1
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Fakharzadeh A, Qu J, Pan F, Sagui C, Roland C. Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA-RNA Hybrids. J Phys Chem B 2023; 127:7907-7924. [PMID: 37681731 PMCID: PMC10519205 DOI: 10.1021/acs.jpcb.3c03538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/11/2023] [Indexed: 09/09/2023]
Abstract
Myotonic dystrophy type 1 is the most frequent form of muscular dystrophy in adults caused by an abnormal expansion of the CTG trinucleotide. Both the expanded DNA and the expanded CUG RNA transcript can fold into hairpins. Co-transcriptional formation of stable RNA·DNA hybrids can also enhance the instability of repeat tracts. We performed molecular dynamics simulations of homoduplexes associated with the disease, d(CTG)n and r(CUG)n, and their corresponding r(CAG)n:d(CTG)n and r(CUG)n:d(CAG)n hybrids that can form under bidirectional transcription and of non-pathological d(GTC)n and d(GUC)n homoduplexes. We characterized their conformations, stability, and dynamics and found that the U·U and T·T mismatches are dynamic, favoring anti-anti conformations inside the helical core, followed by anti-syn and syn-syn conformations. For DNA, the secondary minima in the non-expanding d(GTC)n helices are deeper, wider, and longer-lived than those in d(CTG)n, which constitutes another biophysical factor further differentiating the expanding and non-expanding sequences. The hybrid helices are closer to A-RNA, with the A-T and A-U pairs forming two stable Watson-Crick hydrogen bonds. The neutralizing ion distribution around the non-canonical pairs is also described.
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Affiliation(s)
- Ashkan Fakharzadeh
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Jing Qu
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Feng Pan
- Department
of Statistics, Florida State University, Tallahassee, Florida 32306, USA
| | - Celeste Sagui
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Christopher Roland
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
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2
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Gibaut QR, Bush JA, Tong Y, Baisden JT, Taghavi A, Olafson H, Yao X, Childs-Disney JL, Wang ET, Disney MD. Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG) exp Degrader in Myotonic Dystrophy. ACS CENTRAL SCIENCE 2023; 9:1342-1353. [PMID: 37521782 PMCID: PMC10375898 DOI: 10.1021/acscentsci.2c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 08/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a highly structured RNA repeat expansion, r(CUG)exp, harbored in the 3' untranslated region (3' UTR) of dystrophia myotonica protein kinase (DMPK) mRNA and drives disease through a gain-of-function mechanism. A panel of low-molecular-weight fragments capable of reacting with RNA upon UV irradiation was studied for cross-linking to r(CUG)expin vitro, affording perimidin-2-amine diazirine (1) that bound to r(CUG)exp. The interactions between the small molecule and RNA were further studied by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Binding of 1 in DM1 myotubes was profiled transcriptome-wide, identifying 12 transcripts including DMPK that were bound by 1. Augmenting the functionality of 1 with cleaving capability created a chimeric degrader that specifically targets r(CUG)exp for elimination. The degrader broadly improved DM1-associated defects as assessed by RNA-seq, while having limited effects on healthy myotubes. This study (i) provides a platform to investigate molecular recognition of ligands directly in disease-affected cells; (ii) illustrates that RNA degraders can be more specific than the binders from which they are derived; and (iii) suggests that repeating transcripts can be selectively degraded due to the presence of multiple ligand binding sites.
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Affiliation(s)
- Quentin
M. R. Gibaut
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hailey Olafson
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Xiyuan Yao
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Eric T. Wang
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Matthew D. Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
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3
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Wang SC, Chen YT, Satange R, Chu JW, Hou MH. Structural basis for water modulating RNA duplex formation in the CUG repeats of myotonic dystrophy type 1. J Biol Chem 2023:104864. [PMID: 37245780 PMCID: PMC10316006 DOI: 10.1016/j.jbc.2023.104864] [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: 03/31/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/30/2023] Open
Abstract
Secondary structures formed by expanded CUG RNA are involved in the pathobiology of myotonic dystrophy type 1. Understanding the molecular basis of toxic RNA structures can provide insights into the mechanism of disease pathogenesis and accelerate the drug discovery process. Here, we report the crystal structure of CUG repeat RNA containing three U-U mismatches between C-G and G-C base pairs. The CUG RNA crystallizes as an A-form duplex, with the first and third U-U mismatches adopting a water-mediated asymmetric mirror isoform geometry. We found for the first time that a symmetric, water-bridged U-H2O-U mismatch is well tolerated within the CUG RNA duplex, which was previously suspected but not observed. The new water-bridged U-U mismatch resulted in high base-pair opening and single-sided cross-strand stacking interactions, which in turn dominate the CUG RNA structure. Furthermore, we performed molecular dynamics (MD) simulations that complemented the structural findings and proposed that the first and third U-U mismatches are interchangeable conformations, while the central water-bridged U-U mismatch represents an intermediate state that modulates the RNA duplex conformation. Collectively, the new structural features provided in this work are important for understanding the recognition of U-U mismatches in CUG repeats by external ligands such as proteins or small molecules.
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Affiliation(s)
- Shun-Ching Wang
- 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
| | - Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068 Taiwan
| | - Roshan Satange
- Institute of Genomics and Bioinformatics; National Chung Hsing University, Taichung 402, Taiwan
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068 Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30068 Taiwan; Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 30068 Taiwan.
| | - 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; Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
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4
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An Y, Chen ZS, Chan H, Ngo J. Molecular insights into the interaction of CAG trinucleotide RNA repeats with nucleolin and its implication in polyglutamine diseases. Nucleic Acids Res 2022; 50:7655-7668. [PMID: 35776134 PMCID: PMC9303306 DOI: 10.1093/nar/gkac532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/08/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Polyglutamine (polyQ) diseases are a type of inherited neurodegenerative disorders caused by cytosine-adenine-guanine (CAG) trinucleotide expansion within the coding region of the disease-associated genes. We previously demonstrated that a pathogenic interaction between expanded CAG RNA and the nucleolin (NCL) protein triggers the nucleolar stress and neuronal cell death in polyQ diseases. However, mechanisms behind the molecular interaction remain unknown. Here, we report a 1.45 Å crystal structure of the r(CAG)5 oligo that comprises a full A'-form helical turn with widened grooves. Based on this structure, we simulated a model of r(CAG)5 RNA complexed with the RNA recognition motif 2 (RRM2) of NCL and identified NCL residues that are critical for its binding to CAG RNA. Combined with in vitro and in vivo site-directed mutagenesis studies, our model reveals that CAG RNA binds to NCL sites that are not important for other cellular functions like gene expression and rRNA synthesis regulation, indicating that toxic CAG RNA interferes with NCL functions by sequestering it. Accordingly, an NCL mutant that is aberrant in CAG RNA-binding could rescue RNA-induced cytotoxicity effectively. Taken together, our study provides new molecular insights into the pathogenic mechanism of polyQ diseases mediated by NCL-CAG RNA interaction.
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Affiliation(s)
- Ying An
- School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
| | - Zhefan S Chen
- School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
| | - Ho Yin Edwin Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
| | - Jacky Chi Ki Ngo
- School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
- Center for Novel Biomaterials, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
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5
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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6
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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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7
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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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8
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Hagler LD, Bonson SE, Kocheril PA, Zimmerman SC. Assessing the feasibility and stability of uracil base flipping in RNA–small molecule complexes using molecular dynamics simulations. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small molecules can be used to target RNAs that mediate disease. A fundamental understanding of binding interactions between RNA and small molecules and the structure of their complexes will further inform the design of new targeting agents. Two small molecule ligands were investigated for their ability to recognize the expanded CUG repeat sequence in RNA, the causative agent of myotonic dystrophy type 1. We report the use of molecular dynamics simulations to explore small molecule–RNA complexes and the finding of a stabilized base flipped conformation at UU mismatches. The results of this computational study support experimental observations and suggest that base flipping is feasible for CUG-repeat RNA.
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Affiliation(s)
- Lauren D. Hagler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sarah E. Bonson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Philip A. Kocheril
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steven C. Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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9
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Hale MA, Johnson NE, Berglund JA. Repeat-associated RNA structure and aberrant splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194405. [PMID: 31323433 DOI: 10.1016/j.bbagrm.2019.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Over 30 hereditary disorders attributed to the expansion of microsatellite repeats have been identified. Despite variant nucleotide content, number of consecutive repeats, and different locations in the genome, many of these diseases have pathogenic RNA gain-of-function mechanisms. The repeat-containing RNAs can form structures in vitro predicted to contribute to the disease through assembly of intracellular RNA aggregates termed foci. The expanded repeat RNAs within these foci sequester RNA binding proteins (RBPs) with important roles in the regulation of RNA metabolism, most notably alternative splicing (AS). These deleterious interactions lead to downstream alterations in transcriptome-wide AS directly linked with disease symptoms. This review summarizes existing knowledge about the association between the repeat RNA structures and RBPs as well as the resulting aberrant AS patterns, specifically in the context of myotonic dystrophy. The connection between toxic, structured RNAs and dysregulation of AS in other repeat expansion diseases is also discussed. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Melissa A Hale
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicholas E Johnson
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J Andrew Berglund
- The RNA Institute, Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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10
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Foss DV, Schirle NT, MacRae IJ, Pezacki JP. Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs. FEBS Open Bio 2019; 9:1042-1051. [PMID: 31021526 PMCID: PMC6551489 DOI: 10.1002/2211-5463.12644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/03/2019] [Accepted: 04/24/2019] [Indexed: 12/31/2022] Open
Abstract
Viral suppressors of RNA silencing (VSRSs) are a diverse group of viral proteins that have evolved to disrupt eukaryotic RNA silencing pathways, thereby contributing to viral pathogenicity. The p19 protein is a VSRS that selectively binds to short interfering RNAs (siRNAs) over microRNAs (miRNAs). Mutational analysis has identified single amino acid substitutions that reverse this selectivity through new high-affinity interactions with human miR-122. Herein, we report crystal structures of complexed p19-T111S (2.6 Å), p19-T111H (2.3 Å) and wild-type p19 protein (2.2 Å) from the Carnation Italian ringspot virus with small interfering RNA (siRNA) ligands. Structural comparisons reveal that these mutations do not lead to major changes in p19 architecture, but instead promote subtle rearrangement of residues and solvent molecules along the p19 midline. These observations suggest p19 uses many small interactions to distinguish siRNAs from miRNAs and perturbing these interactions can create p19 variants with novel RNA-recognition properties. DATABASE: Model data are deposited in the PDB database under the accession numbers 6BJG, 6BJH and 6BJV.
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Affiliation(s)
- Dana V Foss
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Canada
| | - Nicole T Schirle
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Canada
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11
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González ÀL, Konieczny P, Llamusi B, Delgado-Pinar E, Borrell JI, Teixidó J, García-España E, Pérez-Alonso M, Estrada-Tejedor R, Artero R. In silico discovery of substituted pyrido[2,3-d]pyrimidines and pentamidine-like compounds with biological activity in myotonic dystrophy models. PLoS One 2017; 12:e0178931. [PMID: 28582438 PMCID: PMC5459475 DOI: 10.1371/journal.pone.0178931] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/22/2017] [Indexed: 12/24/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a rare multisystemic disorder associated with an expansion of CUG repeats in mutant DMPK (dystrophia myotonica protein kinase) transcripts; the main effect of these expansions is the induction of pre-mRNA splicing defects by sequestering muscleblind-like family proteins (e.g. MBNL1). Disruption of the CUG repeats and the MBNL1 protein complex has been established as the best therapeutic approach for DM1, hence two main strategies have been proposed: targeted degradation of mutant DMPK transcripts and the development of CUG-binding molecules that prevent MBNL1 sequestration. Herein, suitable CUG-binding small molecules were selected using in silico approaches such as scaffold analysis, similarity searching, and druggability analysis. We used polarization assays to confirm the CUG repeat binding in vitro for a number of candidate compounds, and went on to evaluate the biological activity of the two with the strongest affinity for CUG repeats (which we refer to as compounds 1–2 and 2–5) in DM1 mutant cells and Drosophila DM1 models with an impaired locomotion phenotype. In particular, 1–2 and 2–5 enhanced the levels of free MBNL1 in patient-derived myoblasts in vitro and greatly improved DM1 fly locomotion in climbing assays. This work provides new computational approaches for rational large-scale virtual screens of molecules that selectively recognize CUG structures. Moreover, it contributes valuable knowledge regarding two compounds with desirable biological activity in DM1 models.
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Affiliation(s)
- Àlex L. González
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
| | - Piotr Konieczny
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
| | - Beatriz Llamusi
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
| | | | - José I. Borrell
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
| | - Jordi Teixidó
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
| | | | - Manuel Pérez-Alonso
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
| | - Roger Estrada-Tejedor
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
- * E-mail:
| | - Rubén Artero
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
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12
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Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ. Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. Front Cell Neurosci 2017; 11:97. [PMID: 28442996 PMCID: PMC5387085 DOI: 10.3389/fncel.2017.00097] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions. A growing body of recent evidence revealed that the RNA structures formed by these mutant RNA repeat tracts exhibit toxic effects on cells. Therefore, in this review article, we present existing knowledge on the structural aspects of different RNA repeat tracts as revealed mainly using well-established biochemical and biophysical methods. Furthermore, in several cases, it was shown that these expanded RNA structures are potent traps for a variety of RNA-binding proteins and that the sequestration of these proteins from their normal intracellular environment causes alternative splicing aberration, inhibition of nuclear transport and export, or alteration of a microRNA biogenesis pathway. Therefore, in this review article, we also present the most studied examples of abnormal interactions that occur between mutant RNAs and their associated proteins.
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Affiliation(s)
- Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Karolina Drazkowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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13
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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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14
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González ÀL, Teixidó J, Borrell JI, Estrada-Tejedor R. On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion. PLoS One 2016; 11:e0152049. [PMID: 27010216 PMCID: PMC4806922 DOI: 10.1371/journal.pone.0152049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 03/08/2016] [Indexed: 11/18/2022] Open
Abstract
Non-coding RNAs play a pivotal role in a number of diseases promoting an aberrant sequestration of nuclear RNA-binding proteins. In the particular case of myotonic dystrophy type 1 (DM1), a multisystemic autosomal dominant disease, the formation of large non-coding CUG repeats set up long-tract hairpins able to bind muscleblind-like proteins (MBNL), which trigger the deregulation of several splicing events such as cardiac troponin T (cTNT) and insulin receptor’s, among others. Evidence suggests that conformational changes in RNA are determinant for the recognition and binding of splicing proteins, molecular modeling simulations can attempt to shed light on the structural diversity of CUG repeats and to understand their pathogenic mechanisms. Molecular dynamics (MD) are widely used to obtain accurate results at atomistic level, despite being very time consuming, and they contrast with fast but simplified coarse-grained methods such as Elastic Network Model (ENM). In this paper, we assess the application of ENM (traditionally applied on proteins) for studying the conformational space of CUG repeats and compare it to conventional and accelerated MD conformational sampling. Overall, the results provided here reveal that ANM can provide useful insights into dynamic rCUG structures at a global level, and that their dynamics depend on both backbone and nucleobase fluctuations. On the other hand, ANM fail to describe local U-U dynamics of the rCUG system, which require more computationally expensive methods such as MD. Given that several limitations are inherent to both methods, we discuss here the usefulness of the current theoretical approaches for studying highly dynamic RNA systems such as CUG trinucleotide repeat overexpansions.
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Affiliation(s)
- Àlex L. González
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS) – Universitat Ramon Llull (URL), Barcelona, Catalonia, 08017, Spain
| | - Jordi Teixidó
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS) – Universitat Ramon Llull (URL), Barcelona, Catalonia, 08017, Spain
| | - José I. Borrell
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS) – Universitat Ramon Llull (URL), Barcelona, Catalonia, 08017, Spain
| | - Roger Estrada-Tejedor
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS) – Universitat Ramon Llull (URL), Barcelona, Catalonia, 08017, Spain
- * E-mail:
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15
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Yildirim I, Chakraborty D, Disney MD, Wales DJ, Schatz GC. Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1. J Chem Theory Comput 2015; 11:4943-58. [PMID: 26500461 PMCID: PMC4606397 DOI: 10.1021/acs.jctc.5b00728] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Indexed: 01/02/2023]
Abstract
Despite the importance of the knowledge of molecular hydration entropy (ΔShyd) in chemical and biological processes, the exact calculation of ΔShyd is very difficult, because of the complexity in solute–water interactions. Although free-energy perturbation (FEP) methods have been employed quite widely in the literature, the poor convergent behavior of the van der Waals interaction term in the potential function limited the accuracy and robustness. In this study, we propose a new method for estimating ΔShyd by means of combining the FEP approach and the scaled particle theory (or information theory) to separately calculate the electrostatic solute–water interaction term (ΔSelec) and the hydrophobic contribution approximated by the cavity formation entropy (ΔScav), respectively. Decomposition of ΔShyd into ΔScav and ΔSelec terms is found to be very effective with a substantial accuracy enhancement in ΔShyd estimation, when compared to the conventional full FEP calculations. ΔScav appears to dominate over ΔSelec in magnitude, even in the case of polar solutes, implying that the major contribution to the entropic cost for hydration comes from the formation of a solvent-excluded volume. Our hybrid scaled particle theory and FEP method is thus found to enhance the accuracy of ΔShyd prediction by effectively complementing the conventional full FEP method.
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Affiliation(s)
- Ilyas Yildirim
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Chemistry, University of Cambridge, Cambridge, United Kingdom CB2 1EW
| | - Debayan Chakraborty
- Department
of Chemistry, University of Cambridge, Cambridge, United Kingdom CB2 1EW
| | - Matthew D. Disney
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - David J. Wales
- Department
of Chemistry, University of Cambridge, Cambridge, United Kingdom CB2 1EW
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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16
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Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
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Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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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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18
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Wong CH, Nguyen L, Peh J, Luu LM, Sanchez J, Richardson SL, Tuccinardi T, Tsoi H, Chan WY, Chan HY, Baranger AM, Hergenrother PJ, Zimmerman SC. Targeting toxic RNAs that cause myotonic dystrophy type 1 (DM1) with a bisamidinium inhibitor. J Am Chem Soc 2014; 136:6355-61. [PMID: 24702247 PMCID: PMC4015652 DOI: 10.1021/ja5012146] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 01/28/2023]
Abstract
A working hypothesis for the pathogenesis of myotonic dystrophy type 1 (DM1) involves the aberrant sequestration of an alternative splicing regulator, MBNL1, by expanded CUG repeats, r(CUG)(exp). It has been suggested that a reversal of the myotonia and potentially other symptoms of the DM1 disease can be achieved by inhibiting the toxic MBNL1-r(CUG)(exp) interaction. Using rational design, we discovered an RNA-groove binding inhibitor (ligand 3) that contains two triaminotriazine units connected by a bisamidinium linker. Ligand 3 binds r(CUG)12 with a low micromolar affinity (K(d) = 8 ± 2 μM) and disrupts the MBNL1-r(CUG)12 interaction in vitro (K(i) = 8 ± 2 μM). In addition, ligand 3 is cell and nucleus permeable, exhibits negligible toxicity to mammalian cells, dissolves MBNL1-r(CUG)(exp) ribonuclear foci, and restores misregulated splicing of IR and cTNT in a DM1 cell culture model. Importantly, suppression of r(CUG)(exp) RNA-induced toxicity in a DM1 Drosophila model was observed after treatment with ligand 3. These results suggest ligand 3 as a lead for the treatment of DM1.
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Affiliation(s)
- Chun-Ho Wong
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Lien Nguyen
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Jessie Peh
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Long M. Luu
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Jeannette
S. Sanchez
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Stacie L. Richardson
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | | | - Ho Tsoi
- Laboratory of Drosophila
Research and School of Life Sciences and School of Biomedical
Sciences, The Chinese University of Hong
Kong, Shatin, N.T., Hong Kong SAR, The People's Republic
of China
| | - Wood Yee Chan
- Laboratory of Drosophila
Research and School of Life Sciences and School of Biomedical
Sciences, The Chinese University of Hong
Kong, Shatin, N.T., Hong Kong SAR, The People's Republic
of China
| | - H. Y.
Edwin Chan
- Laboratory of Drosophila
Research and School of Life Sciences and School of Biomedical
Sciences, The Chinese University of Hong
Kong, Shatin, N.T., Hong Kong SAR, The People's Republic
of China
| | - Anne M. Baranger
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Paul J. Hergenrother
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Steven C. Zimmerman
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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