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Wan L, Zhang C, Liu Y, Zhang J, He L, Zhang Y, Chen G, Guo P, Han D. Small CAG Repeat RNA Forms a Duplex Structure with Sticky Ends That Promote RNA Condensation. J Am Chem Soc 2025; 147:3813-3822. [PMID: 39807887 DOI: 10.1021/jacs.4c16886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
Abstract
Biomolecular condensation lays the foundation of forming biologically important membraneless organelles, but abnormal condensation processes are often associated with human diseases. Ribonucleic acid (RNA) plays a critical role in the formation of biomolecular condensates by mediating the phase transition through its interactions with proteins and other RNAs. However, the physicochemical principles governing RNA phase transitions, especially for short RNAs, remain inadequately understood. Here, we report that small CAG repeat (sCAG) RNAs composed of six to seven CAG repeats, which are pathogenic factors in Huntington's disease, undergo phase transition in vitro and in cells. Leveraging solution nuclear magnetic resonance spectroscopy and advanced coarse-grained molecular dynamic simulations, we reveal that sCAG RNAs form duplex structures with 3'-sticky ends, where the GC stickers initiate intermolecular crosslinking and promote the formation of RNA condensates. Furthermore, we demonstrate that sCAG RNAs can form cellular condensates within nuclear speckles. Our work suggests that the RNA phase transition can be promoted by specific structural motifs, reducing the reliance on sequence length and multivalence. This opens avenues for exploring new functions of RNA in biomolecular condensates and designing novel biomaterials based on RNA condensation.
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Affiliation(s)
- Liqi Wan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | | | - Yu Liu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jiacheng Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Lei He
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yuchao Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | | | - Pei Guo
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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2
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Yildirim I, Andralojc W, Taghavi A, Baranowski D, Gdaniec Z, Kierzek R, Kierzek E. Experimental and computational investigations of RNA duplexes containing N7-regioisomers of adenosine and LNA-adenosine. Nucleic Acids Res 2025; 53:gkae1222. [PMID: 39711475 PMCID: PMC11724317 DOI: 10.1093/nar/gkae1222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/22/2024] [Accepted: 11/27/2024] [Indexed: 12/24/2024] Open
Abstract
Although glycosidic bonds in purines typically involve the N9 position, the chemical synthesis of adenosine produces N7-ribofuranosyladenine (7A) as a kinetically favorable ribosylation product. Similarly, in the synthesis of LNA-adenosine (AL), a minor product, N7-LNA-adenosine (7AL), is observed. While extensive research has focused on investigating the properties of N9-regioisomers of adenosine, 7A has been largely overlooked and considered as a side-product. In this study, we conducted comprehensive experimental and computational investigations to elucidate the structural and thermodynamic properties of 7A and 7AL. Our results reveal that 7A and 7AL primarily enhance the thermodynamic stability of 1 × 1 mismatches when paired with purines but decrease stability when paired with pyrimidines. Utilizing nuclear magnetic resonance and computational techniques, we discovered that 1 × 1 7A:A and 7AL:A prefer anti-anti conformations, while 1 × 1 7A:G and 7AL:G prefer syn-anti orientations, both forming two hydrogen bond states, resulting in enhanced duplex stabilities. Altogether, these findings underscore the unique properties of 7A and 7AL when incorporated in RNA, which could advance structure-based RNA studies and potentially be utilized to modulate binding affinity, selectivity and biostability of RNA molecules.
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Affiliation(s)
- Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Witold Andralojc
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Amirhossein Taghavi
- Department of Chemistry and Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Daniel Baranowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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3
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Singh S, Singh S, Joshi D, Mohanty C, Singh R. In Silico Prediction of Potential Inhibitors for Targeting RNA CAG Repeats via Molecular Docking and Dynamics Simulation: A Drug Discovery Approach. J Cell Biochem 2024; 125:e30611. [PMID: 38884365 DOI: 10.1002/jcb.30611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/03/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Abstract
Spinocerebellar ataxia (SCA) is a rare neurological illness inherited dominantly that causes severe impairment and premature mortality. While each rare disease may affect individuals infrequently, collectively they pose a significant healthcare challenge. It is mainly carried out due to the expansion of RNA triplet (CAG) repeats, although missense or point mutations can also be induced. Unfortunately, there is no cure; only symptomatic treatments are available. To date, SCA has about 48 subtypes, the most common of these being SCA 1, 2, 3, 6, 7, 12, and 17 having CAG repeats. Using molecular docking and molecular dynamics (MD) simulation, this study seeks to investigate effective natural herbal neuroprotective compounds against CAG repeats, which are therapeutically significant in treating SCA. Initially, virtual screening followed by molecular docking was used to estimate the binding affinity of neuroprotective natural compounds toward CAG repeats. The compound with the highest binding affinity, somniferine, was then chosen for MD simulation. The structural stability, interaction mechanism, and conformational dynamics of CAG repeats and somniferine were investigated via MD simulation. The MD study revealed that during the simulation period, the interaction between CAG repeats and somniferine stabilizes and results in fewer conformational variations. This in silico study suggests that Somniferine can be used as a therapeutic medication against RNA CAG repeats in SCA.
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Affiliation(s)
- Surbhi Singh
- Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Suchitra Singh
- Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Chhandamayee Mohanty
- Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Royana Singh
- Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Gallardo A, Dutagaci B. Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability. J Comput Aided Mol Des 2023; 38:1. [PMID: 37987925 PMCID: PMC10663202 DOI: 10.1007/s10822-023-00543-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functions in promoter-proximal pausing and elongation processivity. Spt5 was also recognized for its roles in the transcription of expanded-repeat genes that are related to neurodegenerative diseases. Recently, a set of Spt5-Pol II small molecule inhibitors (SPIs) were reported, which selectively inhibit mutant huntingtin gene transcription. Inhibition mechanisms as well as interaction sites of these SPIs with Pol II and Spt5 are not entirely known. In this study, we predicted the binding sites of three selected SPIs at the Pol II-Spt5 interface by docking and molecular dynamics simulations. Two molecules out of three demonstrated strong binding with Spt5 and Pol II, while the other molecule was more loosely bound and sampled multiple binding sites. Strongly bound SPIs indirectly affected RNA and DNA dynamics at the exit site as DNA became more flexible while RNA was stabilized by increased interactions with Spt5. Our results suggest that the transcription inhibition mechanism induced by SPIs can be related to Spt5-nucleic acid interactions, which were altered to some extent with strong binding of SPIs.
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Affiliation(s)
- Adan Gallardo
- Department of Molecular and Cell Biology, University of California Merced, 5200 North Lake Rd, Merced, CA, 95343, USA
| | - Bercem Dutagaci
- Department of Molecular and Cell Biology, University of California Merced, 5200 North Lake Rd, Merced, CA, 95343, USA.
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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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He W, Naleem N, Kleiman D, Kirmizialtin S. Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA. J Phys Chem Lett 2022; 13:3400-3408. [PMID: 35404614 PMCID: PMC9036580 DOI: 10.1021/acs.jpclett.2c00359] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The growing recognition of the functional and therapeutic roles played by RNA and the difficulties in gaining atomic-level insights by experiments are paving the way for all-atom simulations of RNA. One of the main impediments to the use of all-atom simulations is the imbalance between the energy terms of the RNA force fields. Through exhaustive sampling of an RNA helix-junction-helix (HJH) model using enhanced sampling, we critically assessed the select Amber force fields against small-angle X-ray scattering (SAXS) experiments. The tested AMBER99SB, DES-AMBER, and CUFIX force fields show deviations from measured profiles. First, we identified parameters leading to inconsistencies. Then, as a way to balance the forces governing RNA folding, we adopted strategies to refine hydrogen bonding, backbone, and base-stacking parameters. We validated the modified force field (HB-CUFIX) against SAXS data of the HJH model in different ionic strengths. Moreover, we tested a set of independent RNA systems to cross-validate the force field. Overall, HB-CUFIX demonstrates improved performance in studying thermodynamics and structural properties of realistic RNA motifs.
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Affiliation(s)
- Weiwei He
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003United States
| | - Nawavi Naleem
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Diego Kleiman
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry
Program, Science Division, New York University, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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7
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Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome. Mol Neurobiol 2022; 59:1992-2007. [PMID: 35040038 DOI: 10.1007/s12035-021-02697-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
Expansion of CGG trinucleotide repeats in 5' untranslated region of the FMR1 gene is the causative mutation of neurological diseases such as fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and ovarian disorder such as fragile X-associated primary ovarian insufficiency (FXPOI). CGG repeats containing FMR1 transcripts form the toxic ribonuclear aggregates, abrupt pre-mRNA splicing, and cause repeat-associated non-AUG translation, leading to the disease symptoms. Here, we utilized a small molecule library of ~ 250,000 members obtained from the National Cancer Institute (NCI) and implemented a shape-based screening approach to identify the candidate small molecules that mitigate toxic CGG RNA-mediated pathogenesis. The compounds obtained from screening were further assessed for their affinity and selectivity towards toxic CGG repeat RNA by employing fluorescence-binding experiment and isothermal calorimetry titration assay. Three candidate molecules B1, B4, and B11 showed high affinity and selectivity for expanded CGG repeats RNA. Further, NMR spectroscopy, gel mobility shift assay, CD spectroscopy, UV-thermal denaturation assay, and molecular docking affirmed their high affinity and selectivity for toxic CGG RNAs. Next, these lead compounds selectively improved the pre-mRNA alternative splicing defects with no perturbation in global splicing efficacy and simultaneously reduced the FMR1polyG protein aggregate formation without affecting the downstream expression of the gene. Taken together these findings, we addressed compound B1, B4, and B11 as potential lead molecules for developing promising therapeutics against FXTAS. Herein, this study, we have utilized shape similarity approach to screen the NCI library and found out the potential candidate which improves the pre-mRNA splicing defects and reduces FMR1polyG aggregations.
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Li PP, Moulick R, Feng H, Sun X, Arbez N, Jin J, Marque LO, Hedglen E, Chan HE, Ross CA, Pulst SM, Margolis RL, Woodson S, Rudnicki DD. RNA Toxicity and Perturbation of rRNA Processing in Spinocerebellar Ataxia Type 2. Mov Disord 2021; 36:2519-2529. [PMID: 34390268 PMCID: PMC8884117 DOI: 10.1002/mds.28729] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/03/2021] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disease caused by expansion of a CAG repeat in Ataxin-2 (ATXN2) gene. The mutant ATXN2 protein with a polyglutamine tract is known to be toxic and contributes to the SCA2 pathogenesis. OBJECTIVE Here, we tested the hypothesis that the mutant ATXN2 transcript with an expanded CAG repeat (expATXN2) is also toxic and contributes to SCA2 pathogenesis. METHODS The toxic effect of expATXN2 transcripts on SK-N-MC neuroblastoma cells and primary mouse cortical neurons was evaluated by caspase 3/7 activity and nuclear condensation assay, respectively. RNA immunoprecipitation assay was performed to identify RNA binding proteins (RBPs) that bind to expATXN2 RNA. Quantitative PCR was used to examine if ribosomal RNA (rRNA) processing is disrupted in SCA2 and Huntington's disease (HD) human brain tissue. RESULTS expATXN2 RNA induces neuronal cell death, and aberrantly interacts with RBPs involved in RNA metabolism. One of the RBPs, transducin β-like protein 3 (TBL3), involved in rRNA processing, binds to both expATXN2 and expanded huntingtin (expHTT) RNA in vitro. rRNA processing is disrupted in both SCA2 and HD human brain tissue. CONCLUSION These findings provide the first evidence of a contributory role of expATXN2 transcripts in SCA2 pathogenesis, and further support the role of expHTT transcripts in HD pathogenesis. The disruption of rRNA processing, mediated by aberrant interaction of RBPs with expATXN2 and expHTT transcripts, suggest a point of convergence in the pathogeneses of repeat expansion diseases with potential therapeutic implications. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Pan P. Li
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Roumita Moulick
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Hongxuan Feng
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Xin Sun
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Nicolas Arbez
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jing Jin
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Leonard O. Marque
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Erin Hedglen
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - H.Y. Edwin Chan
- Biochemistry Program, School of Life SciencesThe Chinese University of Hong KongHong KongChina
| | - Christopher A. Ross
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Stefan M. Pulst
- Department of NeurologyUniversity of UtahSalt Lake CityUtahUSA
| | - Russell L. Margolis
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Sarah Woodson
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Dobrila D. Rudnicki
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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Zhang J, Fakharzadeh A, Pan F, Roland C, Sagui C. Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids. Nucleic Acids Res 2020; 48:9899-9917. [PMID: 32821947 PMCID: PMC7515735 DOI: 10.1093/nar/gkaa665] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 11/13/2022] Open
Abstract
Expansion of the GAA/TTC repeats in the first intron of the FXN gene causes Friedreich's ataxia. Non-canonical structures are linked to this expansion. DNA triplexes and R-loops are believed to arrest transcription, which results in frataxin deficiency and eventual neurodegeneration. We present a systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands; the two hybrid duplexes [r(GAA):d(TTC) and d(GAA):r(UUC)] in an R-loop; and three hybrid triplexes that could form during bidirectional transcription when the non-template DNA strand bonds with the hybrid duplex (collapsed R-loops, where the two DNA strands remain antiparallel). For both Y·R:Y and R·R:Y DNA triplexes, the parallel third strand orientation is more stable; both parallel and antiparallel protonated d(GA+A)·d(GAA):d(TTC) triplexes are stable. Apparent contradictions in the literature about the R·R:Y triplex stability is probably due to lack of molecular resolution, since shifting the third strand by a single nucleotide alters the stability ranking. In the collapsed R-loops, antiparallel d(TTC+)·d(GAA):r(UUC) is unstable, while parallel d(GAA)·r(GAA):d(TTC) and d(GA+A)·r(GAA):d(TTC) are stable. In addition to providing new structural perspectives for specific therapeutic aims, our results contribute to a systematic structural basis for the emerging field of quantitative R-loop biology.
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Affiliation(s)
- Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Ashkan Fakharzadeh
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA.,Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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Palomino‐Hernandez O, Margreiter MA, Rossetti G. Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies. Isr J Chem 2020. [DOI: 10.1002/ijch.202000021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Oscar Palomino‐Hernandez
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
- Computation-based Science and Technology Research CenterThe Cyprus Institute Nicosia 2121 Cyprus
- Institute of Life ScienceThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Michael A. Margreiter
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Jülich Supercomputing Centre (JSC)Forschungszentrum Jülich 52425 Jülich Germany
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation University Hospital AachenRWTH Aachen University Pauwelsstraße 30 52074 Aachen Germany
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11
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Xu P, Pan F, Roland C, Sagui C, Weninger K. Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts. Nucleic Acids Res 2020; 48:2232-2245. [PMID: 31974547 PMCID: PMC7049705 DOI: 10.1093/nar/gkaa036] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/11/2019] [Accepted: 01/15/2020] [Indexed: 01/08/2023] Open
Abstract
DNA trinucleotide repeats (TRs) can exhibit dynamic expansions by integer numbers of trinucleotides that lead to neurodegenerative disorders. Strand slipped hairpins during DNA replication, repair and/or recombination may contribute to TR expansion. Here, we combine single-molecule FRET experiments and molecular dynamics studies to elucidate slipping dynamics and conformations of (CAG)n TR hairpins. We directly resolve slipping by predominantly two CAG units. The slipping kinetics depends on the even/odd repeat parity. The populated states suggest greater stability for 5′-AGCA-3′ tetraloops, compared with alternative 5′-CAG-3′ triloops. To accommodate the tetraloop, even(odd)-numbered repeats have an even(odd) number of hanging bases in the hairpin stem. In particular, a paired-end tetraloop (no hanging TR) is stable in (CAG)n = even, but such situation cannot occur in (CAG)n = odd, where the hairpin is “frustrated’’ and slips back and forth between states with one TR hanging at the 5′ or 3′ end. Trinucleotide interrupts in the repeating CAG pattern associated with altered disease phenotypes select for specific conformers with favorable loop sequences. Molecular dynamics provide atomic-level insight into the loop configurations. Reducing strand slipping in TR hairpins by sequence interruptions at the loop suggests disease-associated variations impact expansion mechanisms at the level of slipped hairpins.
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Affiliation(s)
- Pengning Xu
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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12
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Perrone B, La Cognata V, Sprovieri T, Ungaro C, Conforti FL, Andò S, Cavallaro S. Alternative Splicing of ALS Genes: Misregulation and Potential Therapies. Cell Mol Neurobiol 2020; 40:1-14. [PMID: 31385134 PMCID: PMC11448865 DOI: 10.1007/s10571-019-00717-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Parkinson's, Alzheimer's, and Huntington's disease affect a rapidly increasing population worldwide. Although common pathogenic mechanisms have been identified (e.g., protein aggregation or dysfunction, immune response alteration and axonal degeneration), the molecular events underlying timing, dosage, expression, and location of RNA molecules are still not fully elucidated. In particular, the alternative splicing (AS) mechanism is a crucial player in RNA processing and represents a fundamental determinant for brain development, as well as for the physiological functions of neuronal circuits. Although in recent years our knowledge of AS events has increased substantially, deciphering the molecular interconnections between splicing and ALS remains a complex task and still requires considerable efforts. In the present review, we will summarize the current scientific evidence outlining the involvement of AS in the pathogenic processes of ALS. We will also focus on recent insights concerning the tuning of splicing mechanisms by epigenomic and epi-transcriptomic regulation, providing an overview of the available genomic technologies to investigate AS drivers on a genome-wide scale, even at a single-cell level resolution. In the future, gene therapy strategies and RNA-based technologies may be utilized to intercept or modulate the splicing mechanism and produce beneficial effects against ALS.
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Affiliation(s)
- Benedetta Perrone
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Catania, Italy
| | - Teresa Sprovieri
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Carmine Ungaro
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Francesca Luisa Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
- Centro Sanitario, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Catania, Italy.
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13
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Bogomazova AN, Eremeev AV, Pozmogova GE, Lagarkova MA. The Role of Mutant RNA in the Pathogenesis of Huntington’s Disease and Other Polyglutamine Diseases. Mol Biol 2019. [DOI: 10.1134/s0026893319060037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Discovery of a potent small molecule inhibiting Huntington's disease (HD) pathogenesis via targeting CAG repeats RNA and Poly Q protein. Sci Rep 2019; 9:16872. [PMID: 31728006 PMCID: PMC6856162 DOI: 10.1038/s41598-019-53410-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
CAG repeats RNA causes various fatal neurodegenerative diseases exemplified by Huntington's disease (HD) and several spinocerebellar ataxias (SCAs). Although there are differences in the pathogenic mechanisms, these diseases share the common cause, i.e., expansion of CAG repeats. The shared cause of these diseases raises the possibility for the exploiting the common target as a potential therapeutic approach. Oligonucleotide-based therapeutics are designed earlier with the help of the base pairing rule but are not very promiscuous, considering the nonspecific stimulation of the immune system and the poor cellular delivery. Therefore, small molecules-based therapeutics are preferred for targeting the repeats expansion disorders. Here, we have used the chemical similarity search approach to discern the small molecules that selectively target toxic CAG RNA. The lead compounds showed the specificity towards AA mismatch in biophysical studies including CD, ITC, and NMR spectroscopy and thus aided to forestall the polyQ mediated pathogenicity. Furthermore, the lead compounds also explicitly alleviate the polyQ mediated toxicity in HD cell models and patient-derived cells. These findings suggest that the lead compound could act as a chemical probe for AA mismatch containing RNA as well as plays a neuroprotective role in fatal neurodegenerative diseases like HD and SCAs.
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15
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Verma AK, Khan E, Bhagwat SR, Kumar A. Exploring the Potential of Small Molecule-Based Therapeutic Approaches for Targeting Trinucleotide Repeat Disorders. Mol Neurobiol 2019; 57:566-584. [DOI: 10.1007/s12035-019-01724-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/29/2019] [Indexed: 12/18/2022]
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16
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Khan E, Biswas S, Mishra SK, Mishra R, Samanta S, Mishra A, Tawani A, Kumar A. Rationally designed small molecules targeting toxic CAG repeat RNA that causes Huntington's disease (HD) and spinocerebellar ataxia (SCAs). Biochimie 2019; 163:21-32. [DOI: 10.1016/j.biochi.2019.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/01/2019] [Indexed: 12/29/2022]
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17
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Rangadurai A, Zhou H, Merriman DK, Meiser N, Liu B, Shi H, Szymanski ES, Al-Hashimi HM. Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? Nucleic Acids Res 2019; 46:11099-11114. [PMID: 30285154 PMCID: PMC6237737 DOI: 10.1093/nar/gky885] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022] Open
Abstract
A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson–Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical melting experiments, molecular dynamics simulations and modified nucleotides to identify factors that contribute to this destabilization of HG bps in A-RNA. Removing the 2′-hydroxyl at single purine nucleotides in A-RNA duplexes did not stabilize HG bps relative to WC. In contrast, loosening the A-form geometry using a bulge in A-RNA reduced the energy cost of forming HG bps at the flanking sites to B-DNA levels. A structural and thermodynamic analysis of purine-purine HG mismatches reveals that compared to B-DNA, the A-form geometry disfavors syn purines by 1.5–4 kcal/mol due to sugar-backbone rearrangements needed to sterically accommodate the syn base. Based on MD simulations, an additional penalty of 3–4 kcal/mol applies for purine-pyrimidine HG bps due to the higher energetic cost associated with moving the bases to form hydrogen bonds in A-RNA versus B-DNA. These results provide insights into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | | | - Nathalie Meiser
- Goethe University, Institute for Organic Chemistry and Chemical Biology, Frankfurt am Main, Germany
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.,Department of Chemistry, Duke University, Durham, NC, USA
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18
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Thadke SA, Perera JDR, Hridya VM, Bhatt K, Shaikh AY, Hsieh WC, Chen M, Gayathri C, Gil RR, Rule GS, Mukherjee A, Thornton CA, Ly DH. Design of Bivalent Nucleic Acid Ligands for Recognition of RNA-Repeated Expansion Associated with Huntington's Disease. Biochemistry 2018; 57:2094-2108. [PMID: 29562132 PMCID: PMC6091552 DOI: 10.1021/acs.biochem.8b00062] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report the development of a new class of nucleic acid ligands that is comprised of Janus bases and the MPγPNA backbone and is capable of binding rCAG repeats in a sequence-specific and selective manner via, inference, bivalent H-bonding interactions. Individually, the interactions between ligands and RNA are weak and transient. However, upon the installation of a C-terminal thioester and an N-terminal cystine and the reduction of disulfide bond, they undergo template-directed native chemical ligation to form concatenated oligomeric products that bind tightly to the RNA template. In the absence of an RNA target, they self-deactivate by undergoing an intramolecular reaction to form cyclic products, rendering them inactive for further binding. The work has implications for the design of ultrashort nucleic acid ligands for targeting rCAG-repeat expansion associated with Huntington's disease and a number of other related neuromuscular and neurodegenerative disorders.
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Affiliation(s)
- Shivaji A. Thadke
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - J. Dinithi R. Perera
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - V. M. Hridya
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India
| | - Kirti Bhatt
- Department of Neurology, Box 645, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Ashif Y. Shaikh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Che Hsieh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Mengshen Chen
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Chakicherla Gayathri
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Roberto R. Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S. Rule
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India
| | - Charles A. Thornton
- Department of Neurology, Box 645, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Danith H. Ly
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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19
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Khan E, Tawani A, Mishra SK, Verma AK, Upadhyay A, Kumar M, Sandhir R, Mishra A, Kumar A. Myricetin Reduces Toxic Level of CAG Repeats RNA in Huntington's Disease (HD) and Spino Cerebellar Ataxia (SCAs). ACS Chem Biol 2018; 13:180-188. [PMID: 29172480 DOI: 10.1021/acschembio.7b00699] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder that is caused by abnormal expansion of CAG repeats in the HTT gene. The transcribed mutant RNA contains expanded CAG repeats that translate into a mutant huntingtin protein. This expanded CAG repeat also causes mis-splicing of pre-mRNA due to sequestration of muscle blind like-1 splicing factor (MBNL1), and thus both of these elicit the pathogenesis of HD. Targeting the onset as well as progression of HD by small molecules could be a potent therapeutic approach. We have screened a set of small molecules to target this transcript and found Myricetin, a flavonoid, as a lead molecule that interacts with the CAG motif and thus prevents the translation of mutant huntingtin protein as well as sequestration of MBNL1. Here, we report the first solution structure of the complex formed between Myricetin and RNA containing the 5'CAG/3'GAC motif. Myricetin interacts with this RNA via base stacking at the AA mismatch. Moreover, Myricetin was also found reducing the proteo-toxicity generated due to the aggregation of polyglutamine, and further, its supplementation also improves neurobehavioral deficits in the HD mouse model. Our study provides the structural and mechanistic basis of Myricetin as an effective therapeutic candidate for HD and other polyQ related disorders.
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Affiliation(s)
- Eshan Khan
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Arpita Tawani
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Subodh Kumar Mishra
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Arun Kumar Verma
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Arun Upadhyay
- Cellular
and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan 342011, India
| | - Mohit Kumar
- Department
of Biochemistry, Panjab University, Chandigarh 160014, India
| | - Rajat Sandhir
- Department
of Biochemistry, Panjab University, Chandigarh 160014, India
| | - Amit Mishra
- Cellular
and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan 342011, India
| | - Amit Kumar
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
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20
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A brain-targeting lipidated peptide for neutralizing RNA-mediated toxicity in Polyglutamine Diseases. Sci Rep 2017; 7:12077. [PMID: 28935901 PMCID: PMC5608758 DOI: 10.1038/s41598-017-11695-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/29/2017] [Indexed: 01/11/2023] Open
Abstract
Polyglutamine (PolyQ) diseases are progressive neurodegenerative disorders caused by both protein- and RNA-mediated toxicities. We previously showed that a peptidyl inhibitor, P3, which binds directly to expanded CAG RNA can inhibit RNA-induced nucleolar stress and suppress RNA-induced neurotoxicity. Here we report a N-acetylated and C-amidated derivative of P3, P3V8, that showed a more than 20-fold increase in its affinity for expanded CAG RNA. The P3V8 peptide also more potently alleviated expanded RNA-induced cytotoxicity in vitro, and suppressed polyQ neurodegeneration in Drosophila with no observed toxic effects. Further N-palmitoylation of P3V8 (L1P3V8) not only significantly improved its cellular uptake and stability, but also facilitated its systemic exposure and brain uptake in rats via intranasal administration. Our findings demonstrate that concomitant N-acetylation, C-amidation and palmitoylation of P3 significantly improve both its bioactivity and pharmacological profile. L1P3V8 possesses drug/lead-like properties that can be further developed into a lead inhibitor for the treatment of polyQ diseases.
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21
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Pan F, Man VH, Roland C, Sagui C. Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats. Biophys J 2017; 113:19-36. [PMID: 28700917 DOI: 10.1016/j.bpj.2017.05.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/19/2017] [Accepted: 05/26/2017] [Indexed: 12/13/2022] Open
Abstract
CAG trinucleotide repeats are known to cause 10 late-onset progressive neurodegenerative disorders as the repeats expand beyond a threshold, whereas GAC repeats are associated with skeletal dysplasias and expand from the normal five to a maximum of seven repeats. The TR secondary structure is believed to play a role in CAG expansions. We have carried out free energy and molecular dynamics studies to determine the preferred conformations of the A-A noncanonical pairs in (CAG)n and (GAC)n trinucleotide repeats (n = 1, 4) and the consequent changes in the overall structure of the RNA and DNA duplexes. We find that the global free energy minimum corresponds to A-A pairs stacked inside the core of the helix with anti-anti conformations in RNA and (high-anti)-(high-anti) conformations in DNA. The next minimum corresponds to anti-syn conformations, whereas syn-syn conformations are higher in energy. Transition rates of the A-A conformations are higher for RNA than DNA. Mechanisms for these various transitions are identified. Additional structural and dynamical aspects of the helical conformations are explored, with a focus on contrasting CAG and GAC duplexes. The neutralizing ion distribution around the noncanonical pairs is described.
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Affiliation(s)
- Feng Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Viet Hoang Man
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, North Carolina.
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22
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Guo P, Chan HYE, Lam SL. Conformational flexibility in the RNA stem-loop structures formed by CAG repeats. FEBS Lett 2017; 591:1752-1760. [PMID: 28488797 DOI: 10.1002/1873-3468.12672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/28/2017] [Accepted: 05/05/2017] [Indexed: 11/11/2022]
Abstract
The expansion of CAG repeats has been found to be associated with at least nine human genetic disorders. In these disorders, the full-length expanded CAG RNA transcripts are cleaved into small CAG-repeated RNAs which are cytotoxic and known to be capable of forming hairpins. To better understand the RNA pathogenic mechanism, in this study we have performed high-resolution nuclear magnetic resonance structural investigations on the RNA hairpins formed by CAG repeats. Our results show the formation of a type III AGCA tetraloop and reveal the effect of stem rigidity on the loop conformational flexibility.
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Affiliation(s)
- Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ho Yin Edwin Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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23
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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: 54] [Impact Index Per Article: 6.8] [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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24
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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: 2.8] [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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