1
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Masoudi-Sobhanzadeh Y, Li S, Peng Y, Panchenko A. Interpretable deep residual network uncovers nucleosome positioning and associated features. Nucleic Acids Res 2024; 52:8734-8745. [PMID: 39036965 PMCID: PMC11347144 DOI: 10.1093/nar/gkae623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/31/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024] Open
Abstract
Nucleosomes represent elementary building units of eukaryotic chromosomes and consist of DNA wrapped around a histone octamer flanked by linker DNA segments. Nucleosomes are central in epigenetic pathways and their genomic positioning is associated with regulation of gene expression, DNA replication, DNA methylation and DNA repair, among other functions. Building on prior discoveries that DNA sequences noticeably affect nucleosome positioning, our objective is to identify nucleosome positions and related features across entire genome. Here, we introduce an interpretable framework based on the concepts of deep residual networks (NuPoSe). Trained on high-coverage human experimental MNase-seq data, NuPoSe is able to learn sequence and structural patterns associated with nucleosome organization in human genome. NuPoSe can be also applied to unseen data from different organisms and cell types. Our findings point to 43 informative features, most of them constitute tri-nucleotides, di-nucleotides and one tetra-nucleotide. Most features are significantly associated with the nucleosomal structural characteristics, namely, periodicity of nucleosomal DNA and its location with respect to a histone octamer. Importantly, we show that features derived from the 27 bp linker DNA flanking nucleosomes contribute up to 10% to the quality of the prediction model. This, along with the comprehensive training sets, deep-learning architecture, and feature selection method, may contribute to the NuPoSe's 80-89% classification accuracy on different independent datasets.
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Affiliation(s)
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, Canada
| | - Yunhui Peng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, Canada
- Department of Biology and Molecular Sciences, Queen's University, Kingston, K7L3N6, Canada
- School of Computing, Queen's University, Kingston, K7L3N6, Canada
- Ontario Institute of Cancer Research, Toronto, M5G 0A3, Canada
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2
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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3
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Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett 2023; 597:2879-2896. [PMID: 37884438 DOI: 10.1002/1873-3468.14766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.
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Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Sarah Fisher
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Cesar Menor-Salvan
- Department of Biología de Sistemas, Universidad de Alcalá, Madrid, Spain
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Rioux KL, Delaney S. Ionic strength modulates excision of uracil by SMUG1 from nucleosome core particles. DNA Repair (Amst) 2023; 125:103482. [PMID: 36931160 PMCID: PMC10073303 DOI: 10.1016/j.dnarep.2023.103482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023]
Abstract
Ionic strength affects many cellular processes including the packaging of genetic material in eukaryotes. For example, chromatin fibers are compacted in high ionic strength environments as are the minimal unit of packaging in chromatin, nucleosome core particles (NCPs). Furthermore, ionic strength is known to modulate several aspects of NCP dynamics including transient unwrapping of DNA from the histone protein core, nucleosome gaping, and intra- and internucleosomal interactions of the N-terminal histone tails. Changes in NCP structure may also impact interactions of transcriptional, repair, and other cellular machinery with nucleosomal DNA. One repair process, base excision repair (BER), is impacted by NCP structure and may be further influenced by changes in ionic strength. Here we examine the effects of ionic strength on the initiation of BER using biochemical assays. Using a population of NCPs containing uracil (U) at dozens of geometric locations, excision of U by single-strand selective monofunctional uracil DNA glycosylase (SMUG1) is assessed at higher and lower ionic strengths. SMUG1 has increased excision activity in the lower ionic strength conditions. On duplex DNA, however, SMUG1 activity is largely unaffected by ionic strength except at short incubation times, suggesting that changes in SMUG1 activity are likely due to alterations in NCP structure and dynamics. These results allow us to further understand the cellular role of SMUG1 in a changing ionic environment and broadly contribute to the understanding of BER on chromatin and genomic stability.
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Affiliation(s)
- Katelyn L Rioux
- Department of Chemistry, Brown University, Providence, RI, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, USA.
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5
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Hu Y, Ma S, Kartha VK, Duarte FM, Horlbeck M, Zhang R, Shrestha R, Labade A, Kletzien H, Meliki A, Castillo A, Durand N, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers A, Buenrostro JD. Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.533945. [PMID: 37034577 PMCID: PMC10081223 DOI: 10.1101/2023.03.28.533945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cis-regulatory elements control gene expression and are dynamic in their structure, reflecting changes to the composition of diverse effector proteins over time1-3. Here we sought to connect the structural changes at cis-regulatory elements to alterations in cellular fate and function. To do this we developed PRINT, a computational method that uses deep learning to correct sequence bias in chromatin accessibility data and identifies multi-scale footprints of DNA-protein interactions. We find that multi-scale footprints enable more accurate inference of TF and nucleosome binding. Using PRINT with single-cell multi-omics, we discover wide-spread changes to the structure and function of candidate cis-regulatory elements (cCREs) across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Activity segmentation using the co-variance across cell states identifies "sub-cCREs" as modular cCRE subunits of regulatory DNA. We apply this single-cell and PRINT approach to characterize the age-associated alterations to cCREs within hematopoietic stem cells (HSCs). Remarkably, we find a spectrum of aging alterations among HSCs corresponding to a global gain of sub-cCRE activity while preserving cCRE accessibility. Collectively, we reveal the functional importance of cCRE structure across cell states, highlighting changes to gene regulation at single-cell and single-base-pair resolution.
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Affiliation(s)
- Yan Hu
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Sai Ma
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
- Current address: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Vinay K. Kartha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Fabiana M. Duarte
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Max Horlbeck
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Ruochi Zhang
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Rojesh Shrestha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Ajay Labade
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Heidi Kletzien
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115
| | - Alia Meliki
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Andrew Castillo
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Neva Durand
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Eugenio Mattei
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Lauren J. Anderson
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Tristan Tay
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Andrew S. Earl
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Noam Shoresh
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Charles B. Epstein
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Amy Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115
| | - Jason D. Buenrostro
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
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6
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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7
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Mishra P, Sankar SHH, Gosavi N, Bharathavikru RS. RNA nucleoprotein complexes in biological systems. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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8
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Histone variants H3.3 and H2A.Z/H3.3 facilitate excision of uracil from nucleosome core particles. DNA Repair (Amst) 2022; 116:103355. [PMID: 35717761 PMCID: PMC9262417 DOI: 10.1016/j.dnarep.2022.103355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022]
Abstract
At the most fundamental level of chromatin organization, DNA is packaged as nucleosome core particles (NCPs) where DNA is wound around a core of histone proteins. This ubiquitous sequestration of DNA within NCPs presents a significant barrier to many biological processes, including DNA repair. We previously demonstrated that histone variants from the H2A family facilitate excision of uracil (U) lesions by DNA base excision repair (BER) glycosylases. Here, we consider how the histone variant H3.3 and double-variant H2A.Z/H3.3 modulate the BER enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1). Using an NCP model system with U:G base pairs at a wide variety of geometric positions we generate the global repair profile for both glycosylases. Enhanced excision of U by UDG and SMUG1 is observed with the H3.3 variant. We demonstrate that these H3.3-containing NCPs form two species: (1) octasomes, which contain the full complement of eight histone proteins and (2) hexasomes which are sub-nucleosomal particles that contain six histones. Both the octasome and hexasome species facilitate excision activity of UDG and SMUG1, with the largest impacts observed at sterically-occluded lesion sites and in terminal regions of DNA of the hexasome that do not closely interact with histones. For the double-variant H2A.Z/H3.3 NCPs, which exist as octasomes, the global repair profile reveals that UDG but not SMUG1 has increased U excision activity. The enhanced glycosylase activity reveals potential functions for these histone variants to facilitate BER in packaged DNA and contributes to our understanding of DNA repair in chromatin and its significance regarding mutagenesis and genomic integrity.
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9
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Determining translocation orientations of nucleic acid helicases. Methods 2021; 204:160-171. [PMID: 34758393 PMCID: PMC9076756 DOI: 10.1016/j.ymeth.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Helicase enzymes translocate along an RNA or DNA template with a defined polarity to unwind, separate, or remodel duplex strands for a variety of genome maintenance processes. Helicase mutations are commonly associated with a variety of diseases including aging, cancer, and neurodegeneration. Biochemical characterization of these enzymes has provided a wealth of information on the kinetics of unwinding and substrate preferences, and several high-resolution structures of helicases alone and bound to oligonucleotides have been solved. Together, they provide mechanistic insights into the structural translocation and unwinding orientations of helicases. However, these insights rely on structural inferences derived from static snapshots. Instead, continued efforts should be made to combine structure and kinetics to better define active translocation orientations of helicases. This review explores many of the biochemical and biophysical methods utilized to map helicase binding orientation to DNA or RNA substrates and includes several time-dependent methods to unequivocally map the active translocation orientation of these enzymes to better define the active leading and trailing faces.
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10
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Gabriel P, Maranha FG, Nordlander E, Neves A, Terenzi H. A heterotrinuclear bioinspired coordination complex capable of binding to DNA and emulation of nuclease activity. J Inorg Biochem 2021; 226:111631. [PMID: 34717251 DOI: 10.1016/j.jinorgbio.2021.111631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
The investigation of compounds capable of strongly and selectively interacting with DNA comprises a field of research in constant development. In this work, we demonstrate that a trinuclear coordination complex based on a dinuclear Fe(III)Zn(II) core designed for biomimicry of the hydrolytic enzyme kidney bean purple acid phosphatase, containing an additional pendant arm coordinating a Pd(II) ion, has the ability to interact with DNA and to promote its hydrolytic cleavage. These results were found through analysis of plasmid DNA interaction and cleavage by the trinuclear complex 1 and its derivatives 2 and 3, in addition to the analysis of alteration in the DNA structure in the presence of the complexes through circular dichroism and DNA footprinting techniques. The suggested covalent interaction of the palladium-containing complex with DNA was analysed using an electrophoretic mobility assay, circular dichroism, high resolution gel separation techniques and kinetic analysis. This is a new and promising metal complex targeted to nucleic acids and acting in two separate ways: strong DNA interaction and hydrolytic cleavage.
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Affiliation(s)
- Philipe Gabriel
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis 88040-970, Brazil
| | - Filipy Gobbo Maranha
- Laboratório de Bioinorgânica e Cristalografia, Departamernto de Química, Universidade Federal de Santa Catarina, Florianópolis 88040-970, Brazil
| | - Ebbe Nordlander
- Chemical Physics, Department of Chemistry, Lund University, Lund, Box 124, SE-221 00, Sweden
| | - Ademir Neves
- Laboratório de Bioinorgânica e Cristalografia, Departamernto de Química, Universidade Federal de Santa Catarina, Florianópolis 88040-970, Brazil
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis 88040-970, Brazil.
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11
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Fenton-Chemistry-Based Oxidative Modification of Proteins Reflects Their Conformation. Int J Mol Sci 2021; 22:ijms22189927. [PMID: 34576105 PMCID: PMC8469487 DOI: 10.3390/ijms22189927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 11/25/2022] Open
Abstract
In order to understand protein structure to a sufficient extent for, e.g., drug discovery, no single technique can provide satisfactory information on both the lowest-energy conformation and on dynamic changes over time (the ‘four-dimensional’ protein structure). Instead, a combination of complementary techniques is required. Mass spectrometry methods have shown promise in addressing protein dynamics, but often rely on the use of high-end commercial or custom instruments. Here, we apply well-established chemistry to conformation-sensitive oxidative protein labelling on a timescale of a few seconds, followed by analysis through a routine protein analysis workflow. For a set of model proteins, we show that site selectivity of labelling can indeed be rationalised in terms of known structural information, and that conformational changes induced by ligand binding are reflected in the modification pattern. In addition to conventional bottom-up analysis, further insights are obtained from intact mass measurement and native mass spectrometry. We believe that this method will provide a valuable and robust addition to the ‘toolbox’ of mass spectrometry researchers studying higher-order protein structure.
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12
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Bjarnason S, Ruidiaz SF, McIvor J, Mercadante D, Heidarsson PO. Protein intrinsic disorder on a dynamic nucleosomal landscape. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:295-354. [PMID: 34656332 DOI: 10.1016/bs.pmbts.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The complex nucleoprotein landscape of the eukaryotic cell nucleus is rich in dynamic proteins that lack a stable three-dimensional structure. Many of these intrinsically disordered proteins operate directly on the first fundamental level of genome compaction: the nucleosome. Here we give an overview of how disordered interactions with and within nucleosomes shape the dynamics, architecture, and epigenetic regulation of the genetic material, controlling cellular transcription patterns. We highlight experimental and computational challenges in the study of protein disorder and illustrate how integrative approaches are increasingly unveiling the fine details of nuclear interaction networks. We finally dissect sequence properties encoded in disordered regions and assess common features of disordered nucleosome-binding proteins. As drivers of many critical biological processes, disordered proteins are integral to a comprehensive molecular view of the dynamic nuclear milieu.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Sarah F Ruidiaz
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Jordan McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
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13
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Ravi Kumara GS, Seo YJ. Polymerase-mediated synthesis of p-vinylaniline-coupled fluorescent DNA for the sensing of nucleolin protein- c-myc G-quadruplex interactions. Org Biomol Chem 2021; 19:5788-5793. [PMID: 34085078 DOI: 10.1039/d1ob00863c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this paper we report the synthesis of two deoxyuridine derivatives (dUCN2, dUPy)-featuring p-vinylaniline-based fluorophores linked through a propargyl unit at the 5' position-that function as molecular rotors. This probing system proved to be useful for the sensing of gene regulation arising from interactions between this G-quadruplex and nucleolin.
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Affiliation(s)
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
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14
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McCormack LS, Efremov AK, Yan J. Effects of size, cooperativity, and competitive binding on protein positioning on DNA. Biophys J 2021; 120:2040-2053. [PMID: 33771470 DOI: 10.1016/j.bpj.2021.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/26/2021] [Accepted: 03/18/2021] [Indexed: 11/24/2022] Open
Abstract
Accurate positioning of proteins on chromosomal DNA is crucial for its proper organization as well as gene transcription regulation. Recent experiments revealed existence of periodic patterns of nucleoprotein complexes on DNA, which frequently cannot be explained by sequence-dependent binding of proteins. Previous theoretical studies suggest that such patterns typically emerge as a result of the proteins' volume-exclusion effect. However, the role of other physical factors in patterns' formation, such as the length of DNA, its sequence heterogeneity, and protein binding cooperativity/binding competition to DNA, remains unclear. To address these less understood yet important aspects, we investigated potential effects of these factors on protein positioning on finite-size DNA by using transfer-matrix calculations. It has been found that upon binding to DNA, proteins form oscillatory patterns that span over the length of up to ∼10 times the size of the protein binding site, with the shape of the patterns being strongly dependent on the length of DNA and the proteins' binding cooperativity to DNA. Furthermore, calculations showed that small variations in the proteins' affinity to DNA due to its sequence heterogeneity do not much change the main geometric characteristics of the observed protein patterns. Finally, competition between two different types of proteins for binding to DNA has been found to lead to formation of highly diverse and complex alternating positioning of the two proteins. Altogether, these results provide new insights into the roles of physicochemical properties of proteins, the DNA length, and DNA-binding competition between proteins in formation of protein positioning patterns on DNA.
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Affiliation(s)
- Leo S McCormack
- Department of Physics, Imperial College London, London, United Kingdom; Mechanobiology InstituteNational University of Singapore, Singapore, Singapore
| | - Artem K Efremov
- Mechanobiology InstituteNational University of Singapore, Singapore, Singapore.
| | - Jie Yan
- Mechanobiology InstituteNational University of Singapore, Singapore, Singapore; Department of Physics, National University of Singapore, Singapore, Singapore.
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15
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Caffrey PJ, Delaney S. Nucleosome Core Particles Lacking H2B or H3 Tails Are Altered Structurally and Have Differential Base Excision Repair Fingerprints. Biochemistry 2021; 60:210-218. [PMID: 33426868 DOI: 10.1021/acs.biochem.0c00877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A recently discovered post-translational modification of histone proteins is the irreversible proteolytic clipping of the histone N-terminal tail domains. This modification is involved in the regulation of various biological processes, including the DNA damage response. In this work, we used chemical footprinting to characterize the structural alterations to nucleosome core particles (NCPs) that result from a lack of a histone H2B or H3 tail. We also examine the influence of these histone tails on excision of the mutagenic lesion 1,N6-ethenoadenine (εA) by the repair enzyme alkyladenine DNA glycosylase. We found that the absence of the H2B or H3 tail results in altered DNA periodicity relative to that of native NCPs. We correlated these structural alterations to εA excision by utilizing a global analysis of 21 εA sites in NCPs and unincorporated duplex DNA. In comparison to native NCPs, there is enhanced excision of εA in tailless H2B NCPs in regions that undergo DNA unwrapping. This enhanced excision is not observed for tailless H3 NCPs; rather, excision is inhibited in more static areas of the NCP not prone to unwrapping. Our results support in vivo observations of alkylation damage profiles and the potential role of tail clipping as a mechanism for overcoming physical obstructions caused by packaging in NCPs but also reveal the potential inhibition of repair by tail clipping in some locations. Taken together, these results further our understanding of how base excision repair can be facilitated or diminished by histone tail removal and contribute to our understanding of the underlying mechanism that leads to mutational hot spots.
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Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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16
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Lai SM, Gopalan V. Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs. Methods Mol Biol 2021; 2167:147-169. [PMID: 32712919 DOI: 10.1007/978-1-0716-0716-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kink-turns are important RNA structural modules that facilitate long-range tertiary interactions and form binding sites for members of the L7Ae family of proteins. Present in a wide variety of functional RNAs, kink-turns play key organizational roles in many RNA-based cellular processes, including translation, modification, and tRNA biogenesis. It is important to determine the contribution of kink-turns to the overall architecture of resident RNAs, as these modules dictate ribonucleoprotein (RNP) assembly and function. This chapter describes a site-directed, hydroxyl radical-mediated footprinting strategy that utilizes L7Ae-tethered chemical nucleases to experimentally validate computationally identified kink-turns in any RNA and under a wide variety of conditions. The work plan described here uses the catalytic RNase P RNA as an example to provide a blueprint for using this footprinting method to map RNA-protein interactions in other RNP complexes.
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Affiliation(s)
- Stella M Lai
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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17
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Hayashi I. The C-terminal region of the plasmid partitioning protein TubY is a tetramer that can bind membranes and DNA. J Biol Chem 2020; 295:17770-17780. [PMID: 33454013 PMCID: PMC7762940 DOI: 10.1074/jbc.ra120.014705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/13/2020] [Indexed: 01/07/2023] Open
Abstract
Bacterial low-copy-number plasmids require partition (par) systems to ensure their stable inheritance by daughter cells. In general, these systems consist of three components: a centromeric DNA sequence, a centromere-binding protein and a nucleotide hydrolase that polymerizes and functions as a motor. Type III systems, however, segregate plasmids using three proteins: the FtsZ/tubulin-like GTPase TubZ, the centromere-binding protein TubR and the MerR-like transcriptional regulator TubY. Although the TubZ filament is sufficient to transport the TubR-centromere complex in vitro, TubY is still necessary for the stable maintenance of the plasmid. TubY contains an N-terminal DNA-binding helix-turn-helix motif and a C-terminal coiled-coil followed by a cluster of lysine residues. This study determined the crystal structure of the C-terminal domain of TubY from the Bacillus cereus pXO1-like plasmid and showed that it forms a tetrameric parallel four-helix bundle that differs from the typical MerR family proteins with a dimeric anti-parallel coiled-coil. Biochemical analyses revealed that the C-terminal tail with the conserved lysine cluster helps TubY to stably associate with the TubR-centromere complex as well as to nonspecifically bind DNA. Furthermore, this C-terminal tail forms an amphipathic helix in the presence of lipids but must oligomerize to localize the protein to the membrane in vivo. Taken together, these data suggest that TubY is a component of the nucleoprotein complex within the partitioning machinery, and that lipid membranes act as mediators of type III systems.
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Affiliation(s)
- Ikuko Hayashi
- Department of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Kanagawa, Japan
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18
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Nguyen PDM, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen SJ, Zou X, Heng X, Burke DH. Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nucleic Acids Res 2020; 48:2709-2722. [PMID: 31943114 PMCID: PMC7049723 DOI: 10.1093/nar/gkz1224] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022] Open
Abstract
RNA aptamers that bind HIV-1 reverse transcriptase (RT) inhibit RT in enzymatic and viral replication assays. Some aptamers inhibit RT from only a few viral clades, while others show broad-spectrum inhibition. Biophysical determinants of recognition specificity are poorly understood. We investigated the interface between HIV-1 RT and a broad–spectrum UCAA-family aptamer. SAR and hydroxyl radical probing identified aptamer structural elements critical for inhibition and established the role of signature UCAA bulge motif in RT-aptamer interaction. HDX footprinting on RT ± aptamer shows strong contacts with both subunits, especially near the C-terminus of p51. Alanine scanning revealed decreased inhibition by the aptamer for mutants P420A, L422A and K424A. 2D proton nuclear magnetic resonance and SAXS data provided constraints on the solution structure of the aptamer and enable computational modeling of the docked complex with RT. Surprisingly, the aptamer enhanced proteolytic cleavage of precursor p66/p66 by HIV-1 protease, suggesting that it stabilizes the productive conformation to allow maturation. These results illuminate features at the RT-aptamer interface that govern recognition specificity by a broad-spectrum antiviral aptamer, and they open new possibilities for accelerating RT maturation and interfering with viral replication.
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Affiliation(s)
- Phuong D M Nguyen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Liming Qiu
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Dong Zhang
- Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA
| | - Steve Tuske
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Margaret J Lange
- Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
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19
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Caffrey PJ, Kher R, Bian K, Li D, Delaney S. Comparison of the Base Excision and Direct Reversal Repair Pathways for Correcting 1, N6-Ethenoadenine in Strongly Positioned Nucleosome Core Particles. Chem Res Toxicol 2020; 33:1888-1896. [PMID: 32293880 PMCID: PMC7374743 DOI: 10.1021/acs.chemrestox.0c00089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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1,N6-ethenoadenine (εA) is a
mutagenic lesion and biomarker observed in numerous cancerous tissues.
Two pathways are responsible for its repair: base excision repair
(BER) and direct reversal repair (DRR). Alkyladenine DNA glycosylase
(AAG) is the primary enzyme that excises εA in BER, generating
stable intermediates that are processed by downstream enzymes. For
DRR, the Fe(II)/α-ketoglutarate-dependent ALKBH2 enzyme repairs
εA by direct conversion of εA to A. While the molecular
mechanism of each enzyme is well understood on unpackaged duplex DNA,
less is known about their actions on packaged DNA. The nucleosome
core particle (NCP) forms the minimal packaging unit of DNA in eukaryotic
organisms and is composed of 145–147 base pairs wrapped around
a core of eight histone proteins. In this work, we investigated the
activity of AAG and ALKBH2 on εA lesions globally distributed
at positions throughout a strongly positioned NCP. Overall, we examined
the repair of εA at 23 unique locations in packaged DNA. We
observed a strong correlation between rotational positioning of εA
and AAG activity but not ALKBH2 activity. ALKBH2 was more effective
than AAG at repairing occluded εA lesions, but only AAG was
capable of full repair of any εA in the NCP. However, notable
exceptions to these trends were observed, highlighting the complexity
of the NCP as a substrate for DNA repair. Modeling of binding of the
repair enzymes to NCPs revealed that some of these observations can
be explained by steric interference caused by DNA packaging. Specifically,
interactions between ALKBH2 and the histone proteins obstruct binding
to DNA, which leads to diminished activity. Taken together, these
results support in vivo observations of alkylation
damage profiles and contribute to our understanding of mutational
hotspots.
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Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Raadhika Kher
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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20
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Chan C, Kwok CK. Specific Binding of a
d
‐RNA G‐Quadruplex Structure with an
l
‐RNA Aptamer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Chun‐Yin Chan
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
| | - Chun Kit Kwok
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
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21
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Chan CY, Kwok CK. Specific Binding of a d-RNA G-Quadruplex Structure with an l-RNA Aptamer. Angew Chem Int Ed Engl 2020; 59:5293-5297. [PMID: 31975549 DOI: 10.1002/anie.201914955] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/06/2020] [Indexed: 01/24/2023]
Abstract
G-quadruplex (G4) structures are of general importance in chemistry and biology, such as in biosensing, gene regulation, and cancers. Although a large repertoire of G4-binding tools has been developed, no aptamer has been developed to interact with G4. Moreover, the G4 selectivity of current toolkits is very limited. Herein, we report the first l-RNA aptamer that targets a d-RNA G-quadruplex (rG4). Using TERRA rG4 as an example, our results reveal that this l-RNA aptamer, Ap3-7, folds into a unique secondary structure, exhibits high G4 selectivity and effectively interferes with TERRA-rG4-RHAU53 binding. Our approach and findings open a new door in further developing G4-specific tools for diverse applications.
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Affiliation(s)
- Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
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22
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POT1-TPP1 differentially regulates telomerase via POT1 His266 and as a function of single-stranded telomere DNA length. Proc Natl Acad Sci U S A 2019; 116:23527-23533. [PMID: 31685617 PMCID: PMC6876245 DOI: 10.1073/pnas.1905381116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Telomeres cap the ends of linear chromosomes and terminate in a single-stranded DNA (ssDNA) overhang recognized by POT1-TPP1 heterodimers to help regulate telomere length homeostasis. Here hydroxyl radical footprinting coupled with mass spectrometry was employed to probe protein-protein interactions and conformational changes involved in the assembly of telomere ssDNA substrates of differing lengths bound by POT1-TPP1 heterodimers. Our data identified environmental changes surrounding residue histidine 266 of POT1 that were dependent on telomere ssDNA substrate length. We further determined that the chronic lymphocytic leukemia-associated H266L substitution significantly reduced POT1-TPP1 binding to short ssDNA substrates; however, it only moderately impaired the heterodimer binding to long ssDNA substrates containing multiple protein binding sites. Additionally, we identified a telomerase inhibitory role when several native POT1-TPP1 proteins coat physiologically relevant lengths of telomere ssDNA. This POT1-TPP1 complex-mediated inhibition of telomerase is abrogated in the context of the POT1 H266L mutation, which leads to telomere overextension in a malignant cellular environment.
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23
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Guanidine- and purine-functionalized ligands of FeIIIZnII complexes: effects on the hydrolysis of DNA. J Biol Inorg Chem 2019; 24:675-691. [DOI: 10.1007/s00775-019-01680-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/21/2019] [Indexed: 01/01/2023]
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24
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New Heteroleptic Ruthenium(II) Complexes with Sulfamethoxypyridazine and Diimines as Potential Antitumor Agents. Molecules 2019; 24:molecules24112154. [PMID: 31181667 PMCID: PMC6600252 DOI: 10.3390/molecules24112154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 11/21/2022] Open
Abstract
Two new complexes of Ru(II) with mixed ligands were prepared: [Ru(bpy)2smp](PF6) (1) and [Ru(phen)2smp](PF6) (2), in which smp = sulfamethoxypyridazine; bpy = 2,2′-bipyridine; phen = 1,10-phenanthroline. The complexes have been characterized by elemental and conductivity analyses; infrared, NMR, and electrospray ionization mass spectroscopies; and X-ray diffraction of single crystal. Structural analyses reveal a distorted octahedral geometry around Ru(II) that is bound to two bpy (in 1) or two phen (in 2) via their two heterocyclic nitrogens and to two nitrogen atoms from sulfamethoxypyridazine—one of the methoxypyridazine ring and the sulfonamidic nitrogen, which is deprotonated. Both complexes inhibit the growth of chronic myelogenous leukemia cells. The interaction of the complexes with bovine serum albumin and DNA is described. DNA footprinting using an oligonucleotide as substrate showed the complexes’ preference for thymine base rich sites. It is worth notifying that the complexes interact with the Src homology SH3 domain of the Abl tyrosine kinase protein. Abl protein is involved in signal transduction and implicated in the development of chronic myelogenous leukemia. Nuclear magnetic resonance (NMR) studies of the interaction of complex 2 with the Abl-SH3 domain showed that the most affected residues were T79, G97, W99, and Y115.
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25
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Shafirovich V, Kolbanovskiy M, Kropachev K, Liu Z, Cai Y, Terzidis MA, Masi A, Chatgilialoglu C, Amin S, Dadali A, Broyde S, Geacintov NE. Nucleotide Excision Repair and Impact of Site-Specific 5',8-Cyclopurine and Bulky DNA Lesions on the Physical Properties of Nucleosomes. Biochemistry 2019; 58:561-574. [PMID: 30570250 PMCID: PMC6373774 DOI: 10.1021/acs.biochem.8b01066] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The nonbulky 5',8-cyclopurine DNA lesions (cP) and the bulky, benzo[ a]pyrene diol epoxide-derived stereoisomeric cis- and trans- N2-guanine adducts (BPDE-dG) are good substrates of the human nucleotide excision repair (NER) mechanism. These DNA lesions were embedded at the In or Out rotational settings near the dyad axis in nucleosome core particles reconstituted either with native histones extracted from HeLa cells (HeLa-NCP) or with recombinant histones (Rec-NCP). The cP lesions are completely resistant to NER in human HeLa cell extracts. The BPDE-dG adducts are also NER-resistant in Rec-NCPs but are good substrates of NER in HeLa-NCPs. The four BPDE-dG adduct samples are excised with different efficiencies in free DNA, but in HeLa-NCPs, the efficiencies are reduced by a common factor of 2.2 ± 0.2 relative to the NER efficiencies in free DNA. The NER response of the BPDE-dG adducts in HeLa-NCPs is not directly correlated with the observed differences in the thermodynamic destabilization of HeLa-NCPs, the Förster resonance energy transfer values, or hydroxyl radical footprint patterns and is weakly dependent on the rotational settings. These and other observations suggest that NER is initiated by the binding of the DNA damage-sensing NER factor XPC-RAD23B to a transiently opened BPDE-modified DNA sequence that corresponds to the known footprint of XPC-DNA-RAD23B complexes (≥30 bp). These observations are consistent with the hypothesis that post-translational modifications and the dimensions and properties of the DNA lesions are the major factors that have an impact on the dynamics and initiation of NER in nucleosomes.
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Affiliation(s)
- Vladimir Shafirovich
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Marina Kolbanovskiy
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Konstantin Kropachev
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Zhi Liu
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Yuquin Cai
- Department of Biology, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Michael A. Terzidis
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Shantu Amin
- Department of Pharmacology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Alexander Dadali
- Bronx College of the City University of New York, Bronx, NY 10453, United States
| | - Suse Broyde
- Department of Biology, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Nicholas E. Geacintov
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
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26
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Knorr S, Sinn M, Galetskiy D, Williams RM, Wang C, Müller N, Mayans O, Schleheck D, Hartig JS. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat Commun 2018; 9:5071. [PMID: 30498244 PMCID: PMC6265302 DOI: 10.1038/s41467-018-07563-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022] Open
Abstract
Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an α-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate. CsiD is found widespread in bacteria. We present crystal structures of CsiD in complex with glutarate, succinate, and the inhibitor N-oxalyl-glycine, demonstrating strong discrimination between the structurally related ligands. We show that L-2-hydroxyglutarate is converted to α-ketoglutarate by LhgO acting as a membrane-bound, ubiquinone-linked dehydrogenase. Lysine enters the pathway via 5-aminovalerate by the promiscuous enzymes GabT and GabD. We demonstrate that repression of the pathway by CsiR is relieved upon glutarate binding. In conclusion, lysine degradation provides an important link in central metabolism. Our results imply the gut microbiome as a potential source of glutarate and L-2-hydroxyglutarate associated with human diseases such as cancer and organic acidurias.
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Affiliation(s)
- Sebastian Knorr
- Department of Chemistry, University of Konstanz, Konstanz, 78457, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), Konstanz, 78457, Germany
| | - Malte Sinn
- Department of Chemistry, University of Konstanz, Konstanz, 78457, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), Konstanz, 78457, Germany
| | - Dmitry Galetskiy
- Department of Chemistry, University of Konstanz, Konstanz, 78457, Germany
| | - Rhys M Williams
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Changhao Wang
- Department of Chemistry, University of Konstanz, Konstanz, 78457, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Olga Mayans
- Konstanz Research School Chemical Biology (KoRS-CB), Konstanz, 78457, Germany.,Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - David Schleheck
- Konstanz Research School Chemical Biology (KoRS-CB), Konstanz, 78457, Germany.,Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, Konstanz, 78457, Germany. .,Konstanz Research School Chemical Biology (KoRS-CB), Konstanz, 78457, Germany.
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27
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Hayashi I, Oda T, Sato M, Fuchigami S. Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid. J Mol Biol 2018; 430:5015-5028. [PMID: 30414406 DOI: 10.1016/j.jmb.2018.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 11/19/2022]
Abstract
Tubulin/FtsZ-like GTPase TubZ is responsible for maintaining the stability of pXO1-like plasmids in virulent Bacilli. TubZ forms a filament in a GTP-dependent manner, and like other partitioning systems of low-copy-number plasmids, it requires the centromere-binding protein TubR that connects the plasmid to the TubZ filament. Systems regulating TubZ partitioning have been identified in Clostridium prophages as well as virulent Bacillus species, in which TubZ facilitates partitioning by binding and towing the segrosome: the nucleoprotein complex composed of TubR and the centromere. However, the molecular mechanisms of segrosome assembly and the transient on-off interactions between the segrosome and the TubZ filament remain poorly understood. Here, we determined the crystal structure of TubR from Bacillus cereus at 2.0-Å resolution and investigated the DNA-binding ability of TubR using hydroxyl radical footprinting and electrophoretic mobility shift assays. The TubR dimer possesses 2-fold symmetry and binds to a 15-bp palindromic consensus sequence in the tubRZ promoter region. Continuous TubR-binding sites overlap each other, which enables efficient binding of TubR in a cooperative manner. Interestingly, the segrosome adopts an extended DNA-protein filament structure and likely gains conformational flexibility by introducing non-consensus residues into the palindromes in an asymmetric manner. Together, our experimental results and structural model indicate that the unique centromere recognition mechanism of TubR allows transient complex formation between the segrosome and the dynamic polymer of TubZ.
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Affiliation(s)
- Ikuko Hayashi
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
| | - Takashi Oda
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mamoru Sato
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Sotaro Fuchigami
- Department of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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28
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Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nat Protoc 2018; 13:2535-2556. [PMID: 30341436 PMCID: PMC6322412 DOI: 10.1038/s41596-018-0048-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydroxyl-radical footprinting (HRF) is a powerful method for probing structures of nucleic acid-protein complexes with single-nucleotide resolution in solution. To tap the full quantitative potential of HRF, we describe a protocol, hydroxyl-radical footprinting interpretation for DNA (HYDROID), to quantify HRF data and integrate them with atomistic structural models. The stages of the HYDROID protocol are extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at each nucleotide and theoretical estimation of the DNA cleavage frequency from atomistic structural models, followed by comparison of experimental and theoretical results. Example scripts for each step of HRF data analysis and interpretation are provided for several nucleosome systems; they can be easily adapted to analyze user data. As input, HYDROID requires polyacrylamide gel electrophoresis (PAGE) images of HRF products and optionally can use a molecular model of the DNA-protein complex. The HYDROID protocol can be used to quantify HRF over DNA regions of up to 100 nucleotides per gel image. In addition, it can be applied to the analysis of RNA-protein complexes and free RNA or DNA molecules in solution. Compared with other methods reported to date, HYDROID is unique in its ability to simultaneously integrate HRF data with the analysis of atomistic structural models. HYDROID is freely available. The complete protocol takes ~3 h. Users should be familiar with the command-line interface, the Python scripting language and Protein Data Bank (PDB) file formats. A graphical user interface (GUI) with basic functionality (HYDROID_GUI) is also available.
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Affiliation(s)
- Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Grigoriy A Armeev
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Galina A Komarova
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vasily M Studitsky
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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29
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Chea EE, Jones LM. Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting. Analyst 2018; 143:798-807. [DOI: 10.1039/c7an01323j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydroxyl radical footprinting (HRF) has been successfully used to study the structure of both nucleic acids and proteins in live cells.
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Affiliation(s)
- Emily E. Chea
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
| | - Lisa M. Jones
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
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30
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Shaytan AK, Xiao H, Armeev GA, Wu C, Landsman D, Panchenko AR. Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning. Nucleic Acids Res 2017; 45:9229-9243. [PMID: 28934480 PMCID: PMC5765820 DOI: 10.1093/nar/gkx616] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Nucleosomes are the most abundant protein–DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical footprinting (HRF) of protein–DNA complexes is a chemical technique that probes nucleosome organization in solution with a high precision unattainable by other methods. In this work we propose an integrative modeling method for constructing high-resolution atomistic models of nucleosomes based on HRF experiments. Our method precisely identifies DNA positioning on nucleosome by combining HRF data for both DNA strands with the pseudo-symmetry constraints. We performed high-resolution HRF for Saccharomyces cerevisiae centromeric nucleosome of unknown structure and characterized it using our integrative modeling approach. Our model provides the basis for further understanding the cooperative engagement and interplay between Cse4p protein and the A-tracts important for centromere function.
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Affiliation(s)
- Alexey K Shaytan
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, USA.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grigoriy A Armeev
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Carl Wu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.,Department of Biology, Johns Hopkins University, 3400 N. Charles Street-UTL 387, Baltimore, MD 21218, USA.,Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - David Landsman
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, USA
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31
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Bilotti K, Kennedy EE, Li C, Delaney S. Human OGG1 activity in nucleosomes is facilitated by transient unwrapping of DNA and is influenced by the local histone environment. DNA Repair (Amst) 2017; 59:1-8. [PMID: 28892740 DOI: 10.1016/j.dnarep.2017.08.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/30/2017] [Accepted: 08/30/2017] [Indexed: 12/17/2022]
Abstract
If unrepaired, damage to genomic DNA can cause mutations and/or be cytotoxic. Single base lesions are repaired via the base excision repair (BER) pathway. The first step in BER is the recognition and removal of the nucleobase lesion by a glycosylase enzyme. For example, human oxoguanine glycosylase 1 (hOGG1) is responsible for removal of the prototypic oxidatively damaged nucleobase, 8-oxo-7,8-dihydroguanine (8-oxoG). To date, most studies of glycosylases have used free duplex DNA substrates. However, cellular DNA is packaged as repeating nucleosome units, with 145 base pair segments of DNA wrapped around histone protein octamers. Previous studies revealed inhibition of hOGG1 at the nucleosome dyad axis and in the absence of chromatin remodelers. In this study, we reveal that even in the absence of chromatin remodelers or external cofactors, hOGG1 can initiate BER at positions off the dyad axis and that this activity is facilitated by spontaneous and transient unwrapping of DNA from the histones. Additionally, we find that solution accessibility as determined by hydroxyl radical footprinting is not fully predictive of glycosylase activity and that histone tails can suppress hOGG1 activity. We therefore suggest that local nuances in the nucleosome environment and histone-DNA interactions can impact glycosylase activity.
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Affiliation(s)
- Katharina Bilotti
- Department of Chemistry, Brown University, Providence, RI 02912, United States
| | - Erin E Kennedy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, United States
| | - Chuxuan Li
- Department of Chemistry, Brown University, Providence, RI 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, United States.
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32
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Single molecule high-throughput footprinting of small and large DNA ligands. Nat Commun 2017; 8:304. [PMID: 28824174 PMCID: PMC5563512 DOI: 10.1038/s41467-017-00379-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 06/20/2017] [Indexed: 02/04/2023] Open
Abstract
Most DNA processes are governed by molecular interactions that take place in a sequence-specific manner. Determining the sequence selectivity of DNA ligands is still a challenge, particularly for small drugs where labeling or sequencing methods do not perform well. Here, we present a fast and accurate method based on parallelized single molecule magnetic tweezers to detect the sequence selectivity and characterize the thermodynamics and kinetics of binding in a single assay. Mechanical manipulation of DNA hairpins with an engineered sequence is used to detect ligand binding as blocking events during DNA unzipping, allowing determination of ligand selectivity both for small drugs and large proteins with nearly base-pair resolution in an unbiased fashion. The assay allows investigation of subtle details such as the effect of flanking sequences or binding cooperativity. Unzipping assays on hairpin substrates with an optimized flat free energy landscape containing all binding motifs allows determination of the ligand mechanical footprint, recognition site, and binding orientation. Mapping the sequence specificity of DNA ligands remains a challenge, particularly for small drugs. Here the authors develop a parallelized single molecule magnetic tweezers approach using engineered DNA hairpins that can detect sequence selectivity, thermodynamics and kinetics of binding for small drugs and large proteins.
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33
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Olmon ED, Delaney S. Differential Ability of Five DNA Glycosylases to Recognize and Repair Damage on Nucleosomal DNA. ACS Chem Biol 2017; 12:692-701. [PMID: 28085251 DOI: 10.1021/acschembio.6b00921] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Damage to genomic DNA leads to mutagenesis and disease. Repair of single base damage is initiated by DNA glycosylases, the first enzymes in the base excision repair pathway. Although eukaryotic packaging of chromosomal DNA in nucleosomes is known to decrease DNA glycosylase efficiency, the impact on individual glycosylases is unclear. Here, we present a model system in which we examine the repair of site-specific base damage in well-characterized nucleosome core particles by five different DNA glycosylases. We find that DNA glycosylase efficiency on nucleosome substrates depends not only on the geometric orientation of the damaged base but also on its identity, as well as on the size, structure, and mechanism of the glycosylase. We show via molecular modeling that inhibition of glycosylase activity is largely due to steric obstruction by the nucleosome core.
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Affiliation(s)
- Eric D. Olmon
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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34
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The excluded DNA strand is SEW important for hexameric helicase unwinding. Methods 2016; 108:79-91. [DOI: 10.1016/j.ymeth.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 02/04/2023] Open
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35
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Paul R, Greenberg MM. Mechanistic Studies on RNA Strand Scission from a C2'-Radical. J Org Chem 2016; 81:9199-9205. [PMID: 27668445 DOI: 10.1021/acs.joc.6b01760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The C2'-carbon-hydrogen bond in ribonucleotides is significantly weaker than other carbohydrate carbon-hydrogen bonds in RNA or DNA. Independent generation of the C2'-uridine radical (1) in RNA oligonucleotides via Norrish type I photocleavage of a ketone-substituted nucleotide yields direct strand breaks via cleavage of the β-phosphate. The reactivity of 1 in different sequences and under a variety of conditions suggests that the rate constant for strand scission is significantly greater than 106 s-1 at pH 7.2. The initially formed C2'-radical (1) is not trapped under a variety of conditions, consistent with computational studies ( Chem.-Eur. J. 2009 , 15 , 2394 ) that suggest that the barrier to strand scission is very low and that synchronous proton transfer from the 2'-hydroxyl to the departing phosphate group facilitates cleavage. The C2'-radical could be a significant contributor to RNA strand scission by the hydroxyl radical, particularly under anaerobic conditions where 1 can be produced from nucleobase radicals.
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Affiliation(s)
- Rakesh Paul
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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36
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Bortolotto T, Silva-Caldeira PP, Pich CT, Pereira-Maia EC, Terenzi H. Tunable DNA cleavage activity promoted by copper(ii) ternary complexes with N-donor heterocyclic ligands. Chem Commun (Camb) 2016; 52:7130-3. [PMID: 27168172 DOI: 10.1039/c6cc03142k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Several small molecules have the capacity to cleave DNA promptly at high yields, even under mild conditions. Usually, this activity has no constraints, occurring without external or user control. Here, we demonstrate that UV-light exposure can greatly enhance the DNA cleavage activity promoted by four ternary copper(ii) complexes. A remarkable photocontrolled activity was achieved, which may be interesting for chemical and biochemical applications.
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Affiliation(s)
- T Bortolotto
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970, Florianópolis-SC, Brazil.
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37
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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38
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Lu J, Trnka MJ, Roh SH, Robinson PJJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2141-51. [PMID: 26323614 PMCID: PMC5067139 DOI: 10.1007/s13361-015-1235-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 05/11/2023]
Abstract
Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.
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Affiliation(s)
- Jonathan Lu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Princeton University, Princeton, NJ, 08544, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
| | - Soung-Hun Roh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Philip J J Robinson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Carrie Shiau
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, 94158, USA
| | - Danica Galonic Fujimori
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
| | - Shenheng Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA.
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94143, USA.
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39
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Jost M, Fernández-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PYT, Kang G, Padmanabhan S, Elías-Arnanz M, Drennan CL. Structural basis for gene regulation by a B12-dependent photoreceptor. Nature 2015; 526:536-41. [PMID: 26416754 PMCID: PMC4634937 DOI: 10.1038/nature14950] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/14/2015] [Indexed: 12/29/2022]
Abstract
Photoreceptor proteins enable organisms to sense and respond to light. The newly discovered CarH-type photoreceptors use a vitamin B12 derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. Here, we present crystal structures of Thermus thermophilus CarH in all three relevant states: in the dark, both free and bound to operator DNA, and after light exposure. These structures provide a visualization of how adenosylcobalamin mediates CarH tetramer formation in the dark, how this tetramer binds to the promoter −35 element to repress transcription, and how light exposure leads to a large-scale conformational change that activates transcription. In addition to the remarkable functional repurposing of adenosylcobalamin from an enzyme cofactor to a light sensor, we find that nature also repurposed two independent protein modules in assembling CarH. These results expand the biological role of vitamin B12 and provide fundamental insight into a new mode of light-dependent gene regulation.
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Affiliation(s)
- Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Jésus Fernández-Zapata
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - María Carmen Polanco
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Juan Manuel Ortiz-Guerrero
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Montserrat Elías-Arnanz
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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40
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Paul R, Greenberg MM. Rapid RNA strand scission following C2'-hydrogen atom abstraction. J Am Chem Soc 2015; 137:596-9. [PMID: 25580810 DOI: 10.1021/ja511401g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
C2'-Nucleotide radicals have been proposed as key intermediates in direct strand break formation in RNA exposed to ionizing radiation. Uridin-2'-yl radical (1) was independently generated in single- and double-stranded RNA via photolysis of a ketone precursor. Direct stand breaks result from heterolytic cleavage of the adjacent C3'-carbon-oxygen bond. Trapping of 1 by O2 or β-mercaptoethanol (1 M) does not compete with strand scission, indicating that phosphate elimination is >10(6) s(-1). Uracil loss also does not compete with strand scission. When considered in conjunction with reports that nucleobase radicals produce 1, this chemistry explains why RNA is significantly more susceptible to strand scission by ionizing radiation (hydroxyl radical) than is DNA.
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Affiliation(s)
- Rakesh Paul
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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41
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Cappella P, Pulici M, Gasparri F. Application of Click Chemistry Conditions for 5‐Bromo‐2′‐Deoxyuridine Determination Through Fenton and Related Reactions. ACTA ACUST UNITED AC 2015; 71:7.43.1-7.43.17. [DOI: 10.1002/0471142956.cy0743s71] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Paolo Cappella
- Department of Biology, Drug Discovery Oncology, Nerviano Medical Sciences Srl Milan Italy
| | - Maurizio Pulici
- Department of Chemistry, Drug Discovery Oncology, Nerviano Medical Sciences Srl Milan Italy
| | - Fabio Gasparri
- Department of Biology, Drug Discovery Oncology, Nerviano Medical Sciences Srl Milan Italy
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42
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Ellis MJ, Trussler RS, Ross JA, Haniford DB. Probing Hfq:RNA interactions with hydroxyl radical and RNase footprinting. Methods Mol Biol 2015; 1259:403-15. [PMID: 25579599 DOI: 10.1007/978-1-4939-2214-7_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA footprinting and structure probing techniques are used to characterize the interaction between RNA-binding proteins and RNAs in vitro. Hydroxyl radical footprinting results in the identification of protein binding site(s) in an RNA. Ribonuclease (RNase) structure probing is a complementary technique that also provides information about protein binding sites, as well as RNA structure and possible protein-directed RNA remodeling. Here we provide a comprehensive protocol for studying the interaction between Hfq and an mRNA or sRNA of interest using a combination of RNase A, T1, and V1 as well as hydroxyl radical footprinting techniques. Detailed protocols for in vitro synthesis of (32)P-labeled RNA; formation of Hfq:RNA binary complex(es), RNase, and hydroxyl radical footprinting; preparation and running of sequencing gels; and data analysis are provided.
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Affiliation(s)
- Michael J Ellis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, 1151 Richmond St., London, ON, Canada, N6A 5C1
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43
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Volle CB, Delaney S. AGG/CCT interruptions affect nucleosome formation and positioning of healthy-length CGG/CCG triplet repeats. BMC BIOCHEMISTRY 2013; 14:33. [PMID: 24261641 PMCID: PMC3870987 DOI: 10.1186/1471-2091-14-33] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/19/2013] [Indexed: 11/16/2022]
Abstract
Background Fragile X Syndrome (FXS), the most common inherited form of mental retardation, is caused by expansion of a CGG/CCG repeat tract in the 5′-untranslated region of the fragile X mental retardation (FMR1) gene, which changes the functional organization of the gene from euchromatin to heterochromatin. Interestingly, healthy-length repeat tracts possess AGG/CCT interruptions every 9–10 repeats, and clinical data shows that loss of these interruptions is linked to expansion of the repeat tract to disease-length. Thus, it is important to understand how these interruptions alter the behavior of the repeat tract in the packaged gene. Results To investigate how uninterrupted and interrupted CGG/CCG repeat tracts interact with the histone core, we designed experiments using the nucleosome core particle, the most basic unit of chromatin packaging. Using DNA containing 19 CGG/CCG repeats, flanked by either a nucleosome positioning sequence or the FMR1 gene sequence, we determined that the addition of a single AGG/CCT interruption modulates both the ability of the CGG/CCG repeat DNA to incorporate into a nucleosome and the rotational and translational position of the repeat DNA around the histone core when flanked by the nucleosome positioning sequence. The presence of these interruptions also alters the periodicity of the DNA in the nucleosome; interrupted repeat tracts have a greater periodicity than uninterrupted repeats. Conclusions This work defines the ability of AGG/CCT interruptions to modulate the behavior of the repeat tract in the packaged gene and contributes to our understanding of the role that AGG/CCT interruptions play in suppressing expansion and maintaining the correct functional organization of the FMR1 gene, highlighting a protective role played by the interruptions in genomic packaging.
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Affiliation(s)
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, USA.
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44
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Miniaturized Sequencing Gel System for Quick Analysis of DNA by Hydroxyl Radical Cleavage. Appl Biochem Biotechnol 2013; 172:1-8. [DOI: 10.1007/s12010-013-0512-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/08/2013] [Indexed: 11/25/2022]
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45
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Potentiometric sensing of nuclease activities and oxidative damage of single-stranded DNA using a polycation-sensitive membrane electrode. Biosens Bioelectron 2013; 47:559-65. [DOI: 10.1016/j.bios.2013.03.066] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/13/2013] [Accepted: 03/26/2013] [Indexed: 01/09/2023]
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46
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He G, Vasilieva E, Bashkin JK, Dupureur CM. Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis. Anal Biochem 2013; 439:99-101. [PMID: 23608054 PMCID: PMC3713177 DOI: 10.1016/j.ab.2013.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/08/2013] [Accepted: 04/10/2013] [Indexed: 12/17/2022]
Abstract
The mapping of DNA footprints and affinity cleavage sites for small DNA ligands is affected by the choice of sequencing chemistry and end label, and the potential for indexing errors can be significant when mapping small ligand-DNA interactions. Described here is a mechanism for avoiding such errors based on a summary of standard labeling, cleavage, and indexing chemistries and a comparison among them for analysis of these interactions by capillary electrophoresis. The length dependence of the difference between Sanger and Maxam-Gilbert indexing is examined for a number of duplexes of mixed sequence.
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Affiliation(s)
- Gaofei He
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Elena Vasilieva
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - James K. Bashkin
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Cynthia M. Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
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47
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Cappella P, Giansanti V, Pulici M, Gasparri F. From "Click" to "Fenton" chemistry for 5-bromo-2'-deoxyuridine determination. Cytometry A 2013; 83:989-1000. [PMID: 23943293 DOI: 10.1002/cyto.a.22343] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/08/2013] [Accepted: 07/14/2013] [Indexed: 12/24/2022]
Abstract
Ascorbic acid (AA) and copper have been increasingly employed in flow cytometry (FCM) and high content analysis (HCA) since the introduction of "click chemistry" as a non-destructive alternative to classical 5-bromo-2'-deoxyuridine (BrdU) immunodetection for DNA synthesis and proliferation assays. Mixtures of ascorbate and catalytic copper, under certain experimental conditions, act as oxidizing agent, catalyzing the formation of reactive hydroxyl radicals through hydrogen peroxides decomposition via Fenton reaction. We developed a procedure for BrdU incorporation detection based on the use of AA and cupric ions as DNA damaging agents. Optimal DNA damaging conditions were identified and found to provide results comparable with "click" 5-ethynyl-deoxyuridine (EdU) cycloaddition approach and classical BrdU immunodetection. Scavenger agents were found to prevent hydroxyl-induced DNA damages, providing the proof-of-concept for the use of this procedure for DNA denaturation prior to BrdU detection. We demonstrated hydroxyl radicals' reaction to be readily applicable to HCA and FCM assays, for both classical BrdU immunostaining and EdU cycloaddition procedure. This technique was successfully employed for BrdU pulse-chase experiments and in multiparametric immunofluorescence assays for the simultaneous detection of labile phosphoproteins in intact cells. The use of AA/Cu prior to immunodetection for BrdU incorporation assays is a viable alternative to chemical/physical DNA denaturing agents (acids or heat), since it allows preservation of labile epitopes such as phosphoproteins, and over enzymatic agents (digestion with DNases) for its lower cost.
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Affiliation(s)
- Paolo Cappella
- Department of Biology Nerviano Medical Sciences, Via Pasteur 10, 20014, Nerviano, Italy
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48
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Ross JA, Ellis MJ, Hossain S, Haniford DB. Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. RNA (NEW YORK, N.Y.) 2013; 19:670-84. [PMID: 23510801 PMCID: PMC3677282 DOI: 10.1261/rna.037747.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/11/2013] [Indexed: 05/23/2023]
Abstract
Hfq functions in post-transcriptional gene regulation in a wide range of bacteria, usually by promoting base-pairing of mRNAs and trans-encoded sRNAs that share partial sequence complementarity. It is less clear if Hfq is required for pairing of cis-encoded RNAs (i.e., antisense RNAs) with their target mRNAs. In the current work, we have characterized the interactions between Escherichia coli Hfq and the components of the Tn10/IS10 antisense system, RNA-IN and RNA-OUT. We show that Hfq interacts with RNA-OUT through its proximal RNA-binding surface, as is typical for Hfq and trans-encoded sRNAs. In contrast, RNA-IN binds both proximal and distal RNA-binding surfaces in Hfq with a higher affinity for the latter, as is typical for mRNA interactions in canonical sRNA-mRNA pairs. Importantly, an amino acid substitution in Hfq that interferes with RNA binding to the proximal site negatively impacts RNA-IN:OUT pairing in vitro and suppresses the ability of Hfq to negatively regulate IS10 transposition in vivo. We also show that Hfq binding to RNA-IN and RNA-OUT alters secondary structure elements in both of these RNAs and speculate that this could be important in how Hfq facilitates RNA-IN:OUT pairing. Based on the results presented here, we suggest that Hfq could be involved in regulating RNA pairing in other antisense systems, including systems encoded by other transposable elements.
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49
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Volle CB, Delaney S. CAG/CTG repeats alter the affinity for the histone core and the positioning of DNA in the nucleosome. Biochemistry 2012; 51:9814-25. [PMID: 23157165 DOI: 10.1021/bi301416v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trinucleotide repeats (TNRs) occur throughout the genome, and their expansion has been linked to several neurodegenerative disorders, including Huntington's disease. TNRs have been studied using both oligonucleotides and plasmids; however, less is know about how repetitive DNA responds to genomic packaging. Here, we investigate the behavior of CAG/CTG repeats incorporated into nucleosome core particles, the most basic unit of chromatin packaging. To assess the general interaction between CAG/CTG repeats and the histone core, we determined the efficiency with which various TNR-containing DNA substrates form nucleosomes, revealing that even short CAG/CTG tracts are robust incorporators. However, the presence of the Huntington gene flanking sequence (htt) decreases the rate of incorporation. Enzymatic and chemical probing revealed repositioning of the DNA in the nucleosome as the number of CAG/CTG repeats increased, regardless of the flanking sequence. Notably, the periodicity of the repeat tract remained unchanged as a function of length and is consistently 10.7 bp per helical turn. In contrast, the periodicity of the nonrepetitive flanking sequence varies and is smaller than the repeat tract at ~10.0-10.5 bp per turn. Furthermore, while the CAG/CTG repeats remain as a canonical duplex in the nucleosome, nucleosome formation causes kinking in a secondary repeat tract in the htt gene, comprised of CCG/CGG repeats. This work highlights the innate ability of CAG/CTG repeats to incorporate and to position in nucleosomes and how that behavior is modulated by the htt flanking sequence. In addition, it illuminates the differences in packaging of healthy and diseased length repeat tracts within the genome.
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Affiliation(s)
- Catherine B Volle
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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50
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Perry CC, Urata SM, Lee M, Aguilera JA, Milligan JR. Radioprotective effects produced by the condensation of plasmid DNA with avidin and biotinylated gold nanoparticles. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2012; 51:457-468. [PMID: 22825766 DOI: 10.1007/s00411-012-0429-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/28/2012] [Indexed: 06/01/2023]
Abstract
The treatment of aqueous solutions of plasmid DNA with the protein avidin results in significant changes in physical, chemical, and biochemical properties. These effects include increased light scattering, formation of micron-sized particles containing both DNA and protein, and plasmid protection against thermal denaturation, radical attack, and nuclease digestion. All of these changes are consistent with condensation of the plasmid by avidin. Avidin can be displaced from the plasmid at higher ionic strengths. Avidin is not displaced from the plasmid by an excess of a tetra-arginine ligand, nor by the presence of biotin. Therefore, this system offers the opportunity to reversibly bind biotin-labeled species to a condensed DNA-protein complex. An example application is the use of biotinylated gold nanoparticles. This system offers the ability to examine in better detail the chemical mechanisms involved in important radiobiological effects. Examples include protein modulation of radiation damage to DNA, and radiosensitization by gold nanoparticles.
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Affiliation(s)
- Christopher C Perry
- Department of Biochemistry, Loma Linda University, 11085 Campus Street, Loma Linda, CA, 92350, USA
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