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Błaszczyk L, Ryczek M, Das B, Mateja-Pluta M, Bejger M, Śliwiak J, Nakatani K, Kiliszek A. Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand. Nucleic Acids Res 2024; 52:6707-6717. [PMID: 38738637 PMCID: PMC11194091 DOI: 10.1093/nar/gkae376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
The abnormal expansion of GGGGCC/GGCCCC hexanucleotide repeats (HR) in C9orf72 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Structural polymorphisms of HR result in the multifactorial pathomechanism of ALS/FTD. Consequently, many ongoing studies are focused at developing therapies targeting pathogenic HR RNA. One of them involves small molecules blocking sequestration of important proteins, preventing formation of toxic nuclear foci. However, rational design of potential therapeutics is hindered by limited number of structural studies of RNA-ligand complexes. We determined the crystal structure of antisense HR RNA in complex with ANP77 ligand (1.1 Å resolution) and in the free form (0.92 and 1.5 Å resolution). HR RNA folds into a triplex structure composed of four RNA chains. ANP77 interacted with two neighboring single-stranded cytosines to form pseudo-canonical base pairs by adopting sandwich-like conformation and adjusting the position of its naphthyridine units to the helical twist of the RNA. In the unliganded structure, the cytosines formed a peculiar triplex i-motif, assembled by trans C•C+ pair and a third cytosine located at the Hoogsteen edge of the C•C+ pair. These results extend our knowledge of the structural polymorphisms of HR and can be used for rational design of small molecules targeting disease-related RNAs.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Marcin Ryczek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Martyna Mateja-Pluta
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
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Saini S, Goel K, Ghosh S, Das A, Saraogi I. Effects of PNA Sequence and Target Site Selection on Function of a 4.5S Non-Coding RNA. Chembiochem 2024:e202400029. [PMID: 38595046 DOI: 10.1002/cbic.202400029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/11/2024]
Abstract
Peptide nucleic acid (PNA) based antisense strategy is a promising therapeutic approach to specifically inhibit target gene expression. However, unlike protein coding genes, identification of an ideal PNA binding site for non-coding RNA is not straightforward. Here, we compare the inhibitory activities of PNA molecules that bind a non-coding 4.5S RNA called SRP RNA, a key component of the bacterial signal recognition particle (SRP). A 9-mer PNA (PNA9) complementary to the tetraloop region of the RNA was more potent in inhibiting its interaction with the SRP protein, compared to an 8-mer PNA (PNA8) targeting a stem-loop. PNA9, which contained a homo-pyrimidine sequence could form a triplex with the complementary stretch of RNA in vitro as confirmed using a fluorescent derivative of PNA9 (F-PNA13). The RNA-PNA complex formation resulted in inhibition of SRP function with PNA9 and F-PNA13, but not PNA8 highlighting the importance of target site selection. Surprisingly, F-PNA13 which was more potent in inhibiting SRP function in vitro, showed weaker antibacterial activity compared to PNA9 likely due to poor cell penetration of the longer PNA. Our results underscore the importance of suitable target site selection and optimum PNA length to develop better antisense molecules against non-coding RNA.
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Affiliation(s)
- Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Khushboo Goel
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Sudipta Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Anirban Das
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
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Shivakumar KM, Mahendran G, Brown JA. Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels. Int J Mol Sci 2024; 25:1630. [PMID: 38338910 PMCID: PMC10855403 DOI: 10.3390/ijms25031630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENβ triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENβ stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5-13 °C more than the Watson-Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENβ stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENβ. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENβ.
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Affiliation(s)
| | | | - Jessica A. Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.M.S.); (G.M.)
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Aich M, Ansari AH, Ding L, Iesmantavicius V, Paul D, Choudhary C, Maiti S, Buchholz F, Chakraborty D. TOBF1 modulates mouse embryonic stem cell fate through regulating alternative splicing of pluripotency genes. Cell Rep 2023; 42:113177. [PMID: 37751355 DOI: 10.1016/j.celrep.2023.113177] [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: 02/08/2023] [Revised: 06/28/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Embryonic stem cells (ESCs) can undergo lineage-specific differentiation, giving rise to different cell types that constitute an organism. Although roles of transcription factors and chromatin modifiers in these cells have been described, how the alternative splicing (AS) machinery regulates their expression has not been sufficiently explored. Here, we show that the long non-coding RNA (lncRNA)-associated protein TOBF1 modulates the AS of transcripts necessary for maintaining stem cell identity in mouse ESCs. Among the genes affected is serine/arginine splicing factor 1 (SRSF1), whose AS leads to global changes in splicing and expression of a large number of downstream genes involved in the maintenance of ESC pluripotency. By overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and AS upon its knockout, we describe local nuclear territories where these distinct events converge. Collectively, these contribute to the maintenance of mouse ESC identity.
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Affiliation(s)
- Meghali Aich
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Asgar Hussain Ansari
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Vytautas Iesmantavicius
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Deepanjan Paul
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Souvik Maiti
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Debojyoti Chakraborty
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Maldonado R, Längst G. The chromatin - triple helix connection. Biol Chem 2023; 404:1037-1049. [PMID: 37506218 DOI: 10.1515/hsz-2023-0189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order genome organisation, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions. Different mechanisms allow the tethering of these chromatin-associated RNAs (caRNA) to chromosomes, including RNA binding proteins, the RNA polymerases and R-loops. In this review, we focus on the sequence-specific targeting of RNA to DNA by forming triple helical structures and describe its interplay with chromatin. It turns out that nucleosome positioning at triple helix target sites and the nucleosome itself are essential factors in determining the formation and stability of triple helices. The histone H3-tail plays a critical role in triple helix stabilisation, and the role of its epigenetic modifications in this process is discussed.
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Affiliation(s)
- Rodrigo Maldonado
- Institute of Anatomy, Histology, and Pathology, Faculty of Medicine, Universidad Austral de Chile, 5090000 Valdivia, Chile
| | - Gernot Längst
- Regensburg Center for Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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Filho MS, Massi L, Millet A, Michel D, Moussa W, Ronco C, Benhida R. Energy-resolved mass spectrometry to investigate nucleobase triplexes – a study applied to triplex-forming artificial nucleobases. NEW J CHEM 2022. [DOI: 10.1039/d2nj00665k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper discloses the use of an energy-resolved mass spectrometric-based approach to assess the stabilities of base triplexes encompassing artificial nucleobases by using variable energy collision-induced dissociation.
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Affiliation(s)
- Mauro Safir Filho
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Lionel Massi
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Antoine Millet
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Dylan Michel
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Wafa Moussa
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Cyril Ronco
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Rachid Benhida
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
- Mohamed VI Polytechnic University, UM6P, 43150, Ben Guerir, Morocco
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Ren H, Song L, Zhang W, Xu L. Synthesis, Stability, and Anti-Tumour Activity of a New Category of "Stapled" Antisense Oligonucleotides with Stimuli-Responsive Feature. J Pharm Sci 2021; 110:3166-3170. [PMID: 34102202 DOI: 10.1016/j.xphs.2021.05.024] [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: 01/08/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The development of nucleic acid drugs with unique structures and mechanisms has stimulated great research interest. Herein, we report a general strategy to construct "stapled" structures of single-stranded antisense oligonucleotides (ASONs) with a stimuli-responsive feature. "Stapled" cyclic structures can be synthesized with reactive bifunctional handles that react with thiol groups of phosphorothioate (PS)-modified ASONs, and can be alternatively adjusted depending on the desired PS sites in the ASON strand. The disulphide group in the stapled handle can be cleaved in the reducing microenvironment of tumour cells. Thus, "stapled" ASONs may be transformed back to a linear conformation to facilitate binding to target mRNAs. Stapling conferred protection against degradation, and enhanced anti-tumour activity compared to linear counterparts. This study provides a new, effective, and convenient strategy for designing ASONs with "stapled" structures, and also adds a further contribution to facilitate the stability and biological efficacy of novel nucleic acid-based therapeutics.
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Affiliation(s)
- Hongqian Ren
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Liya Song
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Wei Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Liang Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.
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8
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Ong AAL, Toh DFK, Krishna MS, Patil KM, Okamura K, Chen G. Incorporating 2-Thiouracil into Short Double-Stranded RNA-Binding Peptide Nucleic Acids for Enhanced Recognition of A-U Pairs and for Targeting a MicroRNA Hairpin Precursor. Biochemistry 2019; 58:3444-3453. [PMID: 31318532 DOI: 10.1021/acs.biochem.9b00521] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemically modified short peptide nucleic acids (PNAs) recognize RNA duplexes under near physiological conditions by major-groove PNA·RNA-RNA triplex formation and show great promise for the development of RNA-targeting probes and therapeutics. Thymine (T) and uracil (U) are often incorporated into PNAs to recognize A-U pairs through major-groove T·A-U and U·A-U base triple formation. Incorporation of a modified nucleobase, 2-thiouracil (s2U), into triplex-forming oligonucleotides stabilizes both DNA and RNA triplexes. Thiolation of uracil causes a decrease in the dehydration energy penalty for triplex formation as well as a decrease in the pKa of the N3 atom, which may result in improved hydrogen bonding in addition to enhanced base stacking interactions, similar to the previously reported thiolation effect of pseudoisocytosine (J to L substitution). Here, we incorporated s2U into short PNAs, followed by binding studies of a series of s2U-modified PNAs. We demonstrated by nondenaturing polyacrylamide gel electrophoresis and thermal melting experiments that s2U and L incorporated into dsRNA-binding PNAs (dbPNAs) enhance the recognition of A-U and G-C pairs, respectively, in RNA duplexes in a position-independent manner, with no appreciable binding to the DNA duplex. Combining s2U and L modifications in dbPNAs facilitates enhanced recognition of dsRNAs and maintains selective binding to dsRNAs over ssRNAs. We further demonstrated through a cell-free assay the application of the s2U- and L-modified dbPNAs (8-mer, with a molecular mass of ∼2.3 kDa) in the inhibition of the pre-microRNA-198 maturation in a substrate-specific manner. Thus, s2U-modified dbPNAs may be generally useful for the enhanced and selective recognition of RNA duplexes and for the regulation of RNA functions.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Katsutomo Okamura
- Division of Biological Sciences , Nara Institute of Science and Technology , 8916-5 Takayama , Ikoma , Nara 630-0192 , Japan
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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Al-mahamad LL. Synthesis and surface characterization of new triplex polymer of Ag(I) and mixture nucleosides: cytidine and 8-bromoguanosine. Heliyon 2019; 5:e01609. [PMID: 31193246 PMCID: PMC6522667 DOI: 10.1016/j.heliyon.2019.e01609] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/04/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022] Open
Abstract
In this work one-dimensional (1D) triplex polymer of silver (I): mixture nucleosides of cytidine and 8-bromoguanosine was synthesised. The polymer showed high stability due to the presence Ag(I) ions in the structure of the polymer in addition to the stability that produces from the effect of Hoogsteen hydrogen bonding in the triplex CGC. Atomic Force Microscopy (AFM) and transmission electron microscopy (TEM) were used to investigate the morphology of the polymer. The AFM images revealed formation of nanofibres extending many microns in length with height in the range of 2-3 nm. Statistical analyses carried out to analyse the AFM images to determine the height of the loops that formed in the polymer. The data displayed that the height value was in the range between 10 nm to 15 nm. The data of TEM images were consistent with the data of AFM images by displaying a very long fibre. Gwyddion software program was used to investigate surface parameters (roughness and waviness), diameter (size distribution), and probability density of the fibre. The data showed that the diameter of the fibre was ∼0.4 nm.
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Affiliation(s)
- Lamia L.G. Al-mahamad
- Department of Chemistry, College of Science, Mustansiriyah University, Baghdad, Iraq
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