Here, we exploit repression looping with components of the Escherichia coli lac operon to monitor DNA flexibility in living cells. We create a minimal system for testing the shortest possible DNA repression loops that contain an E. coli promoter, and compare the results to prior experiments. Our data reveal that loop-independent repression occurs for certain tight operator/promoter spacings. When only loop-dependent repression is considered, fits to a thermodynamic model show that DNA twisting limits looping in vivo, although the apparent DNA twist flexibility is 2- to 4-fold higher than in vitro. In contrast, length-dependent resistance to DNA bending is not observed in these experiments, even for the shortest loops constraining <0.4 persistence lengths of DNA. As observed previously for other looping configurations, loss of the nucleoid protein heat unstable (HU) markedly disables DNA looping in vivo. Length-independent DNA bending energy may reflect the activities of architectural proteins and the structure of the DNA topological domain. We suggest that the shortest loops are formed in apical loops rather than along the DNA plectonemic superhelix.
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Affiliation(s)
- Laura M. Bond
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Justin P. Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Nicole A. Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Jason D. Kahn
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
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10
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Becker NA, Kahn JD, Maher LJ. Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation. Nucleic Acids Res 2008; 36:4009-21. [PMID: 18515834 PMCID: PMC2475640 DOI: 10.1093/nar/gkn353] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 05/16/2008] [Accepted: 05/16/2008] [Indexed: 01/18/2023] Open
Abstract
DNA looping is important for gene repression and activation in Escherichia coli and is necessary for some kinds of gene regulation and recombination in eukaryotes. We are interested in sequence-nonspecific architectural DNA-binding proteins that alter the apparent flexibility of DNA by producing transient bends or kinks in DNA. The bacterial heat unstable (HU) and eukaryotic high-mobility group B (HMGB) proteins fall into this category. We have exploited a sensitive genetic assay of DNA looping in living E. coli cells to explore the extent to which HMGB proteins and derivatives can complement a DNA looping defect in E. coli lacking HU protein. Here, we show that derivatives of the yeast HMGB protein Nhp6A rescue DNA looping in E. coli lacking HU, in some cases facilitating looping to a greater extent than is observed in E. coli expressing normal levels of HU protein. Nhp6A-induced changes in the DNA length-dependence of repression efficiency suggest that Nhp6A alters DNA twist in vivo. In contrast, human HMGB2-box A derivatives did not rescue looping.
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Affiliation(s)
- Nicole A. Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Jason D. Kahn
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
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Lilja AE, Jenssen JR, Kahn JD. Geometric and dynamic requirements for DNA looping, wrapping and unwrapping in the activation of E.coli glnAp2 transcription by NtrC. J Mol Biol 2004; 342:467-78. [PMID: 15327947 DOI: 10.1016/j.jmb.2004.07.057] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Revised: 07/06/2004] [Accepted: 07/09/2004] [Indexed: 10/26/2022]
Abstract
Transcriptional activation by the E.coli NtrC protein can occur via DNA looping between a DNA-bound activator and the target sigma(54) RNA polymerase. NtrC forms an octamer on DNA that is capable of binding two DNA molecules. Its ATPase activity is required for open complex formation. Geometric requirements for activation were assessed using a library of DNA bending sequences created by random ligation of A-tract oligonucleotides, as well as several designed sequences. Thirty random or designed sequences with a variety of DNA lengths and bending geometries were cloned in plasmids, and the library was used to replace the spacer between the NtrC binding sites and the core glnAp2 promoter. The activity of each promoter construct under nitrogen limitation was determined in vivo, in a lambda phage lacZ reporter system integrated as a single-copy lysogen to avoid titrating NtrC or polymerase. A wide variety of bending geometries was found to support a similar level of transcriptional activation ( approximately 3-4-fold). Computer modeling of the DNA trajectories suggests that the most inactive promoters have short spacer DNA and the NtrC sites on the opposite side of the helix as the wild-type sites; otherwise, the loop can form effectively. Flexibility and multivalency of the NtrC-Esigma(54) interaction apparently provides substantial independence from DNA stiffness constraints, and in general activation requires less efficient looping than repression. However, none of the random templates were as active as wild-type promoter. Subsidiary activator binding sites in the wild-type were found to be required for full activity, but, surprisingly, these sites could not be functionally replaced by strong binding sites. This suggests that one or more protomers in the NtrC octamer must form and then release contacts with DNA in order to complete the ATPase cycle and act as an AAA(+) activator of the Esigma(54). This dynamic DNA wrapping around the NtrC octamer is proposed to be necessary for efficient activation, and the wrapping may also reduce adventitious activation of other promoters.
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Affiliation(s)
- Anders E Lilja
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
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Darst RP, Wang D, Auble DT. MOT1-catalyzed TBP-DNA disruption: uncoupling DNA conformational change and role of upstream DNA. EMBO J 2001; 20:2028-40. [PMID: 11296235 PMCID: PMC125425 DOI: 10.1093/emboj/20.8.2028] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SNF2/SWI2-related ATPases employ ATP hydrolysis to disrupt protein-DNA interactions, but how ATP hydrolysis is coupled to disruption is not understood. Here we examine the mechanism of action of MOT1, a yeast SNF2/SWI2-related ATPase that uses ATP hydrolysis to remove TATA binding protein (TBP) from DNA. MOT1 function requires a 17 bp DNA 'handle' upstream of the TATA box, which must be double stranded. Remarkably, MOT1-catalyzed disruption of TBP-DNA does not appear to require DNA strand separation, DNA bending or twisting of the DNA helix. Thus, TBP-DNA disruption is accomplished in a reaction apparently not driven by a change in DNA structure. MOT1 action is supported by DNA templates in which the handle is connected to the TATA box via single-stranded DNA, indicating that the upstream duplex DNA can be conformationally uncoupled from the TATA box. Combining these results with proposed similarities between SNF2/SWI2 ATPases and helicases, we suggest that MOT1 uses ATP hydrolysis to translocate along the handle and thereby disrupt interactions between TBP and DNA.
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Affiliation(s)
| | | | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health Science Center, 1300 Jefferson Park Avenue, Room 6213, Charlottesville, VA 22908-0733, USA
Corresponding author e-mail:
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