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Błaszczyk L, Ryczek M, Das B, Mateja-Pluta M, Bejger M, Śliwiak J, Nakatani K, Kiliszek A. Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand. Nucleic Acids Res 2024; 52:6707-6717. [PMID: 38738637 PMCID: PMC11194091 DOI: 10.1093/nar/gkae376] [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: 10/24/2023] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
The abnormal expansion of GGGGCC/GGCCCC hexanucleotide repeats (HR) in C9orf72 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Structural polymorphisms of HR result in the multifactorial pathomechanism of ALS/FTD. Consequently, many ongoing studies are focused at developing therapies targeting pathogenic HR RNA. One of them involves small molecules blocking sequestration of important proteins, preventing formation of toxic nuclear foci. However, rational design of potential therapeutics is hindered by limited number of structural studies of RNA-ligand complexes. We determined the crystal structure of antisense HR RNA in complex with ANP77 ligand (1.1 Å resolution) and in the free form (0.92 and 1.5 Å resolution). HR RNA folds into a triplex structure composed of four RNA chains. ANP77 interacted with two neighboring single-stranded cytosines to form pseudo-canonical base pairs by adopting sandwich-like conformation and adjusting the position of its naphthyridine units to the helical twist of the RNA. In the unliganded structure, the cytosines formed a peculiar triplex i-motif, assembled by trans C•C+ pair and a third cytosine located at the Hoogsteen edge of the C•C+ pair. These results extend our knowledge of the structural polymorphisms of HR and can be used for rational design of small molecules targeting disease-related RNAs.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Marcin Ryczek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Martyna Mateja-Pluta
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
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Taghavi A, Baisden JT, Childs-Disney JL, Yildirim I, Disney M. Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies. Nucleic Acids Res 2023; 51:5325-5340. [PMID: 37216594 PMCID: PMC10287959 DOI: 10.1093/nar/gkad403] [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: 01/08/2023] [Revised: 04/15/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
G4C2 and G2C4 repeat expansions in chromosome 9 open reading frame 72 (C9orf72) are the most common cause of genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), or c9ALS/FTD. The gene is bidirectionally transcribed, producing G4C2 repeats [r(G4C2)exp] and G2C4 repeats [r(G2C4)exp]. The c9ALS/FTD repeat expansions are highly structured, and structural studies showed that r(G4C2)exp predominantly folds into a hairpin with a periodic array of 1 × 1 G/G internal loops and a G-quadruplex. A small molecule probe revealed that r(G4C2)exp also adopts a hairpin structure with 2 × 2 GG/GG internal loops. We studied the conformational dynamics adopted by 2 × 2 GG/GG loops using temperature replica exchange molecular dynamics (T-REMD) and further characterized the structure and underlying dynamics using traditional 2D NMR techniques. These studies showed that the loop's closing base pairs influence both structure and dynamics, particularly the configuration adopted around the glycosidic bond. Interestingly, r(G2C4) repeats, which fold into an array of 2 × 2 CC/CC internal loops, are not as dynamic. Collectively, these studies emphasize the unique sensitivity of r(G4C2)exp to small changes in stacking interactions, which is not observed in r(G2C4)exp, providing important considerations for further principles in structure-based drug design.
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Affiliation(s)
- Amirhossein Taghavi
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jared T Baisden
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
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3
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Satange R, Rode AB, Hou MH. Revisiting recent unusual drug-DNA complex structures: Implications for cancer and neurological disease diagnostics and therapeutics. Bioorg Med Chem 2022; 76:117094. [PMID: 36410206 DOI: 10.1016/j.bmc.2022.117094] [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: 09/14/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
DNA plays a crucial role in various biological processes such as protein production, replication, recombination etc. by adopting different conformations. Targeting these conformations by small molecules is not only important for disease therapy, but also improves our understanding of the mechanisms of disease development. In this review, we provide an overview of some of the most recent ligand-DNA complexes that have diagnostic and therapeutic applications in neurological diseases caused by abnormal repeat expansions and in cancer associated with mismatches. In addition, we have discussed important implications of ligands targeting higher-order structures, such as four-way junctions, G-quadruplexes and triplexes for drug discovery and DNA nanotechnology. We provide an overview of the results and perspectives of such structural studies on ligand-DNA interactions.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Ambadas B Rode
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
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4
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A Structural Potential of Rare Trinucleotide Repeat Tracts in RNA. Int J Mol Sci 2022; 23:ijms23105850. [PMID: 35628656 PMCID: PMC9144543 DOI: 10.3390/ijms23105850] [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: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/27/2023] Open
Abstract
Among types of trinucleotide repeats, there is some disproportion in the frequency of their occurrence in the human exome. This research presents new data describing the folding and thermodynamic stability of short, tandem RNA repeats of 23 types, focusing on the rare, yet poorly analyzed ones. UV-melting experiments included the presence of PEG or potassium and magnesium ions to determine their effect on the stability of RNA repeats structures. Rare repeats predominantly stayed single-stranded but had the potential for base pairing with other partially complementary repeat tracts. A coexistence of suitably complementary repeat types in a single RNA creates opportunities for interaction in the context of the secondary structure of RNA. We searched the human transcriptome for model RNAs in which different, particularly rare trinucleotide repeats coexist and selected the GABRA4 and CHIC1 RNAs to study intramolecular interactions between the repeat tracts that they contain. In vitro secondary structure probing results showed that the UAA and UUG repeat tracts, present in GABRA4 3' UTR, form a double helix, which separates one of its structural domains. For the RNA CHIC1 ORF fragment containing four short AGG repeat tracts and the CGU tract, we proved the formation of quadruplexes that blocked reverse transcription.
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Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops. Comput Struct Biotechnol J 2021; 19:2819-2832. [PMID: 34093995 PMCID: PMC8138726 DOI: 10.1016/j.csbj.2021.04.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 01/05/2023] Open
Abstract
Pathogenic DNA secondary structures have been identified as a common and causative factor for expansion in trinucleotide, hexanucleotide, and other simple sequence repeats. These expansions underlie about fifty neurological and neuromuscular disorders known as “anticipation diseases”. Cell toxicity and death have been linked to the pathogenic conformations and functional changes of the RNA transcripts, of DNA itself and, when trinucleotides are present in exons, of the translated proteins. We review some of our results for the conformations and dynamics of pathogenic structures for both RNA and DNA, which include mismatched homoduplexes formed by trinucleotide repeats CAG and GAC; CCG and CGG; CTG(CUG) and GTC(GUC); the dynamics of DNA CAG hairpins; mismatched homoduplexes formed by hexanucleotide repeats (GGGGCC) and (GGCCCC); and G-quadruplexes formed by (GGGGCC) and (GGGCCT). We also discuss the dynamics of strand slippage in DNA hairpins formed by CAG repeats as observed with single-molecule Fluorescence Resonance Energy Transfer. This review focuses on the rich behavior exhibited by the mismatches associated with these simple sequence repeat noncanonical structures.
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Mak CH, Phan ENH. Diagrammatic approaches to RNA structures with trinucleotide repeats. Biophys J 2021; 120:2343-2354. [PMID: 33887227 PMCID: PMC8390803 DOI: 10.1016/j.bpj.2021.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 11/30/2022] Open
Abstract
Trinucleotide repeat expansion disorders are associated with the overexpansion of (CNG) repeats on the genome. Messenger RNA transcripts of sequences with greater than 60–100 (CNG) tandem units have been implicated in trinucleotide repeat expansion disorder pathogenesis. In this work, we develop a diagrammatic theory to study the structural diversity of these (CNG)n RNA sequences. Representing structural elements on the chain’s conformation by a set of graphs and employing elementary diagrammatic methods, we have formulated a renormalization procedure to re-sum these graphs and arrive at a closed-form expression for the ensemble partition function. With a simple approximation for the renormalization and applied to extended (CNG)n sequences, this theory can comprehensively capture an infinite set of conformations with any number and any combination of duplexes, hairpins, multiway junctions, and quadruplexes. To quantify the diversity of different (CNG)n ensembles, the analytical equations derived from the diagrammatic theory were solved numerically to derive equilibrium estimates for the secondary structural contents of the chains. The results suggest that the structural ensembles of (CNG)n repeat sequence with n ∼60 are surprisingly diverse, and the distribution is sensitive to the ability of the N nucleotide to make noncanonical pairs and whether the (CNG)n sequence can sustain stable quadruplexes. The results show how perturbations in the form of biases on the stabilities of the various structural motifs, duplexes, junctions, helices, and quadruplexes could affect the secondary structures of the chains and how these structures may switch when they are perturbed.
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Affiliation(s)
- Chi H Mak
- Department of Chemistry, Center of Applied Mathematical Sciences and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California.
| | - Ethan N H Phan
- Department of Chemistry, University of Southern California, Los Angeles, California
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Ajjugal Y, Kolimi N, Rathinavelan T. Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS. Sci Rep 2021; 11:8163. [PMID: 33854084 PMCID: PMC8046799 DOI: 10.1038/s41598-021-87097-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
CGG tandem repeat expansion in the 5'-untranslated region of the fragile X mental retardation-1 (FMR1) gene leads to unusual nucleic acid conformations, hence causing genetic instabilities. We show that the number of G…G (in CGG repeat) or C…C (in CCG repeat) mismatches (other than A…T, T…A, C…G and G…C canonical base pairs) dictates the secondary structural choice of the sense and antisense strands of the FMR1 gene and their corresponding transcripts in fragile X-associated tremor/ataxia syndrome (FXTAS). The circular dichroism (CD) spectra and electrophoretic mobility shift assay (EMSA) reveal that CGG DNA (sense strand of the FMR1 gene) and its transcript favor a quadruplex structure. CD, EMSA and molecular dynamics (MD) simulations also show that more than four C…C mismatches cannot be accommodated in the RNA duplex consisting of the CCG repeat (antisense transcript); instead, it favors an i-motif conformational intermediate. Such a preference for unusual secondary structures provides a convincing justification for the RNA foci formation due to the sequestration of RNA-binding proteins to the bidirectional transcripts and the repeat-associated non-AUG translation that are observed in FXTAS. The results presented here also suggest that small molecule modulators that can destabilize FMR1 CGG DNA and RNA quadruplex structures could be promising candidates for treating FXTAS.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
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8
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Nakagawa O, Aoyama H, Fujii A, Kishimoto Y, Obika S. Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids. Chemistry 2021; 27:3842-3848. [PMID: 33274789 DOI: 10.1002/chem.202004819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of AgI ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of AgI -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing AgI -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of AgI -mediated base pairs in the central region. The bent duplex structure induced by the addition of AgI ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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9
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Mukherjee S, Błaszczyk L, Rypniewski W, Falschlunger C, Micura R, Murata A, Dohno C, Nakatani K, Kiliszek A. Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats. Nucleic Acids Res 2019; 47:10906-10913. [PMID: 31566242 PMCID: PMC6847237 DOI: 10.1093/nar/gkz832] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/07/2019] [Accepted: 09/26/2019] [Indexed: 12/17/2022] Open
Abstract
The trinucleotide repeat expansion disorders (TREDs) constitute of a group of >40 hereditary neurodegenerative human diseases associated with abnormal expansion of repeated sequences, such as CAG repeats. The pathogenic factor is a transcribed RNA or protein whose function in the cell is compromised. The disorders are progressive and incurable. Consequently, many ongoing studies are oriented at developing therapies. We have analyzed crystal structures of RNA containing CAG repeats in complex with synthetic cyclic mismatch-binding ligands (CMBLs). The models show well-defined interactions between the molecules in which the CMBLs mimic nucleobases as they form pseudo-canonical base pairs with adenosine residues and engage in extensive stacking interactions with neighboring nucleotides. The binding of ligands is associated with major structural changes of the CAG repeats, which is consistent with results of biochemical studies. The results constitute an early characterization of the first lead compounds in the search for therapy against TREDs. The crystallographic data indicate how the compounds could be further refined in future biomedical studies.
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Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Pan F, Man VH, Roland C, Sagui C. Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats. J Phys Chem B 2018; 122:4491-4512. [PMID: 29617130 DOI: 10.1021/acs.jpcb.8b01658] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expansions of both GGC and CCG sequences lead to a number of expandable, trinucleotide repeat (TR) neurodegenerative diseases. Understanding of these diseases involves, among other things, the structural characterization of the atypical DNA and RNA secondary structures. We have performed molecular dynamics simulations of (GCC) n and (GGC) n homoduplexes in order to characterize their conformations, stability, and dynamics. Each TR has two reading frames, which results in eight nonequivalent RNA/DNA homoduplexes, characterized by CpG or GpC steps between the Watson-Crick base pairs. Free energy maps for the eight homoduplexes indicate that the C-mismatches prefer anti-anti conformations, while G-mismatches prefer anti-syn conformations. Comparison between three modifications of the DNA AMBER force field shows good agreement for the mismatch free energy maps. The mismatches in DNA-GCC (but not CCG) are extrahelical, forming an extended e-motif. The mismatched duplexes exhibit characteristic sequence-dependent step twist, with strong variations in the G-rich sequences and the e-motif. The distribution of Na+ is highly localized around the mismatches, especially G-mismatches. In the e-motif, there is strong Na+ binding by two G(N7) atoms belonging to the pseudo GpC step created when cytosines are extruded and by extrahelical cytosines. Finally, we used a novel technique based on fast melting by means of an infrared laser pulse to classify the relative stability of the different DNA-CCG and -GGC homoduplexes.
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Affiliation(s)
- Feng Pan
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
| | - Viet Hoang Man
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
| | - Christopher Roland
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
| | - Celeste Sagui
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
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11
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703989] [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)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences; Academia Sinica; 128 Sec. 2, Academia Rd. Nankang Taipei Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center; College of Science; National Taiwan University; No.1, Sec. 4, Roosevelt Rd. Taipei Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology; Chi Mei Medical Center; No.901, Zhonghua Rd. Tainan Taiwan
| | - Stephen Neidle
- The School of Pharmacy; University College London; London WC1N 1AX UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
- Institute of Biotechnology; National Chung Hsing University; 250 Kuo-kuang Rd. Taichung Taiwan
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12
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Tseng WH, Chang CK, Wu PC, Hu NJ, Lee GH, Tzeng CC, Neidle S, Hou MH. Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation. Angew Chem Int Ed Engl 2017; 56:8761-8765. [PMID: 28544401 DOI: 10.1002/anie.201703989] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 01/23/2023]
Abstract
Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII (Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII (Chro)2 . The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm.
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Affiliation(s)
- Wen-Hsuan Tseng
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Rd. Nankang, Taipei, Taiwan
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center, College of Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ching-Cherng Tzeng
- Department of Pathology, Chi Mei Medical Center, No.901, Zhonghua Rd., Tainan, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
- Institute of Biotechnology, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan
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13
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Phan A, Mailey K, Saeki J, Gu X, Schroeder SJ. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops. RNA (NEW YORK, N.Y.) 2017; 23:770-781. [PMID: 28213527 PMCID: PMC5393185 DOI: 10.1261/rna.059865.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/13/2017] [Indexed: 05/24/2023]
Abstract
Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites.
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Affiliation(s)
- Andy Phan
- Department of Chemistry and Biochemistry
| | | | | | - Xiaobo Gu
- Department of Chemistry and Biochemistry
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Susan J Schroeder
- Department of Chemistry and Biochemistry
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
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14
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Zhang Y, Roland C, Sagui C. Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases. ACS Chem Neurosci 2017; 8:578-591. [PMID: 27933757 PMCID: PMC5423440 DOI: 10.1021/acschemneuro.6b00348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A (GGGGCC) hexanucleotide repeat (HR) expansion in the C9ORF72 gene, and its associated antisense (CCCCGG) expansion, are considered the major cause behind frontotemporal dementia and amyotrophic lateral sclerosis. We have performed molecular dynamics simulations to characterize the conformation and dynamics of the 12 duplexes that result from the three different reading frames in sense and antisense HRs for both DNA and RNA. These duplexes display atypical structures relevant not only for a molecular level understanding of these diseases but also for enlarging the repertoire of nucleic-acid structural motifs. G-rich helices share common features. The inner G-G mismatches stay inside the helix in Gsyn-Ganti conformations and form two hydrogen bonds (HBs) between the Watson-Crick edge of Ganti and the Hoogsteen edge of Gsyn. In addition, Gsyn in RNA forms a base-phosphate HB. Inner G-G mismatches cause local unwinding of the helix. G-rich double helices are more stable than C-rich helices due to better stacking and HBs of G-G mismatches. C-rich helix conformations vary wildly. C mismatches flip out of the helix in DNA but not in RNA. Least (most) stable C-rich RNA and DNA helices have single (double) mismatches separated by two (four) Watson-Crick basepairs. The most stable DNA structure displays an "e-motif" where mismatched bases flip toward the minor groove and point in the 5' direction. There are two RNA conformations, where the orientation and HB pattern of the mismatches is coupled to bending of the helix.
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Affiliation(s)
- Yuan Zhang
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
- Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695-8202, United States
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
- Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695-8202, United States
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
- Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695-8202, United States
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15
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Błaszczyk L, Rypniewski W, Kiliszek A. Structures of RNA repeats associated with neurological diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28130835 DOI: 10.1002/wrna.1412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/25/2016] [Accepted: 11/12/2016] [Indexed: 01/04/2023]
Abstract
All RNA molecules possess a 'propensity' to fold into complex secondary and tertiary structures. Although they are composed of only four types of nucleotides, they show an enormous structural richness which reflects their diverse functions in the cell. However, in some cases the folding of RNA can have deleterious consequences. Aberrantly expanded, repeated RNA sequences can exhibit gain-of-function abnormalities and become pathogenic, giving rise to many incurable neurological diseases. Most RNA repeats form long hairpin structures whose stem consists of noncanonical base pairs interspersed among Watson-Crick pairs. The expanded hairpins have an ability to sequester important proteins and form insoluble nuclear foci. The RNA pathology, common to many repeat disorders, has drawn attention to the structures of the RNA repeats. In this review, we summarize secondary structure probing and crystallographic studies of disease-related RNA repeat sequences. We discuss the unique structural features which can contribute to the pathogenic properties of the repeated runs. In addition, we present the newest reports concerning structural data linked to therapeutic approaches. WIREs RNA 2017, 8:e1412. doi: 10.1002/wrna.1412 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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16
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Krans A, Kearse MG, Todd PK. Repeat-associated non-AUG translation from antisense CCG repeats in fragile X tremor/ataxia syndrome. Ann Neurol 2016; 80:871-881. [PMID: 27761921 DOI: 10.1002/ana.24800] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Repeat-associated non-AUG (RAN) translation drives production of toxic proteins from pathogenic repeat sequences in multiple untreatable neurodegenerative disorders. Fragile X-associated tremor/ataxia syndrome (FXTAS) is one such condition, resulting from a CGG trinucleotide repeat expansion in the 5' leader sequence of the FMR1 gene. RAN proteins from the CGG repeat accumulate in ubiquitinated inclusions in FXTAS patient brains and elicit toxicity. In addition to the CGG repeat, an antisense mRNA containing a CCG repeat is also transcribed from the FMR1 locus. We evaluated whether this antisense CCG repeat supports RAN translation and contributes to pathology in FXTAS patients. METHODS We generated a series of CCG RAN translation-specific reporters and utilized them to measure RAN translation from CCG repeats in multiple reading frames in transfected cells. We also developed antibodies against predicted CCG RAN proteins and used immunohistochemistry and immunofluorescence on FXTAS patient tissues to measure their accumulation and distribution. RESULTS RAN translation from CCG repeats is supported in all 3 potential reading frames, generating polyproline, polyarginine, and polyalanine proteins, respectively. Their production occurs whether or not the natural AUG start upstream of the repeat in the proline reading frame is present. All 3 frames show greater translation at larger repeat sizes. Antibodies targeted to the antisense FMR polyproline and polyalanine proteins selectively stain nuclear and cytoplasmic aggregates in FXTAS patients and colocalize with ubiquitinated neuronal inclusions. INTERPRETATION RAN translation from antisense CCG repeats generates novel proteins that accumulate in ubiquitinated inclusions in FXTAS patients. Ann Neurol 2016;80:871-881.
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Affiliation(s)
- Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI.,VA Medical Center, Ann Arbor, MI
| | | | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI.,VA Medical Center, Ann Arbor, MI
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17
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Rolle K, Piwecka M, Belter A, Wawrzyniak D, Jeleniewicz J, Barciszewska MZ, Barciszewski J. The Sequence and Structure Determine the Function of Mature Human miRNAs. PLoS One 2016; 11:e0151246. [PMID: 27031951 PMCID: PMC4816427 DOI: 10.1371/journal.pone.0151246] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/15/2016] [Indexed: 12/31/2022] Open
Abstract
Micro RNAs (miRNAs) (19–25 nucleotides in length) belong to the group of non-coding RNAs are the most abundant group of posttranscriptional regulators in multicellular organisms. They affect a gene expression by binding of fully or partially complementary sequences to the 3’-UTR of target mRNA. Furthermore, miRNAs present a mechanism by which genes with diverse functions on multiple pathways can be simultaneously regulated at the post-transcriptional level. However, little is known about the specific pathways through which miRNAs with specific sequence or structural motifs regulate the cellular processes. In this paper we showed the broad and deep characteristics of mature miRNAs according to their sequence and structural motifs. We investigated a distinct group of miRNAs characterized by the presence of specific sequence motifs, such as UGUGU, GU-repeats and purine/pyrimidine contents. Using computational function and pathway analysis of their targeted genes, we were able to observe the relevance of sequence and the type of targeted mRNAs. As the consequence of the sequence analysis we finally provide the comprehensive description of pathways, biological processes and proteins associated with the distinct group of characterized miRNAs. Here, we found that the specific group of miRNAs with UGUGU can activate the targets associated to the interferon induction pathway or pathways prominently observed during carcinogenesis. GU-rich miRNAs are prone to regulate mostly processes in neurogenesis, whereas purine/pyrimidine rich miRNAs could be involved rather in transport and/or degradation of RNAs. Additionally, we have also analyzed the simple sequence repeats (SSRs). Their variation within mature miRNAs might be critical for normal miRNA regular activity. Expansion or contraction of SSRs in mature miRNA might directly affect its mRNA interaction or even change the function of that distinct miRNA. Our results prove that due to the specific sequence features, these molecules can also be involved in well-defined cellular processes depending on their sequence contents. The pathway mapping and theoretical gene target identification allowed us to create a biological framework to show the relevance of the specific miRNAs in regulation the distinct type of targets.
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Affiliation(s)
- Katarzyna Rolle
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail: (JB); (KR)
| | - Monika Piwecka
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Jaroslaw Jeleniewicz
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Miroslawa Z. Barciszewska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail: (JB); (KR)
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18
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Dodd DW, Tomchick DR, Corey DR, Gagnon KT. Pathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches. Biochemistry 2016; 55:1283-6. [PMID: 26878348 DOI: 10.1021/acs.biochem.6b00136] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Expansion of a GGGGCC/CCCCGG repeat sequence in the first intron of the C9ORF72 gene is a leading cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). In this combined disorder, called c9FTD/ALS, the expansion is bidirectionally transcribed into sense and antisense repeat RNA associated with disease. To better understand the role of C9ORF72 repeat RNA in molecular disease pathology, we determined crystal structures of a [(CCCCGG)3(CCCC)] model antisense repeat RNA to 1.47 Å resolution. The RNA structure was an A-form-like double helix composed of repeating and regularly spaced tandem C:C mismatch pairs that perturbed helical geometry and surface charge. Solution studies revealed a preference for A-form-like helical conformations as the repeat number increased. Results provide a structural starting point for rationalizing the contribution of repeat RNA to c9FTD/ALS molecular disease mechanisms and for developing molecules to target C9ORF72 repeat RNA as potential therapeutics.
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Affiliation(s)
- David W Dodd
- Department of Pharmacology, ‡Department of Biophysics, and §Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States.,Department of Biochemistry and Molecular Biology, School of Medicine, and ⊥Department of Chemistry and Biochemistry, Southern Illinois University , Carbondale, Illinois 62901, United States
| | - Diana R Tomchick
- Department of Pharmacology, ‡Department of Biophysics, and §Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States.,Department of Biochemistry and Molecular Biology, School of Medicine, and ⊥Department of Chemistry and Biochemistry, Southern Illinois University , Carbondale, Illinois 62901, United States
| | - David R Corey
- Department of Pharmacology, ‡Department of Biophysics, and §Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States.,Department of Biochemistry and Molecular Biology, School of Medicine, and ⊥Department of Chemistry and Biochemistry, Southern Illinois University , Carbondale, Illinois 62901, United States
| | - Keith T Gagnon
- Department of Pharmacology, ‡Department of Biophysics, and §Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States.,Department of Biochemistry and Molecular Biology, School of Medicine, and ⊥Department of Chemistry and Biochemistry, Southern Illinois University , Carbondale, Illinois 62901, United States
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19
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Rypniewski W, Banaszak K, Kuliński T, Kiliszek A. Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation. RNA (NEW YORK, N.Y.) 2016; 22:22-31. [PMID: 26543073 PMCID: PMC4691832 DOI: 10.1261/rna.052399.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/19/2015] [Indexed: 05/16/2023]
Abstract
RNA transcripts that include expanded CCUG repeats are associated with myotonic dystrophy type 2. Crystal structures of two CCUG-containing oligomers show that the RNA strands associate into slipped duplexes that contain noncanonical C-U pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual Watson-Crick-like pairing. The overhanging ends of the duplexes interact forming U-U pairs, which also show tautomerism. Duplexes consisting of CCUG repeats are thermodynamically less stable than the trinucleotide repeats involved in the TRED genetic disorders, but introducing LNA residues increases their stability and raises the melting temperature of the studied oligomers by ∼10°C, allowing detailed crystallographic studies. Quantum mechanical calculations were performed to test the possibility of the tautomeric transitions or protonation within the noncanonical pairs. The results indicate that tautomeric or ionic shifts of nucleobases can manifest themselves in biological systems, supplementing the canonical "rules of engagement."
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Affiliation(s)
- Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Katarzyna Banaszak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tadeusz Kuliński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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20
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Svidritskiy E, Korostelev AA. Ribosome Structure Reveals Preservation of Active Sites in the Presence of a P-Site Wobble Mismatch. Structure 2015; 23:2155-61. [PMID: 26412335 DOI: 10.1016/j.str.2015.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/07/2015] [Accepted: 08/13/2015] [Indexed: 11/17/2022]
Abstract
Translation initiation in the P site occasionally occurs at atypical (non-AUG) start codons, including those forming a mismatch in the third (wobble) position. During elongation, however, a pyrimidine-pyrimidine wobble mismatch may trigger a translation quality-control mechanism, whereby the P-site mismatch is thought to perturb the downstream A-site codon or the decoding center, thereby reducing translation fidelity and inducing termination of aberrant translation. We report a crystal structure of the 70S initiation complex containing an AUC codon in the ribosomal P site. Remarkably, the ribosome stabilizes the mismatched codon-anticodon helix, arranging a normally disruptive cytosine-cytosine pair into a Watson-Crick-like conformation. Translation-competent conformations of the tRNA, mRNA, and decoding center suggest that a P-site wobble-position mismatch in the 70S initiation complex does not pre-arrange the mRNA or decoding center to favor subsequent miscoding events.
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Affiliation(s)
- Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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21
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Park H, González ÀL, Yildirim I, Tran T, Lohman JR, Fang P, Guo M, Disney MD. Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10). Biochemistry 2015; 54:3851-9. [PMID: 26039897 DOI: 10.1021/acs.biochem.5b00551] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide (5')UCU(3')/(3')UCU(5') internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.
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Affiliation(s)
| | - Àlex L González
- ∥Grup d'Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)-Universitat Ramon Llull (URL), Barcelona 08017, Spain
| | - Ilyas Yildirim
- ⊥Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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22
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Chen YW, Jhan CR, Neidle S, Hou MH. Structural Basis for the Identification of an i-Motif Tetraplex Core with a Parallel-Duplex Junction as a Structural Motif in CCG Triplet Repeats. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Chen YW, Jhan CR, Neidle S, Hou MH. Structural basis for the identification of an i-motif tetraplex core with a parallel-duplex junction as a structural motif in CCG triplet repeats. Angew Chem Int Ed Engl 2014; 53:10682-6. [PMID: 25139267 DOI: 10.1002/anie.201405637] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 11/12/2022]
Abstract
CCG triplet repeats can fold into tetraplex structures, which are associated with the expansion of (CCG)n trinucleotide sequences in certain neurological diseases. These structures are stabilized by intertwining i-motifs. However, the structural basis for tetraplex i-motif formation in CCG triplet repeats remains largely unknown. We report the first crystal structure of a CCG-repeat sequence, which shows that two dT(CCG)3 A strands can associate to form a tetraplex structure with an i-motif core containing four C:C(+) pairs flanked by two G:G homopurine base pairs as a structural motif. The tetraplex core is attached to a short parallel-stranded duplex. Each hairpin itself contains a central CCG loop in which the nucleotides are flipped out and stabilized by stacking interactions. The helical twists between adjacent cytosine residues of this structure in the i-motif core have an average value of 30°, which is greater than those previously reported for i-motif structures.
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Affiliation(s)
- Yi-Wen Chen
- Institute of Genomics and Bioinformatics and Institute of Biochemistry, National Chung Hsing University, No. 250 Kuo-Kuang Road, Taichung (Taiwan)
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24
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Abstract
CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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25
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Cleary JD, Ranum LPW. Repeat associated non-ATG (RAN) translation: new starts in microsatellite expansion disorders. Curr Opin Genet Dev 2014; 26:6-15. [PMID: 24852074 DOI: 10.1016/j.gde.2014.03.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/31/2014] [Accepted: 03/11/2014] [Indexed: 12/14/2022]
Abstract
Microsatellite-expansion diseases are a class of neurological and neuromuscular disorders caused by the expansion of short stretches of repetitive DNA (e.g. GGGGCC, CAG, CTG …) within the human genome. Since their discovery 20 years ago, research into how microsatellites expansions cause disease has been examined using the model that these genes are expressed in one direction and that expansion mutations only encode proteins when located in an ATG-initiated open reading frame. The fact that these mutations are often bidirectionally transcribed combined with the recent discovery of repeat associated non-ATG (RAN) translation provides new perspectives on how these expansion mutations are expressed and impact disease. Two expansion transcripts and a set of unexpected RAN proteins must now be considered for both coding and 'non-coding' expansion disorders. RAN proteins have been reported in a growing number of diseases, including spinocerebellar ataxia type 8 (SCA8), myotonic dystrophy type 1 (DM1), Fragile-X tremor ataxia syndrome (FXTAS), and C9ORF72 amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD).
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Affiliation(s)
- John Douglas Cleary
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL, USA; Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA; Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Laura P W Ranum
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL, USA; Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA; Department of Neurology, College of Medicine, University of Florida, Gainesville, FL, USA; Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA.
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26
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Ananth P, Goldsmith G, Yathindra N. An innate twist between Crick's wobble and Watson-Crick base pairs. RNA (NEW YORK, N.Y.) 2013; 19:1038-1053. [PMID: 23861536 PMCID: PMC3708525 DOI: 10.1261/rna.036905.112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Non-Watson-Crick pairs like the G·U wobble are frequent in RNA duplexes. Their geometric dissimilarity (nonisostericity) with the Watson-Crick base pairs and among themselves imparts structural variations decisive for biological functions. Through a novel circular representation of base pairs, a simple and general metric scheme for quantification of base-pair nonisostericity, in terms of residual twist and radial difference that can also envisage its mechanistic effect, is proposed. The scheme is exemplified by G·U and U·G wobble pairs, and their predicable local effects on helical twist angle are validated by MD simulations. New insights into a possible rationale for contextual occurrence of G·U and other non-WC pairs, as well as the influence of a G·U pair on other non-Watson-Crick pair neighborhood and RNA-protein interactions are obtained from analysis of crystal structure data. A few instances of RNA-protein interactions along the major groove are documented in addition to the well-recognized interaction of the G·U pair along the minor groove. The nonisostericity-mediated influence of wobble pairs for facilitating helical packing through long-range interactions in ribosomal RNAs is also reviewed.
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27
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Coonrod LA, Lohman JR, Berglund JA. Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix. Biochemistry 2012; 51:8330-7. [PMID: 23025897 DOI: 10.1021/bi300829w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a microsatellite expansion disorder caused by the aberrant expansion of CTG repeats in the 3'-untranslated region of the DMPK gene. When transcribed, the toxic RNA CUG repeats sequester RNA binding proteins, which leads to disease symptoms. The expanded CUG repeats can adopt a double-stranded structure, and targeting this helix is a therapeutic strategy for DM1. To improve our understanding of the 5'CUG/3'GUC motif and how it may interact with proteins and small molecules, we designed a short CUG helix attached to a GAAA tetraloop/receptor to facilitate crystal packing. Here we report the highest-resolution structure (1.95 Å) to date of a GAAA tetraloop/receptor and the CUG helix it was used to crystallize. Within the CUG helix, we identify two different forms of noncanonical U-U pairs and reconfirm that CUG repeats are essentially A-form. An analysis of all noncanonical U-U pairs in the context of CUG repeats revealed six different classes of conformations that the noncanonical U-U pairs are able to adopt.
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Affiliation(s)
- Leslie A Coonrod
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA
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