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El-Khoury R, Cabrero C, Movilla S, Kaur H, Friedland D, Domínguez A, Thorpe J, Roman M, Orozco M, González C, Damha MJ. Formation of left-handed helices by C2'-fluorinated nucleic acids under physiological salt conditions. Nucleic Acids Res 2024; 52:7414-7428. [PMID: 38874502 PMCID: PMC11260457 DOI: 10.1093/nar/gkae508] [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: 08/25/2023] [Revised: 05/06/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024] Open
Abstract
Recent findings in cell biology have rekindled interest in Z-DNA, the left-handed helical form of DNA. We report here that two minimally modified nucleosides, 2'F-araC and 2'F-riboG, induce the formation of the Z-form under low ionic strength. We show that oligomers entirely made of these two nucleosides exclusively produce left-handed duplexes that bind to the Zα domain of ADAR1. The effect of the two nucleotides is so dramatic that Z-form duplexes are the only species observed in 10 mM sodium phosphate buffer and neutral pH, and no B-form is observed at any temperature. Hence, in contrast to other studies reporting formation of Z/B-form equilibria by a preference for purine glycosidic angles in syn, our NMR and computational work revealed that sequential 2'F…H2N and intramolecular 3'H…N3' interactions stabilize the left-handed helix. The equilibrium between B- and Z- forms is slow in the 19F NMR time scale (≥ms), and each conformation exhibited unprecedented chemical shift differences in the 19F signals. This observation led to a reliable estimation of the relative population of B and Z species and enabled us to monitor B-Z transitions under different conditions. The unique features of 2'F-modified DNA should thus be a valuable addition to existing techniques for specific detection of new Z-binding proteins and ligands.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Cristina Cabrero
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Santiago Movilla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Harneesh Kaur
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - David Friedland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Arnau Domínguez
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
- IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - James D Thorpe
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Morgane Roman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Carlos González
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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2
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Nichols PJ, Krall JB, Henen MA, Welty R, MacFadden A, Vicens Q, Vögeli B. Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate. J Am Chem Soc 2024; 146:677-694. [PMID: 38131335 PMCID: PMC11155437 DOI: 10.1021/jacs.3c10406] [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] [Indexed: 12/23/2023]
Abstract
The left-handed Z-conformation of nucleic acids can be adopted by both DNA and RNA when bound by Zα domains found within a variety of innate immune response proteins. Zα domains stabilize this higher-energy conformation by making specific interactions with the unique geometry of Z-DNA/Z-RNA. However, the mechanism by which a right-handed helix contorts to become left-handed in the presence of proteins, including the intermediate steps involved, is poorly understood. Through a combination of nuclear magnetic resonance (NMR) and other biophysical measurements, we have determined that in the absence of Zα, under low salt conditions at room temperature, d(CpG) and r(CpG) constructs show no observable evidence of transient Z-conformations greater than 0.5% on either the intermediate or slow NMR time scales. At higher temperatures, we observed a transient unfolded intermediate. The ease of melting a nucleic acid duplex correlates with Z-form adoption rates in the presence of Zα. The largest contributing factor to the activation energies of Z-form adoption as calculated by Arrhenius plots is the ease of flipping the sugar pucker, as required for Z-DNA and Z-RNA. Together, these data validate the previously proposed "zipper model" for Z-form adoption in the presence of Zα. Overall, Z-conformations are more likely to be adopted by double-stranded DNA and RNA regions flanked by less stable regions and by RNAs experiencing torsional/mechanical stress.
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Affiliation(s)
- Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
| | - Jeffrey B. Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Robb Welty
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
- Present address: Department of Biology and Biochemistry, Center for Nuclear Receptors and Cellular Signaling, University of Houston, Houston, Texas 77204, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
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3
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Langeberg CJ, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Differential Structural Features of Two Mutant ADAR1p150 Zα Domains Associated with Aicardi-Goutières Syndrome. J Mol Biol 2023; 435:168040. [PMID: 36889460 PMCID: PMC10109538 DOI: 10.1016/j.jmb.2023.168040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
The Zα domain of ADARp150 is critical for proper Z-RNA substrate binding and is a key factor in the type-I interferon response pathway. Two point-mutations in this domain (N173S and P193A), which cause neurodegenerative disorders, are linked to decreased A-to-I editing in disease models. To understand this phenomenon at the molecular level, we biophysically and structurally characterized these two mutated domains, revealing that they bind Z-RNA with a decreased affinity. Less efficient binding to Z-RNA can be explained by structural changes in beta-wing, part of the Z-RNA-protein interface, and alteration of conformational dynamics of the proteins.
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Affiliation(s)
- Conner J Langeberg
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
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4
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Nichols PJ, Krall JB, Henen MA, Vögeli B, Vicens Q. Z-RNA biology: a central role in the innate immune response? RNA (NEW YORK, N.Y.) 2023; 29:273-281. [PMID: 36596670 PMCID: PMC9945438 DOI: 10.1261/rna.079429.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Z-RNA is a higher-energy, left-handed conformation of RNA, whose function has remained elusive. A growing body of work alludes to regulatory roles for Z-RNA in the immune response. Here, we review how Z-RNA features present in cellular RNAs-especially containing retroelements-could be recognized by a family of winged helix proteins, with an impact on host defense. We also discuss how mutations to specific Z-contacting amino acids disrupt their ability to stabilize Z-RNA, resulting in functional losses. We end by highlighting knowledge gaps in the field, which, if addressed, would significantly advance this active area of research.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jeffrey B Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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5
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Yang S, Miao C, Liu W, Zhang G, Shao J, Chang H. Structure and function of African swine fever virus proteins: Current understanding. Front Microbiol 2023; 14:1043129. [PMID: 36846791 PMCID: PMC9950752 DOI: 10.3389/fmicb.2023.1043129] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
African swine fever virus (ASFV) is a highly infectious and lethal double-stranded DNA virus that is responsible for African swine fever (ASF). ASFV was first reported in Kenya in 1921. Subsequently, ASFV has spread to countries in Western Europe, Latin America, and Eastern Europe, as well as to China in 2018. ASFV epidemics have caused serious pig industry losses around the world. Since the 1960s, much effort has been devoted to the development of an effective ASF vaccine, including the production of inactivated vaccines, attenuated live vaccines, and subunit vaccines. Progress has been made, but unfortunately, no ASF vaccine has prevented epidemic spread of the virus in pig farms. The complex ASFV structure, comprising a variety of structural and non-structural proteins, has made the development of ASF vaccines difficult. Therefore, it is necessary to fully explore the structure and function of ASFV proteins in order to develop an effective ASF vaccine. In this review, we summarize what is known about the structure and function of ASFV proteins, including the most recently published findings.
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Affiliation(s)
| | | | - Wei Liu
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Guanglei Zhang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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6
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Bao HL, Xu Y. Oligonucleotide Containing 8-Trifluoromethyl-2'-Deoxyguanosine as a Z-DNA Probe. Methods Mol Biol 2023; 2651:115-130. [PMID: 36892763 DOI: 10.1007/978-1-0716-3084-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Z-DNA structure is a noncanonical left-handed alternative form of DNA, which has been suggested to be biologically important and is related to several genetic diseases and cancer. Therefore, investigation of Z-DNA structure associated with biological events is of great importance to understanding the functions of these molecules. Here, we described the development of a trifluoromethyl labeled deoxyguanosine derivative and employed it as a 19F NMR probe to study Z-form DNA structure in vitro and in living cells.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Miyazaki, Japan.,Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Kiyotake, Miyazaki, Japan.
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7
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NMR Titration Studies in Z-DNA Dynamics. Methods Mol Biol 2023; 2651:69-83. [PMID: 36892760 DOI: 10.1007/978-1-0716-3084-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Chemical shift perturbation (CSP) is a simple NMR technique for studying the DNA binding of proteins. Titration of the unlabeled DNA into the 15N-labeled protein is monitored by acquiring a two-dimensional (2D) heteronuclear single-quantum correlation (HSQC) spectrum at each step of the titration. CSP can also provide information on the DNA-binding dynamics of proteins, as well as protein-induced conformational changes in DNA. Here, we describe the titration of DNA for the 15N-labeled Z-DNA-binding protein, monitored via 2D HSQC spectra. NMR titration data can be analyzed with the active B-Z transition model to provide the protein-induced B-Z transition dynamics of DNA.
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8
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Salt Dependence of DNA Binding Activity of Human Transcription Factor Dlx3. Int J Mol Sci 2022; 23:ijms23169497. [PMID: 36012753 PMCID: PMC9409194 DOI: 10.3390/ijms23169497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Distal-less 3 (Dlx3) is a homeobox-containing transcription factor and plays a crucial role in the development and differentiation process. Human Dlx3 consists of two transactivation domains and a homeobox domain (HD) that selectively binds to the consensus site (5'-TAATT-3') of the DNA duplex. Here, we performed chemical shift perturbation experiments on Dlx3-HD in a complex with a 10-base-paired (10-bp) DNA duplex under various salt conditions. We also acquired the imino proton spectra of the 10-bp DNA to monitor the changes in base-pair stabilities during titration with Dlx3-HD. Our study demonstrates that Dlx3-HD selectively recognizes its consensus DNA sequences through the α3 helix and L1 loop regions with a unique dynamic feature. The dynamic properties of the binding of Dlx3-HD to its consensus DNA sequence can be modulated by varying the salt concentrations. Our study suggested that this unique structural and dynamic feature of Dlx3-HD plays an important role in target DNA recognition, which might be associated with tricho-dento-osseous syndrome.
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9
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Sun L, Miao Y, Wang Z, Chen H, Dong P, Zhang H, Wu L, Jiang M, Chen L, Yang W, Lin P, Jing D, Luo Z, Zhang Y, Jung Y, Wu X, Qian Y, Wu Y. Structural insight into African Swine Fever Virus I73R protein reveals it as a Z‐DNA binding protein. Transbound Emerg Dis 2022; 69:e1923-e1935. [DOI: 10.1111/tbed.14527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/04/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Yurun Miao
- MOE Joint International Research Laboratory of Animal Health and Food Safety College of Veterinary Medicine, Nanjing Agricultural University Nanjing Jiangsu China
| | - Zhenzhong Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety College of Veterinary Medicine, Nanjing Agricultural University Nanjing Jiangsu China
- China Animal Health and Epidemiology Center Qingdao China
| | - Huan Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety College of Veterinary Medicine, Nanjing Agricultural University Nanjing Jiangsu China
| | - Panpan Dong
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Hong Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Linjiao Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Meiqin Jiang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Lifei Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Wendi Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Pingdong Lin
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Dingding Jing
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
| | - Zhipu Luo
- Institute of Molecular Enzymology School of Biology and Basic Medical Sciences Soochow University Suzhou Jiangsu China
| | | | - Yong‐Sam Jung
- MOE Joint International Research Laboratory of Animal Health and Food Safety College of Veterinary Medicine, Nanjing Agricultural University Nanjing Jiangsu China
| | - Xiaodong Wu
- China Animal Health and Epidemiology Center Qingdao China
| | - Yingjuan Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety College of Veterinary Medicine, Nanjing Agricultural University Nanjing Jiangsu China
- Jiangsu Agri‐animal Husbandry Vocational College Veterinary Bio‐pharmaceutical Jiangsu Key Laboratory for High‐Tech Research and Development of Veterinary Biopharmaceuticals Taizhou Jiangsu China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Science Fujian Normal University Fuzhou 350117 China
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10
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Go Y, Ahn HB, Kim BS, Lee AR, Oh KI, Lee JH. Conformational exchange of the Zα domain of human RNA editing enzyme ADAR1 studied by NMR spectroscopy. Biochem Biophys Res Commun 2021; 580:63-66. [PMID: 34624571 DOI: 10.1016/j.bbrc.2021.09.084] [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: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/26/2022]
Abstract
Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune responses, and viral infections. Numerous studies have implicated a role for conformational motions during ZBPs binding upon DNA, but the quantitative intrinsic conformational exchanges of ZBP have not been elucidated. To understand the correlation between the biological function and dynamic feature of the Zα domains of human ADAR1 (hZαADAR1), we have performed the 15N backbone amide Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments on the free hZαADAR1 at two different magnetic fields at 35 °C. The robust inter-dependence of parameters in the global fitting process using multi-magnetic field CPMG profiles allows us characterizing the dynamic properties of conformational changes in hZαADAR1. This study found that free hZαADAR1 exhibited the conformational exchange with a kex of 5784 s-1 between the states "A" (89% population) and "B" (11% population). The different hydrophobic interactions among helices α1, α2, and α3 between these two states might correlate with efficient Z-DNA binding achieved by the hydrogen bonding interactions between its side-chains and the phosphate backbone of Z-DNA.
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Affiliation(s)
- Youyeon Go
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Hye-Bin Ahn
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Byeong-Seon Kim
- Department of Chemistry Education and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
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11
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Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions. Nat Commun 2021; 12:793. [PMID: 33542240 PMCID: PMC7862695 DOI: 10.1038/s41467-021-21039-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) editing of eukaryotic cellular RNAs is essential for protection against auto-immune disorders. Editing is carried out by ADAR1, whose innate immune response-specific cytoplasmic isoform possesses a Z-DNA binding domain (Zα) of unknown function. Zα also binds to CpG repeats in RNA, which are a hallmark of Z-RNA formation. Unexpectedly, Zα has been predicted — and in some cases even shown — to bind to specific regions within mRNA and rRNA devoid of such repeats. Here, we use NMR, circular dichroism, and other biophysical approaches to demonstrate and characterize the binding of Zα to mRNA and rRNA fragments. Our results reveal a broad range of RNA sequences that bind to Zα and adopt Z-RNA conformations. Binding is accompanied by destabilization of neighboring A-form regions which is similar in character to what has been observed for B-Z-DNA junctions. The binding of Zα to non-CpG sequences is specific, cooperative and occurs with an affinity in the low micromolar range. This work allows us to propose a model for how Zα could influence the RNA binding specificity of ADAR1. ADAR1 is an interferon-induced enzyme that catalyzes editing of adenine to inosine across the transcriptome as part of the immune response. Here the authors establish how ADAR1 recognizes non-CpG RNA sequences to facilitate the formation of A-Z junctions.
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12
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Bao HL, Masuzawa T, Oyoshi T, Xu Y. Oligonucleotides DNA containing 8-trifluoromethyl-2'-deoxyguanosine for observing Z-DNA structure. Nucleic Acids Res 2020; 48:7041-7051. [PMID: 32678885 PMCID: PMC7367190 DOI: 10.1093/nar/gkaa505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/01/2020] [Accepted: 06/10/2020] [Indexed: 01/05/2023] Open
Abstract
Z-DNA is known to be a left-handed alternative form of DNA and has important biological roles as well as being related to cancer and other genetic diseases. It is therefore important to investigate Z-DNA structure and related biological events in living cells. However, the development of molecular probes for the observation of Z-DNA structures inside living cells has not yet been realized. Here, we have succeeded in developing site-specific trifluoromethyl oligonucleotide DNA by incorporation of 8-trifluoromethyl-2′-deoxyguanosine (FG). 2D NMR strongly suggested that FG adopted a syn conformation. Trifluoromethyl oligonucleotides dramatically stabilized Z-DNA, even under physiological salt concentrations. Furthermore, the trifluoromethyl DNA can be used to directly observe Z-form DNA structure and interaction of DNA with proteins in vitro, as well as in living human cells by19F NMR spectroscopy for the first time. These results provide valuable information to allow understanding of the structure and function of Z-DNA.
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Affiliation(s)
- Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Tatsuki Masuzawa
- Faculty of Science, Department of Chemistry, Shizuoka University, 836 Ohya Suruga Shizuoka 422-8529, Japan
| | - Takanori Oyoshi
- Faculty of Science, Department of Chemistry, Shizuoka University, 836 Ohya Suruga Shizuoka 422-8529, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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13
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Jin HS, Kim NH, Choi SR, Oh KI, Lee JH. Protein-induced B-Z transition of DNA duplex containing a 2'-OMe guanosine. Biochem Biophys Res Commun 2020; 533:417-423. [PMID: 32972754 DOI: 10.1016/j.bbrc.2020.09.017] [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: 08/31/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
Abstract
Structural transformation of the canonical right-handed helix, B-DNA, to the non-canonical left-handed helix, Z-DNA, can be induced by the Zα domain of the human RNA editing enzyme ADAR1 (hZαADAR1). To characterize the site-specific preferences of binding and structural changes in DNA containing the 2'-O-methyl guanosine derivative (mG), titration of the imino proton spectra and chemical shift perturbations were performed on hZαADAR1 upon binding to Z-DNA. The structural transition between B-Z conformation as the changing ratio between DNA and protein showed a binding affinity of the modified DNA onto the Z-DNA binding protein similar to wild-type DNA or RNA. The chemical shift perturbation results showed that the overall structure and environment of the modified DNA revealed DNA-like properties rather than RNA-like characteristics. Moreover, we found evidence for two distinct regimes, "Z-DNA Sensing" and "Modification Sensing", based on the site-specific chemical shift perturbation between the DNA (or RNA) binding complex and the modified DNA-hZαADAR1 complex. Thus, we propose that modification of the sugar backbone of DNA with 2'-O-methyl guanosine promotes the changes in the surrounding α3 helical structural segment as well as the non-perturbed feature of the β-hairpin region.
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Affiliation(s)
- Ho-Seong Jin
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Na-Hyun Kim
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
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14
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Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
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15
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Kim SH, Lim SH, Lee AR, Kwon DH, Song HK, Lee JH, Cho M, Johner A, Lee NK, Hong SC. Unveiling the pathway to Z-DNA in the protein-induced B-Z transition. Nucleic Acids Res 2019; 46:4129-4137. [PMID: 29584891 PMCID: PMC5934635 DOI: 10.1093/nar/gky200] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/13/2018] [Indexed: 12/31/2022] Open
Abstract
Left-handed Z-DNA is an extraordinary conformation of DNA, which can form by special sequences under specific biological, chemical or physical conditions. Human ADAR1, prototypic Z-DNA binding protein (ZBP), binds to Z-DNA with high affinity. Utilizing single-molecule FRET assays for Z-DNA forming sequences embedded in a long inactive DNA, we measure thermodynamic populations of ADAR1-bound DNA conformations in both GC and TG repeat sequences. Based on a statistical physics model, we determined quantitatively the affinities of ADAR1 to both Z-form and B-form of these sequences. We also reported what pathways it takes to induce the B–Z transition in those sequences. Due to the high junction energy, an intermediate B* state has to accumulate prior to the B–Z transition. Our study showing the stable B* state supports the active picture for the protein-induced B–Z transition that occurs under a physiological setting.
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Affiliation(s)
- Sook Ho Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Physics, Korea University, Seoul 02841, South Korea
| | - So-Hee Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju 52828, South Korea
| | - Do Hoon Kwon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Hyun Kyu Song
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju 52828, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Albert Johner
- Institute Charles Sadron, CNRS 23 rue du Loess 67034, Strasbourg cedex 2, France.,Department of Physics, Sejong University, Seoul 05006, South Korea
| | - Nam-Kyung Lee
- Institute Charles Sadron, CNRS 23 rue du Loess 67034, Strasbourg cedex 2, France.,Department of Physics, Sejong University, Seoul 05006, South Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Physics, Korea University, Seoul 02841, South Korea
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16
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Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function. Comput Struct Biotechnol J 2019; 17:797-804. [PMID: 31312417 PMCID: PMC6607312 DOI: 10.1016/j.csbj.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
Base-pair opening is a conformational transition that is required for proper biological function of nucleic acids. Hydrogen exchange, observed by NMR spectroscopic experiments, is a widely used method to study the thermodynamics and kinetics of base-pair opening in nucleic acids. The hydrogen exchange data of imino protons are analyzed based on a two-state (open/closed) model for the base-pair, where hydrogen exchange only occurs from the open state. In this review, we discuss examples of how hydrogen exchange data provide insight into several interesting biological processes involving functional interactions of nucleic acids: i) selective recognition of DNA by proteins; ii) regulation of RNA cleavage by site-specific mutations; iii) intermolecular interaction of proteins with their target DNA or RNA; iv) formation of PNA:DNA hybrid duplexes. This review systematically summarizes hydrogen exchange theory for base-paired imino protons of nucleic acids. Base-pair opening kinetics explain how the DNA can be selectively recognized by its target proteins. Base-pair opening kinetics explain the mechanisms by which site-specific mutations regulate RNA cleavage. Hydrogen exchange studies can elucidate the intermolecular interaction of proteins with their target DNA or RNA.
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17
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Lee AR, Hwang J, Hur JH, Ryu KS, Kim KK, Choi BS, Kim NK, Lee JH. NMR Dynamics Study Reveals the Zα Domain of Human ADAR1 Associates with and Dissociates from Z-RNA More Slowly than Z-DNA. ACS Chem Biol 2019; 14:245-255. [PMID: 30592616 DOI: 10.1021/acschembio.8b00914] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human RNA editing enzyme ADAR1 deaminates adenosine in pre-mRNA to yield inosine. The Zα domain of human ADAR1 (hZαADAR1) binds specifically to left-handed Z-RNA as well as Z-DNA and stabilizes the Z-conformation. To answer the question of how hZαADAR1 can induce both the B-Z transition of DNA and the A-Z transition of RNA, we investigated the structure and dynamics of hZαADAR1 in complex with 6-base-pair Z-DNA or Z-RNA. We performed chemical shift perturbation and relaxation dispersion experiments on hZαADAR1 upon binding to Z-DNA as well as Z-RNA. Our study demonstrates the unique dynamics of hZαADAR1 during the A-Z transition of RNA, in which the hZαADAR1 protein forms a thermodynamically stable complex with Z-RNA, similar to Z-DNA, but kinetically converts RNA to the Z-form more slowly than DNA. We also discovered some distinct structural features of hZαADAR1 in the Z-RNA binding conformation. Our results suggest that the A-Z transition of RNA facilitated by hZαADAR1 displays unique structural and dynamic features that may be involved in targeting ADAR1 for a role in recognition of RNA substrates.
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Affiliation(s)
- Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
| | - Jihyun Hwang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jeong Hwan Hur
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, South Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team, Korea Basic Science Institute, Chungbuk 28119, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, South Korea
| | - Byong-Seok Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
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18
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Balasubramaniyam T, Ishizuka T, Xu Y. Stability and properties of Z-DNA containing artificial nucleobase 2'-O-methyl-8-methyl guanosine. Bioorg Med Chem 2018; 27:364-369. [PMID: 30545733 DOI: 10.1016/j.bmc.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
We synthesized several DNA oligonucleotides containing one or several 2'-O-methyl-8-methyl guanosine (m8Gm) and demonstrated that these oligonucleotides not only stabilize the Z-DNA with a wide range of sequences under low salt conditions but also possess high thermal stability. Using artificial nucleobase-containing oligonucleotides, we studied the interaction of the Zα domain with Z-DNA. Furthermore, we showed that the m8Gm-contained oligonucleotides allow to study the photochemical reaction of Z-DNA.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan.
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19
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Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins. Molecules 2018; 23:molecules23112748. [PMID: 30355979 PMCID: PMC6278649 DOI: 10.3390/molecules23112748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/21/2018] [Accepted: 10/23/2018] [Indexed: 01/10/2023] Open
Abstract
Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.
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20
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2'- O-Methyl-8-methylguanosine as a Z-Form RNA Stabilizer for Structural and Functional Study of Z-RNA. Molecules 2018; 23:molecules23102572. [PMID: 30304782 PMCID: PMC6222775 DOI: 10.3390/molecules23102572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/28/2018] [Accepted: 10/07/2018] [Indexed: 11/16/2022] Open
Abstract
In contrast to Z-DNA that was stabilized and well-studied for its structure by chemical approaches, the stabilization and structural study of Z-RNA remains a challenge. In this study, we developed a Z-form RNA stabilizer m⁸Gm, and demonstrated that incorporation of m⁸Gm into RNA can markedly stabilize the Z-RNA at low salt conditions. Using the m⁸Gm-contained Z-RNA, we determined the structure of Z-RNA and investigated the interaction of protein and Z-RNA.
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21
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Lee AR, Seo YJ, Choi SR, Ryu KS, Cheong HK, Lee SS, Katahira M, Park CJ, Lee JH. NMR elucidation of reduced B-Z transition activity of PKZ protein kinase at high NaCl concentration. Biochem Biophys Res Commun 2017; 482:335-340. [DOI: 10.1016/j.bbrc.2016.11.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 01/09/2023]
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22
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Lee JY, Lee AR, Choi SR, Seo YJ, Lee SS, Lee JH. Zα Domain of Goldfish PKR-like Protein Kinase Exhibits the Flexible Backbone Structure of β-Hairpin for Efficient Z-DNA Binding. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jin-Young Lee
- Department of Chemistry and Research Institute of Natural Science; Gyeongsang National University; Jinju 52828 Korea
| | - Ae-Ree Lee
- Department of Chemistry and Research Institute of Natural Science; Gyeongsang National University; Jinju 52828 Korea
| | - Seo-Ree Choi
- Department of Chemistry and Research Institute of Natural Science; Gyeongsang National University; Jinju 52828 Korea
| | - Yeo-Jin Seo
- Department of Chemistry and Research Institute of Natural Science; Gyeongsang National University; Jinju 52828 Korea
| | - Shim Sung Lee
- Department of Chemistry and Research Institute of Natural Science; Gyeongsang National University; Jinju 52828 Korea
| | - Joon-Hwa Lee
- Department of Chemistry and Research Institute of Natural Science; Gyeongsang National University; Jinju 52828 Korea
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23
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Subramani VK, Kim D, Yun K, Kim KK. Structural and functional studies of a large winged Z-DNA-binding domain of Danio rerio protein kinase PKZ. FEBS Lett 2016; 590:2275-85. [PMID: 27265117 DOI: 10.1002/1873-3468.12238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/19/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022]
Abstract
The Z-DNA-binding domain of PKZ from zebrafish (Danio rerio; drZαPKZ ) contains the largest β-wing among known Z-DNA-binding domains. To elucidate the functional implication of the β-wing, we solved the crystal structure of apo-drZαPKZ . Structural comparison with its Z-DNA-bound form revealed a large conformational change within the β-wing during Z-DNA binding. Biochemical studies of protein mutants revealed that two basic residues in the β-wing are responsible for Z-DNA recognition as well as fast B-Z transition. Therefore, the extra basic residues in the β-wing of drZαPKZ are necessary for the fast B-Z transition activity.
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Affiliation(s)
- Vinod Kumar Subramani
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Doyoun Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kyunghee Yun
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
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