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Haque US, Yokota T. Enhancing Antisense Oligonucleotide-Based Therapeutic Delivery with DG9, a Versatile Cell-Penetrating Peptide. Cells 2023; 12:2395. [PMID: 37830609 PMCID: PMC10572411 DOI: 10.3390/cells12192395] [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: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
Antisense oligonucleotide-based (ASO) therapeutics have emerged as a promising strategy for the treatment of human disorders. Charge-neutral PMOs have promising biological and pharmacological properties for antisense applications. Despite their great potential, the efficient delivery of these therapeutic agents to target cells remains a major obstacle to their widespread use. Cellular uptake of naked PMO is poor. Cell-penetrating peptides (CPPs) appear as a possibility to increase the cellular uptake and intracellular delivery of oligonucleotide-based drugs. Among these, the DG9 peptide has been identified as a versatile CPP with remarkable potential for enhancing the delivery of ASO-based therapeutics due to its unique structural features. Notably, in the context of phosphorodiamidate morpholino oligomers (PMOs), DG9 has shown promise in enhancing delivery while maintaining a favorable toxicity profile. A few studies have highlighted the potential of DG9-conjugated PMOs in DMD (Duchenne Muscular Dystrophy) and SMA (Spinal Muscular Atrophy), displaying significant exon skipping/inclusion and functional improvements in animal models. The article provides an overview of a detailed understanding of the challenges that ASOs face prior to reaching their targets and continued advances in methods to improve their delivery to target sites and cellular uptake, focusing on DG9, which aims to harness ASOs' full potential in precision medicine.
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Affiliation(s)
- Umme Sabrina Haque
- Department of Neuroscience, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research, Edmonton, AB T6G 2H7, Canada
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2
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Batistatou N, Kritzer JA. Investigation of Sequence-Penetration Relationships of Antisense Oligonucleotides. Chembiochem 2023; 24:e202300009. [PMID: 36791388 PMCID: PMC10305730 DOI: 10.1002/cbic.202300009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/17/2023]
Abstract
A major limitation for the development of more effective oligonucleotide therapeutics has been a lack of understanding of their penetration into the cytosol. While prior work has shown how backbone modifications affect cytosolic penetration, it is unclear how cytosolic penetration is affected by other features including base composition, base sequence, length, and degree of secondary structure. We have applied the chloroalkane penetration assay, which exclusively reports on material that reaches the cytosol, to investigate the effects of these characteristics on the cytosolic uptake of druglike oligonucleotides. We found that base composition and base sequence had moderate effects, while length did not correlate directly with the degree of cytosolic penetration. Investigating further, we found that the degree of secondary structure had the largest and most predictable correlations with cytosolic penetration. These methods and observations add a layer of design for maximizing the efficacy of new oligonucleotide therapeutics.
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Affiliation(s)
- Nefeli Batistatou
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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3
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Brinkman HF, Jauregui Matos V, Mendoza HG, Doherty EE, Beal PA. Nucleoside analogs in ADAR guide strands targeting 5'-UA̲ sites. RSC Chem Biol 2023; 4:74-83. [PMID: 36685257 PMCID: PMC9811522 DOI: 10.1039/d2cb00165a] [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: 07/11/2022] [Accepted: 10/30/2022] [Indexed: 11/07/2022] Open
Abstract
Adenosine deaminases that act on RNA (ADARs) can be directed to predetermined sites in transcriptomes by forming duplex structures with exogenously delivered guide RNAs (gRNAs). They can then catalyze the hydrolytic deamination of adenosine to inosine in double stranded RNA, which is read as guanosine during translation. High resolution structures of ADAR2-RNA complexes revealed a unique conformation for the nucleotide in the guide strand base paired to the editing site's 5' nearest neighbor (-1 position). Here we describe the effect of 16 different nucleoside analogs at this position in a gRNA that targets a 5'-UA̲-3' site. We found that several analogs increase editing efficiency for both catalytically active human ADARs. In particular, 2'-deoxynebularine (dN) increased the ADAR1 and ADAR2 in vitro deamination rates when at the -1 position of gRNAs targeting the human MECP2 W104X site, the mouse IDUA W392X site, and a site in the 3'-UTR of human ACTB. Furthermore, a locked nucleic acid (LNA) modification at the -1 position was found to eliminate editing. When placed -1 to a bystander editing site in the MECP2 W104X sequence, bystander editing was eliminated while maintaining on-target editing. In vitro trends for four -1 nucleoside analogs were validated by directed editing of the MECP2 W104X site expressed on a reporter transcript in human cells. This work demonstrates the importance of the -1 position of the gRNA to ADAR editing and discloses nucleoside analogs for this site that modulate ADAR editing efficiency.
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Affiliation(s)
- Hannah F. Brinkman
- Department of Chemistry, University of California, One Shields AvenueDavisCA 95616USA
| | | | - Herra G. Mendoza
- Department of Chemistry, University of California, One Shields AvenueDavisCA 95616USA
| | - Erin E. Doherty
- Department of Chemistry, University of California, One Shields AvenueDavisCA 95616USA
| | - Peter A. Beal
- Department of Chemistry, University of California, One Shields AvenueDavisCA 95616USA
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4
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Yuan E, Liu K, Lee J, Tsung K, Chow F, Attenello FJ. Modulating glioblastoma chemotherapy response: Evaluating long non-coding RNA effects on DNA damage response, glioma stem cell function, and hypoxic processes. Neurooncol Adv 2022; 4:vdac119. [PMID: 36105389 PMCID: PMC9466271 DOI: 10.1093/noajnl/vdac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive primary adult brain tumor, with an estimated annual incidence of 17 000 new cases in the United States. Current treatments for GBM include chemotherapy, surgical resection, radiation therapy, and antiangiogenic therapy. However, despite the various therapeutic options, the 5-year survival rate remains at a dismal 5%. Temozolomide (TMZ) is the first-line chemotherapy drug for GBM; however, poor TMZ response is one of the main contributors to the dismal prognosis. Long non-coding RNAs (lncRNAs) are nonprotein coding transcripts greater than 200 nucleotides that have been implicated to mediate various GBM pathologies, including chemoresistance. In this review, we aim to frame the TMZ response in GBM via exploration of the lncRNAs mediating three major mechanisms of TMZ resistance: (1) regulation of the DNA damage response, (2) maintenance of glioma stem cell identity, and (3) exploitation of hypoxia-associated responses.
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Affiliation(s)
- Edith Yuan
- Corresponding Author: Edith Yuan, BA, Keck School of Medicine, University of Southern California, 1200 North State St. Suite 3300, Los Angeles, CA 90033, USA ()
| | - Kristie Liu
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin Lee
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kathleen Tsung
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Frances Chow
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Frank J Attenello
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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5
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Su Y, Raguraman P, Veedu RN, Filichev VV. Phosphorothioate modification improves exon-skipping of antisense oligonucleotides based on sulfonyl phosphoramidates in mdx mouse myotubes. Org Biomol Chem 2022; 20:3790-3797. [PMID: 35438707 DOI: 10.1039/d2ob00304j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2'-O-Methyl (2'-OMe) antisense oligonucleotides (AOs) possessing a various number of 4-(trimethylammonio)butylsulfonyl or tosyl phosphoramidates (N+ and Ts-modifications, respectively) instead of a native phosphodiester linkage were designed to skip exon-23 in dystrophin pre-mRNA transcript in mdx mice myotubes. AOs bearing several zwitterionic N+ modifications in the sequence had remarkably increased thermal stability towards complementary mRNA in comparison with 2'-OMe-RNAs having negatively charged Ts and phosphorothioate (PS) linkages. However, only Ts-modified AOs exhibited a similar level of exon skipping in comparison with fully modified PS-containing 2'-OMe-RNA, whereas the exon skipping induced by N+ modified AOs was much lower with no exon-skipping detected for AOs having seven N+ modifications. The level of exon-skipping was improved once Ts and especially N+ moieties were used in combination with PS-modification, most likely through improved cellular and nuclear uptake of AOs. These results provide new insights on expanding the design of novel chemically modified AOs based on phosphate modifications.
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Affiliation(s)
- Yongdong Su
- School of Natural Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Prithi Raguraman
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia. .,Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia. .,Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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6
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Shadid M, Badawi M, Abulrob A. Antisense oligonucleotides: absorption, distribution, metabolism, and excretion. Expert Opin Drug Metab Toxicol 2021; 17:1281-1292. [PMID: 34643122 DOI: 10.1080/17425255.2021.1992382] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Antisense oligonucleotides (ASOs) have emerged as a promising novel drug modality that aims to address unmet medical needs. A record of six ASO drugs have been approved since 2016, and more candidates are in clinical development. ASOs are the most advanced class within the RNA-based therapeutics field. AREAS COVERED This review highlights the two major backbones that are currently used to build the most advanced ASO platforms - the phosphorodiamidate morpholino oligomers (PMOs) and the phosphorothioates (PSs). The absorption, distribution, metabolism, and excretion (ADME) properties of the PMO and PS platforms are discussed in detail. EXPERT OPINION Understanding the ADME properties of existing ASOs can foster further improvement of this cutting-edge therapy, thereby enabling researchers to safely develop ASO drugs and enhancing their ability to innovate. ABBREVIATIONS 2'-MOE, 2'-O-methoxyethyl; 2'PS, 2 modified PS; ADME, absorption, distribution, metabolism, and excretion; ASO, antisense oligonucleotide; AUC, area under the curve; BNA, bridged nucleic acid; CPP, cell-penetrating peptide; CMV, cytomegalovirus; CNS, central nervous system; CYP, cytochrome P; DDI, drug-drug interaction; DMD, Duchenne muscular dystrophy; FDA, Food and Drug Administration; GalNAc3, triantennary N-acetyl galactosamine; IT, intrathecal; IV, intravenous; LNA, locked nucleic acid; mRNA, messenger RNA; NA, not applicable; PBPK, physiologically based pharmacokinetics; PD, pharmacodynamic; PK, pharmacokinetic; PMO, phosphorodiamidate morpholino oligomer; PMOplus, PMOs with positionally specific positive molecular charges; PPMO, peptide-conjugated PMO; PS, phosphorothioate; SC, subcutaneous; siRNA, small-interfering RNA; SMA, spinal muscular atrophy.
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Affiliation(s)
- Mohammad Shadid
- Nonclinical Development, Sarepta Therapeutics, Inc, Cambridge, MA, USA
| | - Mohamed Badawi
- Clinical Pharmacology Fellow, Ohio State University, Columbus, OH, USA
| | - Abedelnasser Abulrob
- Senior Research Officer, Human Health Therapeutics Centre, Translational Bioscience, National Research Council Canada, Ottawa, Ontario, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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7
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Kabza AM, Kundu N, Zhong W, Sczepanski JT. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1743. [PMID: 34328690 DOI: 10.1002/wnan.1743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 01/21/2023]
Abstract
Watson-Crick base pairing rules provide a powerful approach for engineering DNA-based nanodevices with programmable and predictable behaviors. In particular, DNA strand displacement reactions have enabled the development of an impressive repertoire of molecular devices with complex functionalities. By relying on DNA to function, dynamic strand displacement devices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation in living systems has been a slow process due to several persistent challenges, including nuclease degradation. To circumvent these issues, researchers are increasingly turning to chemically modified nucleotides as a means to increase device performance and reliability within harsh biological environments. In this review, we summarize recent progress toward the integration of chemically modified nucleotides with DNA strand displacement reactions, highlighting key successes in the development of robust systems and devices that operate in living cells and in vivo. We discuss the advantages and disadvantages of commonly employed modifications as they pertain to DNA strand displacement, as well as considerations that must be taken into account when applying modified oligonucleotide to living cells. Finally, we explore how chemically modified nucleotides fit into the broader goal of bringing dynamic DNA nanotechnology into the cell, and the challenges that remain. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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8
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [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: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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Mattelaer CA, Mattelaer HP, Rihon J, Froeyen M, Lescrinier E. Efficient and Accurate Potential Energy Surfaces of Puckering in Sugar-Modified Nucleosides. J Chem Theory Comput 2021; 17:3814-3823. [PMID: 34000809 DOI: 10.1021/acs.jctc.1c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Puckering of the sugar unit in nucleosides and nucleotides is an important structural aspect that directly influences the helical structure of nucleic acids. The preference for specific puckering modes in nucleic acids can be analyzed via in silico conformational analysis, but the large amount of conformations and the accuracy of the analysis leads to an extensive amount of computational time. In this paper, we show that the combination of geometry optimizations with the HF-3c method with single point energies at the RI-MP2 level results in accurate results for the puckering potential energy surface (PES) of DNA and RNA nucleosides while significantly reducing the necessary computational time. Applying this method to a series of known xeno nucleic acids (XNAs) allowed us to rapidly explore the puckering PES of each of the respective nucleosides and to explore the puckering PES of six-membered modified XNA (HNA and β-homo-DNA) for the first time.
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Affiliation(s)
- Charles-Alexandre Mattelaer
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Campus Drie Eiken, Laboratory of Medicinal Chemistry, UAntwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jérôme Rihon
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
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10
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Opportunities and challenges for microRNA-targeting therapeutics for epilepsy. Trends Pharmacol Sci 2021; 42:605-616. [PMID: 33992468 DOI: 10.1016/j.tips.2021.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/30/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022]
Abstract
Epilepsy is a common and serious neurological disorder characterised by recurrent spontaneous seizures. Frontline pharmacotherapy includes small-molecule antiseizure drugs that typically target ion channels and neurotransmitter systems, but these fail in 30% of patients and do not prevent either the development or progression of epilepsy. An emerging therapeutic target is microRNA (miRNA), small noncoding RNAs that negatively regulate sets of proteins. Their multitargeting action offers unique advantages for certain forms of epilepsy with complex underlying pathophysiology, such as temporal lobe epilepsy (TLE). miRNA can be inhibited by designed antisense oligonucleotides (ASOs; e.g., antimiRs). Here, we outline the prospects for miRNA-based therapies. We review design considerations for nucleic acid-based approaches and the challenges and next steps in developing therapeutic miRNA-targeting molecules for epilepsy.
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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Chen Y, Li Z, Chen X, Zhang S. Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B 2021; 11:340-354. [PMID: 33643816 PMCID: PMC7893121 DOI: 10.1016/j.apsb.2020.10.001] [Citation(s) in RCA: 254] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Enormous studies have corroborated that long non-coding RNAs (lncRNAs) extensively participate in crucial physiological processes such as metabolism and immunity, and are closely related to the occurrence and development of tumors, cardiovascular diseases, nervous system disorders, nephropathy, and other diseases. The application of lncRNAs as biomarkers or intervention targets can provide new insights into the diagnosis and treatment of diseases. This paper has focused on the emerging research into lncRNAs as pharmacological targets and has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research. Cutting-edge strategies for lncRNA modulation have been summarized, including the sources of lncRNA-related drugs, such as genetic technology and small-molecule compounds, and related delivery methods. The current progress of clinical trials of lncRNA-targeting drugs is also discussed. This information will form a latest updated reference for research and development of lncRNA-based drugs.
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Key Words
- AD, Alzheimer's disease
- ANRIL, antisense noncoding RNA gene at the INK4 locus
- ASO, antisense oligonucleotide
- ASncmtRNA
- ASncmtRNA, antisense noncoding mitochondrial RNA
- BCAR4, breast cancer anti-estrogen resistance 4
- BDNF-AS, brain-derived neurotrophic factor antisense
- CASC9, cancer susceptibility candidate 9
- CDK, cyclin dependent kinase 1
- CHRF, cardiac hypertrophy related factor
- CRISPR, clustered regularly interspaced short palindromic repeats
- Clinical trials
- DACH1, dachshund homolog 1
- DANCR, differentiation antagonizing non-protein coding RNA
- DKD, diabetic kidney disease
- DPF, diphenyl furan
- Delivery
- EBF3-AS, early B cell factor 3-antisense
- ENE, element for nuclear expression
- Erbb4-IR, Erb-B2 receptor tyrosine kinase 4-immunoreactivity
- FDA, U.S. Food and Drug Administration
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GAS5, growth arrest specific 5
- Gene therapy
- HISLA, HIF-1α-stabilizing long noncoding RNA
- HOTAIR, HOX transcript antisense intergenic RNA
- HULC, highly upregulated in liver cancer
- LIPCAR, long intergenic noncoding RNA predicting cardiac remodeling
- LNAs, locked nucleic acids
- LncRNAs
- MALAT1, metastasis associated lung adenocarcinoma transcript 1
- MEG3, maternally expressed gene 3
- MHRT, myosin heavy chain associated RNA transcripts
- MM, multiple myeloma
- NEAT1, nuclear enriched abundant transcript 1
- NKILA, NF-kappaB interacting lncRNA
- NPs, nanoparticles
- Norad, non-coding RNA activated by DNA damage
- OIP5-AS1, opa-interacting protein 5 antisense transcript 1
- PD, Parkinson's disease
- PEG, polyethylene glycol
- PNAs, peptide nucleic acids
- PTO, phosphorothioate
- PVT1, plasmacytoma variant translocation 1
- RGD, arginine-glycine-aspartic acid peptide
- RISC, RNA-induced silencing complex
- SALRNA1, senescence associated long non-coding RNA 1
- SNHG1, small nucleolar RNA host gene 1
- Small molecules
- SncmtRNA, sense noncoding mitochondrial RNA
- THRIL, TNF and HNRNPL related immunoregulatory
- TTTY15, testis-specific transcript, Y-linked 15
- TUG1, taurine-upregulated gene 1
- TWIST1, twist family BHLH transcription factor 1
- Targeted drug
- TncRNA, trophoblast-derived noncoding RNA
- Translational medicine
- UCA1, urothelial carcinoma-associated 1
- UTF1, undifferentiated transcription factor 1
- XIST, X-inactive specific transcript
- lincRNA-p21, long intergenic noncoding RNA p21
- lncRNAs, long non-coding RNAs
- mtlncRNA, mitochondrial long noncoding RNA
- pHLIP, pH-low insertion peptide
- sgRNA, single guide RNA
- siRNAs, small interfering RNAs
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Jin HS, Kim NH, Choi SR, Oh KI, Lee JH. Protein-induced B-Z transition of DNA duplex containing a 2'-OMe guanosine. Biochem Biophys Res Commun 2020; 533:417-423. [PMID: 32972754 DOI: 10.1016/j.bbrc.2020.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
Abstract
Structural transformation of the canonical right-handed helix, B-DNA, to the non-canonical left-handed helix, Z-DNA, can be induced by the Zα domain of the human RNA editing enzyme ADAR1 (hZαADAR1). To characterize the site-specific preferences of binding and structural changes in DNA containing the 2'-O-methyl guanosine derivative (mG), titration of the imino proton spectra and chemical shift perturbations were performed on hZαADAR1 upon binding to Z-DNA. The structural transition between B-Z conformation as the changing ratio between DNA and protein showed a binding affinity of the modified DNA onto the Z-DNA binding protein similar to wild-type DNA or RNA. The chemical shift perturbation results showed that the overall structure and environment of the modified DNA revealed DNA-like properties rather than RNA-like characteristics. Moreover, we found evidence for two distinct regimes, "Z-DNA Sensing" and "Modification Sensing", based on the site-specific chemical shift perturbation between the DNA (or RNA) binding complex and the modified DNA-hZαADAR1 complex. Thus, we propose that modification of the sugar backbone of DNA with 2'-O-methyl guanosine promotes the changes in the surrounding α3 helical structural segment as well as the non-perturbed feature of the β-hairpin region.
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Affiliation(s)
- Ho-Seong Jin
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Na-Hyun Kim
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea
| | - Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea.
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14
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Pickard MAG, Brylow KB, Cisco LA, Anecelle MR, Pershun ML, Chandrasekaran AR, Halvorsen K, Gleghorn ML. Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique. RNA (NEW YORK, N.Y.) 2020; 26:1118-1130. [PMID: 32414856 PMCID: PMC7430668 DOI: 10.1261/rna.075408.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Polyriboadenylic [poly(rA)] strands of sufficient length form parallel double helices in acidic and/or ammonium-containing conditions. Poly(rA) duplexes in acidic conditions are held together by A+-A+ base-pairing also involving base interactions with the phosphate backbone. Traditional UV-melting studies of parallel poly(A) duplexes have typically examined homo-duplex formation of a single nucleic acid species in solution. We have adapted a technique utilizing a DNA nanoswitch that detects interaction of two different strands either with similar or differing lengths or modifications. Our method detected parallel duplex formation as a function of length, chemical modifications, and pH, and at a sensitivity that required over 100-fold less concentration of sample than prior UV-melting methods. While parallel polyriboadenylic acid and poly-2'-O-methyl-adenylic acid homo-duplexes formed, we did not detect homo-duplexes of polydeoxyriboadenylic acid strands or poly-locked nucleic acid (LNA)-adenylic strands. Importantly however, a poly-locked nucleic acid (LNA)-adenylic strand, as well as a poly-2'-O-methyl-adenylic strand, formed a hetero-duplex with a polyriboadenylic strand. Overall, our work validates a new tool for studying parallel duplexes and reveals fundamental properties of poly(A) parallel duplex formation. Parallel duplexes may find use in DNA nanotechnology and in molecular biology applications such as a potential poly(rA) tail capture tool as an alternative to traditional oligo(dT) based purification.
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Affiliation(s)
- Martha Anne G Pickard
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Karl B Brylow
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Lily A Cisco
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Matthew R Anecelle
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Mackenzie L Pershun
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
| | | | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, USA
| | - Michael L Gleghorn
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
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15
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Xue K, MacLaren RE. Antisense oligonucleotide therapeutics in clinical trials for the treatment of inherited retinal diseases. Expert Opin Investig Drugs 2020; 29:1163-1170. [PMID: 32741234 DOI: 10.1080/13543784.2020.1804853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Antisense oligonucleotides (ASOs) represent a class of drugs which can be rationally designed to complement the coding or non-coding regions of target RNA transcripts. They could modulate pre-messenger RNA splicing, induce mRNA knockdown, or block translation of disease-causing genes, thereby slowing disease progression. The pharmacokinetics of intravitreal delivery may enable ASOs to be effective in the treatment of inherited retinal diseases. AREAS COVERED We review the current status of clinical trials of ASO therapies for inherited retinal diseases, which have demonstrated safety, viable durability, and early efficacy. Future applications are discussed in the context of alternative genetic approaches, including gene augmentation and gene editing. EXPERT OPINION Early efficacy data suggest that the splicing-modulating ASO, sepofarsen, is a promising treatment for Leber congenital amaurosis associated with the common c.2991+1655A>G mutation in CEP290. However, potential variability in clinical response to ASO-mediated correction of splicing defect on one allele in patients who are compound heterozygotes needs to be assessed. ASOs hold great therapeutic potential for numerous other inherited retinal diseases with common deep-intronic and dominant gain-of-function mutations. These would complement viral vector-mediated gene augmentation which is generally limited by the size of the transgene and to the treatment of recessive diseases.
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Affiliation(s)
- Kanmin Xue
- Wellcome Trust Clinical Research Career Development Fellow, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford & Honorary Consultant Vitreoretinal Surgeon, Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK
| | - Robert E MacLaren
- Professor of Ophthalmology, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford & Honorary Consultant Vitreoretinal Surgeon, Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK
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16
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Doxakis E. Therapeutic antisense oligonucleotides for movement disorders. Med Res Rev 2020; 41:2656-2688. [PMID: 32656818 DOI: 10.1002/med.21706] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/11/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022]
Abstract
Movement disorders are a group of neurological conditions characterized by abnormalities of movement and posture. They are broadly divided into akinetic and hyperkinetic syndromes. Until now, no effective symptomatic or disease-modifying therapies have been available. However, since many of these disorders are monogenic or have some well-defined genetic component, they represent strong candidates for antisense oligonucleotide (ASO) therapies. ASO therapies are based on the use of short synthetic single-stranded ASOs that bind to disease-related target RNAs via Watson-Crick base-pairing and pleiotropically modulate their function. With information arising from the RNA sequence alone, it is possible to design ASOs that not only alter the expression levels but also the splicing defects of any protein, far exceeding the intervention repertoire of traditional small molecule approaches. Following the regulatory approval of ASO therapies for spinal muscular atrophy and Duchenne muscular dystrophy in 2016, there has been tremendous momentum in testing such therapies for other neurological disorders. This review article initially focuses on the chemical modifications aimed at improving ASO effectiveness, the mechanisms by which ASOs can interfere with RNA function, delivery systems and pharmacokinetics, and the common set of toxicities associated with their application. It, then, describes the pathophysiology and the latest information on preclinical and clinical trials utilizing ASOs for the treatment of Parkinson's disease, Huntington's disease, and ataxias 1, 2, 3, and 7. It concludes with issues that require special attention to realize the full potential of ASO-based therapies.
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Affiliation(s)
- Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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17
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Silva AC, Lobo DD, Martins IM, Lopes SM, Henriques C, Duarte SP, Dodart JC, Nobre RJ, Pereira de Almeida L. Antisense oligonucleotide therapeutics in neurodegenerative diseases: the case of polyglutamine disorders. Brain 2020; 143:407-429. [PMID: 31738395 DOI: 10.1093/brain/awz328] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/09/2019] [Accepted: 08/22/2019] [Indexed: 12/20/2022] Open
Abstract
Polyglutamine (polyQ) disorders are a group of nine neurodegenerative diseases that share a common genetic cause, which is an expansion of CAG repeats in the coding region of the causative genes that are otherwise unrelated. The trinucleotide expansion encodes for an expanded polyQ tract in the respective proteins, resulting in toxic gain-of-function and eventually in neurodegeneration. Currently, no disease-modifying therapies are available for this group of disorders. Nevertheless, given their monogenic nature, polyQ disorders are ideal candidates for therapies that target specifically the gene transcripts. Antisense oligonucleotides (ASOs) have been under intense investigation over recent years as gene silencing tools. ASOs are small synthetic single-stranded chains of nucleic acids that target specific RNA transcripts through several mechanisms. ASOs can reduce the levels of mutant proteins by breaking down the targeted transcript, inhibit mRNA translation or alter the maturation of the pre-mRNA via splicing correction. Over the years, chemical optimization of ASO molecules has allowed significant improvement of their pharmacological properties, which has in turn made this class of therapeutics a very promising strategy to treat a variety of neurodegenerative diseases. Indeed, preclinical and clinical strategies have been developed in recent years for some polyQ disorders using ASO therapeutics. The success of ASOs in several animal models, as well as encouraging results in the clinic for Huntington's disease, points towards a promising future regarding the application of ASO-based therapies for polyQ disorders in humans, offering new opportunities to address unmet medical needs for this class of disorders. This review aims to present a brief overview of key chemical modifications, mechanisms of action and routes of administration that have been described for ASO-based therapies. Moreover, it presents a review of the most recent and relevant preclinical and clinical trials that have tested ASO therapeutics in polyQ disorders.
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Affiliation(s)
- Ana C Silva
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Diana D Lobo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Inês M Martins
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Sara M Lopes
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Carina Henriques
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,ViraVector, Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal
| | - Sónia P Duarte
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | | | - Rui Jorge Nobre
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.,ViraVector, Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal
| | - Luis Pereira de Almeida
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,ViraVector, Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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18
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Tuske S, Zheng J, Olson ED, Ruiz FX, Pascal BD, Hoang A, Bauman JD, Das K, DeStefano JJ, Musier-Forsyth K, Griffin PR, Arnold E. Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer. Curr Res Struct Biol 2020; 2:116-129. [PMID: 33870216 PMCID: PMC8052095 DOI: 10.1016/j.crstbi.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/03/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
The high-resolution crystal structure of HIV-1 reverse transcriptase (RT) bound to a 38-mer DNA hairpin aptamer with low pM affinity was previously described. The high-affinity binding aptamer contained 2'-O-methyl modifications and a seven base-pair GC-rich tract and the structure of the RT-aptamer complex revealed specific contacts between RT and the template strand of the aptamer. Similar to all crystal structures of RT bound to nucleic acid template-primers, the aptamer bound RT with a bend in the duplex DNA. To understand the structural basis for the ultra-high-affinity aptamer binding, an integrative structural biology approach was used. Hydrogen-deuterium exchange coupled to liquid chromatography-mass spectrometry (HDX-MS) was used to examine the structural dynamics of RT alone and in the presence of the DNA aptamer. RT was selectively labeled with 15N to unambiguously identify peptides from each subunit. HDX of unliganded RT shows a mostly stable core. The p66 fingers and thumb subdomains, and the RNase H domain are relatively dynamic. HDX indicates that both the aptamer and a scrambled version significantly stabilize regions of RT that are dynamic in the absence of DNA. No substantial differences in RT dynamics are observed between aptamer and scrambled aptamer binding, despite a large difference in binding affinity. Small-angle X-ray scattering and circular dichroism spectroscopy were used to investigate the aptamer conformation in solution and revealed a pre-bent DNA that possesses both A- and B-form helical character. Both the 2'-O-methyl modifications and the GC tract appear to contribute to an energetically favorable conformation for binding to RT that contributes to the aptamer's ultra-high affinity for RT. The X-ray structure of RT with an RNA/DNA version of the aptamer at 2.8 Å resolution revealed a potential role of the hairpin positioning in affinity. Together, the data suggest that both the 2'-O-methyl modifications and the GC tract contribute to an energetically favorable conformation for high-affinity binding to RT.
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Affiliation(s)
- Steve Tuske
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Bruce D. Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Anthony Hoang
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20740, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
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19
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Thayer MB, Humphreys SC, Chung KS, Lade JM, Cook KD, Rock BM. POE Immunoassay: Plate-based oligonucleotide electro-chemiluminescent immunoassay for the quantification of nucleic acids in biological matrices. Sci Rep 2020; 10:10425. [PMID: 32591626 PMCID: PMC7319975 DOI: 10.1038/s41598-020-66829-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/26/2020] [Indexed: 12/29/2022] Open
Abstract
Oligonucleotide therapeutics use short interfering RNA (siRNA) or antisense oligonucleotide (ASO) molecules to exploit endogenous systems-neutralizing target RNA to prevent subsequent protein translation. While the potential clinical application is vast, delivery efficiency and extrahepatic targeting is challenging. Bioanalytical assays are important in building understanding of these complex relationships. The literature currently lacks description of robust and sensitive methods to measure siRNA and ASOs in complex biological matrices. Described herein is a non-enzymatic hybridization-based immunoassay that enables quantification of individual siRNA strands (antisense or sense) in serum, urine, bile, and liver and kidney homogenates. Assay utility is also demonstrated in ASOs. The assay improves upon previous works by abolishing enzymatic steps and further incorporating Locked Nucleic Acid (LNA) nucleotide modifications to increase analyte hybridization affinity and improve sensitivity, specificity, and robustness. We report an assay with an ultrasensitive dynamic range of 0.3 to 16,700 pM for siRNA in serum. The assay was submitted to full qualification for accuracy and precision in both serum and tissue matrices and assay performance was assessed with single and mixed analytes. The reliable LNA-hybridization-based approach removes the need for matrix sample extraction, enrichment or amplification steps which may be impeded by more advanced chemical modifications.
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Affiliation(s)
- Mai B Thayer
- Amgen Research, Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, CA, US
| | - Sara C Humphreys
- Amgen Research, Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, CA, US
| | - Kyu S Chung
- Amgen Research, Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, CA, US
| | - Julie M Lade
- Amgen Research, Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, CA, US
| | - Kevin D Cook
- Amgen Research, Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, CA, US
| | - Brooke M Rock
- Amgen Research, Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, CA, US.
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20
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Glazier DA, Liao J, Roberts BL, Li X, Yang K, Stevens CM, Tang W. Chemical Synthesis and Biological Application of Modified Oligonucleotides. Bioconjug Chem 2020; 31:1213-1233. [PMID: 32227878 DOI: 10.1021/acs.bioconjchem.0c00060] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA plays a myriad of roles in the body including the coding, decoding, regulation, and expression of genes. RNA oligonucleotides have garnered significant interest as therapeutics via antisense oligonucleotides or small interfering RNA strategies for the treatment of diseases ranging from hyperlipidemia, HCV, and others. Additionally, the recently developed CRISPR-Cas9 mediated gene editing strategy also relies on Cas9-associated RNA strands. However, RNA presents numerous challenges as both a synthetic target and a potential therapeutic. RNA is inherently unstable, difficult to deliver into cells, and potentially immunogenic by itself or upon modification. Despite these challenges, with the help of chemically modified oligonucleotides, multiple RNA-based drugs have been approved by the FDA. The progress is made possible due to the nature of chemically modified oligonucleotides bearing advantages of nuclease stability, stronger binding affinity, and some other unique properties. This review will focus on the chemical synthesis of RNA and its modified versions. How chemical modifications of the ribose units and of the phosphatediester backbone address the inherent issues with using native RNA for biological applications will be discussed along the way.
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Affiliation(s)
- Daniel A Glazier
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junzhuo Liao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Brett L Roberts
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xiaolei Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ka Yang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Christopher M Stevens
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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21
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Lin J, Jo SB, Kim TH, Kim HW, Chew SY. RNA interference in glial cells for nerve injury treatment. J Tissue Eng 2020; 11:2041731420939224. [PMID: 32670539 PMCID: PMC7338726 DOI: 10.1177/2041731420939224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/13/2020] [Indexed: 12/12/2022] Open
Abstract
Drivers of RNA interference are potent for manipulating gene and protein levels, which enable the restoration of dysregulated mRNA expression that is commonly associated with injuries and diseases. This review summarizes the potential of targeting neuroglial cells, using RNA interference, to treat nerve injuries sustained in the central nervous system. In addition, the various methods of delivering these RNA interference effectors will be discussed.
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Affiliation(s)
- Junquan Lin
- School of Chemical and Biomedical
Engineering, Nanyang Technological University, Singapore
| | - Seung Bin Jo
- Institute of Tissue Regeneration
Engineering (ITREN), Dankook University, Cheonan, Republic of Korea
| | - Tae-Hyun Kim
- Institute of Tissue Regeneration
Engineering (ITREN), Dankook University, Cheonan, Republic of Korea
- Department of Nanobiomedical Science
& BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook
University, Cheonan, Republic of Korea
| | - Hae-Won Kim
- Institute of Tissue Regeneration
Engineering (ITREN), Dankook University, Cheonan, Republic of Korea
- Department of Nanobiomedical Science
& BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook
University, Cheonan, Republic of Korea
- UCL Eastman-Korea Dental Medicine
Innovation Centre, Dankook University, Cheonan, Republic of Korea
| | - Sing Yian Chew
- School of Chemical and Biomedical
Engineering, Nanyang Technological University, Singapore
- Lee Kong Chian School of Medicine,
Nanyang Technological University, Singapore
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22
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He CC, Hamlow LA, Zhu Y, Nei YW, Fan L, McNary CP, Maître P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2318-2334. [PMID: 31435890 DOI: 10.1007/s13361-019-02300-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.
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Affiliation(s)
- C C He
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L Fan
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - C P McNary
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - P Maître
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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23
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O'Reilly D, Kartje ZJ, Ageely EA, Malek-Adamian E, Habibian M, Schofield A, Barkau CL, Rohilla KJ, DeRossett LB, Weigle AT, Damha MJ, Gagnon KT. Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity. Nucleic Acids Res 2019; 47:546-558. [PMID: 30517736 PMCID: PMC6344873 DOI: 10.1093/nar/gky1214] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeat) endonucleases are at the forefront of biotechnology, synthetic biology and gene editing. Methods for controlling enzyme properties promise to improve existing applications and enable new technologies. CRISPR enzymes rely on RNA cofactors to guide catalysis. Therefore, chemical modification of the guide RNA can be used to characterize structure-activity relationships within CRISPR ribonucleoprotein (RNP) enzymes and identify compatible chemistries for controlling activity. Here, we introduce chemical modifications to the sugar–phosphate backbone of Streptococcus pyogenes Cas9 CRISPR RNA (crRNA) to probe chemical and structural requirements. Ribose sugars that promoted or accommodated A-form helical architecture in and around the crRNA ‘seed’ region were tolerated best. A wider range of modifications were acceptable outside of the seed, especially D-2′-deoxyribose, and we exploited this property to facilitate exploration of greater chemical diversity within the seed. 2′-fluoro was the most compatible modification whereas bulkier O-methyl sugar modifications were less tolerated. Activity trends could be rationalized for selected crRNAs using RNP stability and DNA target binding experiments. Cas9 activity in vitro tolerated most chemical modifications at predicted 2′-hydroxyl contact positions, whereas editing activity in cells was much less tolerant. The biochemical principles of chemical modification identified here will guide CRISPR-Cas9 engineering and enable new or improved applications.
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Affiliation(s)
- Daniel O'Reilly
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Zachary J Kartje
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Eman A Ageely
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Elise Malek-Adamian
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Maryam Habibian
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Annabelle Schofield
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Christopher L Barkau
- Department of Biochemistry & Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Kushal J Rohilla
- Department of Biochemistry & Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Lauren B DeRossett
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Austin T Weigle
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Keith T Gagnon
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA.,Department of Biochemistry & Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, USA
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24
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Moon SB, Kim DY, Ko JH, Kim JS, Kim YS. Improving CRISPR Genome Editing by Engineering Guide RNAs. Trends Biotechnol 2019; 37:870-881. [PMID: 30846198 DOI: 10.1016/j.tibtech.2019.01.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
CRISPR technology is a two-component gene editing system in which the effector protein induces genetic alterations with the aid of a gene targeting guide RNA. Guide RNA can be produced through chemical synthesis, in vitro transcription, or intracellular transcription. Guide RNAs can be engineered to have chemical modifications, alterations in the spacer length, sequence modifications, fusion of RNA or DNA components, and incorporation of deoxynucleotides. Engineered guide RNA can improve genome editing efficiency and target specificity, regulation of biological toxicity, sensitive and specific molecular imaging, multiplexing, and editing flexibility. Therefore, engineered guide RNA will enable more specific, efficient, and safe gene editing, ultimately improving the clinical benefits of gene therapy.
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Affiliation(s)
- Su Bin Moon
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea; These authors contributed equally to this work
| | - Do Yon Kim
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea; These authors contributed equally to this work
| | - Jeong-Heon Ko
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea; IBS School, Korea University of Science and Technology (UST), Daejeon, Republic of Korea; Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.
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25
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Harp JM, Guenther DC, Bisbe A, Perkins L, Matsuda S, Bommineni GR, Zlatev I, Foster DJ, Taneja N, Charisse K, Maier MA, Rajeev KG, Manoharan M, Egli M. Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity. Nucleic Acids Res 2019; 46:8090-8104. [PMID: 30107495 PMCID: PMC6144868 DOI: 10.1093/nar/gky703] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
Chemical modification is a prerequisite of oligonucleotide therapeutics for improved metabolic stability, uptake and activity, irrespective of their mode of action, i.e. antisense, RNAi or aptamer. Phosphate moiety and ribose C2′/O2′ atoms are the most common sites for modification. Compared to 2′-O-substituents, ribose 4′-C-substituents lie in proximity of both the 3′- and 5′-adjacent phosphates. To investigate potentially beneficial effects on nuclease resistance we combined 2′-F and 2′-OMe with 4′-Cα- and 4′-Cβ-OMe, and 2′-F with 4′-Cα-methyl modification. The α- and β-epimers of 4′-C-OMe-uridine and the α-epimer of 4′-C-Me-uridine monomers were synthesized and incorporated into siRNAs. The 4′α-epimers affect thermal stability only minimally and show increased nuclease stability irrespective of the 2′-substituent (H, F, OMe). The 4′β-epimers are strongly destabilizing, but afford complete resistance against an exonuclease with the phosphate or phosphorothioate backbones. Crystal structures of RNA octamers containing 2′-F,4′-Cα-OMe-U, 2′-F,4′-Cβ-OMe-U, 2′-OMe,4′-Cα-OMe-U, 2′-OMe,4′-Cβ-OMe-U or 2′-F,4′-Cα-Me-U help rationalize these observations and point to steric and electrostatic origins of the unprecedented nuclease resistance seen with the chain-inverted 4′β-U epimer. We used structural models of human Argonaute 2 in complex with guide siRNA featuring 2′-F,4′-Cα-OMe-U or 2′-F,4′-Cβ-OMe-U at various sites in the seed region to interpret in vitro activities of siRNAs with the corresponding 2′-/4′-C-modifications.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Dale C Guenther
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Lydia Perkins
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Donald J Foster
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Nate Taneja
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Martin A Maier
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
- To whom correspondence should be addressed. Tel: +1 615 343 8070; Fax: +1 615 343 0704; . Correspondence may also be addressed to Muthiah Manoharan. Tel: +1 617 551 8319; Fax: +1 617 551 8101;
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
- To whom correspondence should be addressed. Tel: +1 615 343 8070; Fax: +1 615 343 0704; . Correspondence may also be addressed to Muthiah Manoharan. Tel: +1 617 551 8319; Fax: +1 617 551 8101;
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Roovers J, De Jonghe P, Weckhuysen S. The therapeutic potential of RNA regulation in neurological disorders. Expert Opin Ther Targets 2018; 22:1017-1028. [PMID: 30372655 DOI: 10.1080/14728222.2018.1542429] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Gene regulation is the term used to describe the mechanisms by which a cell increases or decreases the amount of a gene product (RNA or protein). In complex organs such as the brain, gene regulation is of the utmost importance; aberrations in the regulation of specific genes can lead to neurological disorders. Understanding these mechanisms can create new strategies for targeting these disorders and progress is being made. Two drugs that function at the RNA level (nusinersen and eteplirsen) have now been approved by the FDA for the treatment of Spinomuscular atrophy and Duchenne muscular dystrophy, respectively; several other compounds for neurological disease are currently being investigated in preclinical studies and clinical trials. Areas covered: We highlight how gene regulation at the level of RNA molecules can be used as a therapeutic strategy to treat neurological disorders. We provide examples of how such an approach is being studied or used and discuss the current hurdles. Expert opinion: Targeting gene expression at the RNA level is a promising strategy to treat genetic neurological disorders. Safe administration, long-term efficacy, and potential side effects, however, still need careful evaluation before RNA therapeutics can be applied on a larger scale.
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Affiliation(s)
- Jolien Roovers
- a Neurogenetics Group , Center for Molecular Neurology, VIB , Antwerp , Belgium.,b Laboratory of Neurogenetics, Institute Born-Bunge , University of Antwerp , Antwerp , Belgium
| | - Peter De Jonghe
- a Neurogenetics Group , Center for Molecular Neurology, VIB , Antwerp , Belgium.,b Laboratory of Neurogenetics, Institute Born-Bunge , University of Antwerp , Antwerp , Belgium.,c Department of Neurology , University Hospital Antwerp , Antwerp , Belgium
| | - Sarah Weckhuysen
- a Neurogenetics Group , Center for Molecular Neurology, VIB , Antwerp , Belgium.,b Laboratory of Neurogenetics, Institute Born-Bunge , University of Antwerp , Antwerp , Belgium.,c Department of Neurology , University Hospital Antwerp , Antwerp , Belgium
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27
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He CC, Hamlow LA, Devereaux ZJ, Zhu Y, Nei YW, Fan L, McNary CP, Maitre P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Purine Nucleosides. J Phys Chem B 2018; 122:9147-9160. [PMID: 30203656 DOI: 10.1021/acs.jpcb.8b07687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The chemical difference between DNA and RNA nucleosides is their 2'-hydrogen versus 2'-hydroxyl substituents. Modification of the ribosyl moiety at the 2'-position and 2'-O-methylation in particular, is common among natural post-transcriptional modifications of RNA. 2'-Modification may alter the electronic properties and hydrogen-bonding characteristics of the nucleoside and thus may lead to enhanced stabilization or malfunction. The structures and relative glycosidic bond stabilities of the protonated forms of the 2'-O-methylated purine nucleosides, 2'-O-methyladenosine (Adom) and 2'-O-methylguanosine (Guom), were examined using two complementary tandem mass spectrometry approaches, infrared multiple photon dissociation action spectroscopy and energy-resolved collision-induced dissociation. Theoretical calculations were also performed to predict the structures and relative stabilities of stable low-energy conformations of the protonated forms of the 2'-O-methylated purine nucleosides and their infrared spectra in the gas phase. Low-energy conformations highly parallel to those found for the protonated forms of the canonical DNA and RNA purine nucleosides are also found for the protonated 2'-O-methylated purine nucleosides. Importantly, the preferred site of protonation, nucleobase orientation, and sugar puckering are preserved among the DNA, RNA, and 2'-O-methylated variants of the protonated purine nucleosides. The 2'-substituent does however influence hydrogen-bond stabilization as the 2'-O-methyl and 2'-hydroxyl substituents enable a hydrogen-bonding interaction between the 2'- and 3'-substituents, whereas a 2'-hydrogen atom does not. Further, 2'-O-methylation reduces the number of stable low-energy hydrogen-bonded conformations possible and importantly inverts the preferred polarity of this interaction versus that of the RNA analogues. Trends in the CID50% values extracted from survival yield analyses of the 2'-O-methylated and canonical DNA and RNA forms of the protonated purine nucleosides are employed to elucidate their relative glycosidic bond stabilities. The glycosidic bond stability of Adom is found to exceed that of its DNA and RNA analogues. The glycosidic bond stability of Guom is also found to exceed that of its DNA analogue; however, this modification weakens this bond relative to its RNA counterpart. The glycosidic bond stability of the protonated purine nucleosides appears to be correlated with the hydrogen-bond stabilization of the sugar moiety.
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Affiliation(s)
- C C He
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L A Hamlow
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Zachary J Devereaux
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y Zhu
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - Y-W Nei
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - L Fan
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - C P McNary
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - P Maitre
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), CNRS, Université Paris-Sud, Université Paris-Saclay , 91405 Orsay , France
| | - B Schindler
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - I Compagnon
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
| | - P B Armentrout
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
| | - M T Rodgers
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
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28
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Rinaldi C, Wood MJA. Antisense oligonucleotides: the next frontier for treatment of neurological disorders. Nat Rev Neurol 2017; 14:9-21. [PMID: 29192260 DOI: 10.1038/nrneurol.2017.148] [Citation(s) in RCA: 471] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antisense oligonucleotides (ASOs) were first discovered to influence RNA processing and modulate protein expression over two decades ago; however, progress translating these agents into the clinic has been hampered by inadequate target engagement, insufficient biological activity, and off-target toxic effects. Over the years, novel chemical modifications of ASOs have been employed to address these issues. These modifications, in combination with elucidation of the mechanism of action of ASOs and improved clinical trial design, have provided momentum for the translation of ASO-based strategies into therapies. Many neurological conditions lack an effective treatment; however, as research progressively disentangles the pathogenic mechanisms of these diseases, they provide an ideal platform to test ASO-based strategies. This steady progress reached a pinnacle in the past few years with approvals of ASOs for the treatment of spinal muscular atrophy and Duchenne muscular dystrophy, which represent landmarks in a field in which disease-modifying therapies were virtually non-existent. With the rapid development of improved next-generation ASOs toward clinical application, this technology now holds the potential to have a dramatic effect on the treatment of many neurological conditions in the near future.
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Affiliation(s)
- Carlo Rinaldi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK
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29
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Elkayam E, Parmar R, Brown CR, Willoughby JL, Theile CS, Manoharan M, Joshua-Tor L. siRNA carrying an (E)-vinylphosphonate moiety at the 5΄ end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2. Nucleic Acids Res 2017; 45:3528-3536. [PMID: 27903888 PMCID: PMC5389677 DOI: 10.1093/nar/gkw1171] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/20/2023] Open
Abstract
Efficient gene silencing by RNA interference (RNAi) in vivo requires the recognition and binding of the 5΄- phosphate of the guide strand of an siRNA by the Argonaute protein. However, for exogenous siRNAs it is limited by the rapid removal of the 5΄- phosphate of the guide strand by metabolic enzymes. Here, we have determined the crystal structure of human Argonaute-2 in complex with the metabolically stable 5΄-(E)-vinylphosphonate (5΄-E-VP) guide RNA at 2.5-Å resolution. The structure demonstrates how the 5΄ binding site in the Mid domain of human Argonaute-2 is able to adjust the key residues in the 5΄-nucleotide binding pocket to compensate for the change introduced by the modified nucleotide. This observation also explains improved binding affinity of the 5΄-E-VP -modified siRNA to human Argonaute-2 in-vitro, as well as the enhanced silencing in the context of the trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA in mice relative to the un-modified siRNA.
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Affiliation(s)
- Elad Elkayam
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Rubina Parmar
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | | | | | | | - Leemor Joshua-Tor
- Keck Structural Biology Lab, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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30
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Mitsuoka Y, Aoyama H, Kugimiya A, Fujimura Y, Yamamoto T, Waki R, Wada F, Tahara S, Sawamura M, Noda M, Hari Y, Obika S. Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure. Org Biomol Chem 2016; 14:6531-8. [PMID: 27296230 DOI: 10.1039/c6ob01051b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A sulfonamide-bridged nucleic acid without an N-substituent (SuNA[NH]) was successfully synthesized. A comparison of the SuNA[NMe]- and SuNA[NH]-modified oligonucleotides revealed that the duplex-forming abilities of the SuNA[NMe]-modified oligonucleotides with complementary DNA and RNA were higher than those of the SuNA[NH]-modified oligonucleotides. The crystal structures of DNA duplexes containing a SuNA[NR] revealed that the helical structures of the two duplexes and hydration patterns around the bridge moiety were different. These results provide insights into hydration patterns and rationale for the high RNA affinity of SuNA-modified oligonucleotides.
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Affiliation(s)
- Yasunori Mitsuoka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. and Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Akira Kugimiya
- Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuko Fujimura
- Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Reiko Waki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Saori Tahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Motoki Sawamura
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Mio Noda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. and Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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31
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Koga Y, Taniguchi Y, Kikukawa Y, Sasaki S. Recognition and detection of 8-oxo-rG in RNA using the DNA/OMeRNA chimera probes containing fluorescent adenosine-diazaphenoxazine analog. Bioorg Med Chem 2016; 24:1308-13. [PMID: 26872394 DOI: 10.1016/j.bmc.2016.02.001] [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: 12/10/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
Abstract
Recent studies indicate that oxidative damage to RNA results in dysfunction of translation and eventual pathogenesis. A representative oxidized base in RNA is 8-hydroxyguanosine (8-oxo-rG), however, unlike its DNA counterpart (8-oxo-dG), its role in pathogenesis has not attracted much attention until recently. The 2'-deoxyadenosine derivative with a diazaphenoxazine skeleton at the 6-amino group (Adap) was shown to be selective for 8-oxo-dG in DNA. In this study, the 2'-O-methoxy derivative of Adap (2'-OMeAdap) was designed as a selective molecule for 8-oxo-rG in RNA. 8-Oxo-rG in the homopurine RNA was selectively recognized by the ODN probe incorporating Adap. In contrast, although it was not possible by the Adap-containing ODN prove due to the instability of the corresponding duplex, 8-oxo-rG in homopyrimidine RNA was selectively detected by the 2'-OMeRNA probe incorporating 2'-OMeAdap.
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Affiliation(s)
- Yohei Koga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Yoshiya Kikukawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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32
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Xu Y, Vanommeslaeghe K, Aleksandrov A, MacKerell AD, Nilsson L. Additive CHARMM force field for naturally occurring modified ribonucleotides. J Comput Chem 2016; 37:896-912. [PMID: 26841080 PMCID: PMC4801715 DOI: 10.1002/jcc.24307] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 01/13/2023]
Abstract
More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, HUDDINGE, SE-141 83, Sweden
| | - Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland, 21201.,Department of Analytical Chemistry and Pharmaceutical Technology (FABI), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, B-1090, Belgium
| | - Alexey Aleksandrov
- Department of Biology, Ecole Polytechnique, Laboratoire De Biochimie (CNRS UMR7654), Palaiseau, F-91128, France
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland, 21201
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, HUDDINGE, SE-141 83, Sweden
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33
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Suresh G, Priyakumar UD. Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study. J Mol Graph Model 2015; 61:150-9. [PMID: 26254870 DOI: 10.1016/j.jmgm.2015.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/22/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.
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Affiliation(s)
- Gorle Suresh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India.
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34
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Evers MM, Toonen LJ, van Roon-Mom WM. Antisense oligonucleotides in therapy for neurodegenerative disorders. Adv Drug Deliv Rev 2015; 87:90-103. [PMID: 25797014 DOI: 10.1016/j.addr.2015.03.008] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 03/02/2015] [Accepted: 03/12/2015] [Indexed: 12/14/2022]
Abstract
Antisense oligonucleotides are synthetic single stranded strings of nucleic acids that bind to RNA and thereby alter or reduce expression of the target RNA. They can not only reduce expression of mutant proteins by breakdown of the targeted transcript, but also restore protein expression or modify proteins through interference with pre-mRNA splicing. There has been a recent revival of interest in the use of antisense oligonucleotides to treat several neurodegenerative disorders using different approaches to prevent disease onset or halt disease progression and the first clinical trials for spinal muscular atrophy and amyotrophic lateral sclerosis showing promising results. For these trials, intrathecal delivery is being used but direct infusion into the brain ventricles and several methods of passing the blood brain barrier after peripheral administration are also under investigation.
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35
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Yamamoto S, Park S, Sugiyama H. Development of a visible nanothermometer with a highly emissive 2′-O-methylated guanosine analogue. RSC Adv 2015. [DOI: 10.1039/c5ra24756j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have synthesized a fluorescent base analogue, 2-aminothieno[3,4-d]pyrimidine based G-mimic deoxyribonucleoside, 2′-OMe-thG, and investigated its photophysical properties and DNA incorporation.
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Affiliation(s)
- Seigi Yamamoto
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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36
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Yildirim I, Kierzek E, Kierzek R, Schatz GC. Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results. J Phys Chem B 2014; 118:14177-87. [PMID: 25268896 DOI: 10.1021/jp506703g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2'-O-methyl RNA residues enhance the duplex stabilities, and this makes it possible to create much better RNA aptamers to target specific molecules in cells. Thus, LNA and 2'-O-methyl RNA residues are finding increasingly widespread use in RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations and UV melting experiments to investigate the structural and thermodynamic properties of 13 nucleic acid duplexes, including full DNA, RNA, LNA, and 2'-O-methyl RNA duplexes as well as hybrid systems such as LNA:RNA, 2'-O-methyl RNA:RNA, LNA/2'-O-methyl RNA:RNA, and RNA/2'-O-methyl RNA:RNA duplexes. The MD simulations are based on a version of the Amber force field revised specifically for RNA and LNA residues. Our results indicate that LNA and 2'-O-methyl RNA residues have two different hybridization mechanisms when included in hybrid duplexes with RNA wherein the former underwinds while the latter overwinds the duplexes. These computational predictions are supported by X-ray structures of LNA and 2'-O-methyl RNA duplexes that were recently presented by different groups, and there is also good agreement with the measured thermal stabilities of the duplexes. We find out that the "underwinding" phenomenon seen in LNA and LNA:RNA hybrid duplexes happens due to expansion of the major groove widths (Mgw) of the duplexes that is associated with decrease in the slide and twist values in base-pair steps. In contrast, 2'-O-methyl RNA residues in RNA duplexes slightly overwind the duplexes while the backbone is forced to stay in C3'-endo. Moreover, base-pair stacking in the LNA and LNA:RNA hybrid systems is gradually reduced with the inclusion of LNA residues in the duplexes while no such effect is seen in the 2'-O-methyl RNA systems. Our results show how competition between base stacking and structural rigidity in these RNA hybrid systems influences structures and stabilities. Even though both LNA and 2'-O-methyl RNA residues have C3'-endo sugar puckering, structurally LNA residues have a frozen sugar backbone which provides entropic enhancement of stabilities while the 2'-O-methyl RNA residues are more flexible and maintain base stacking that is almost untouched compared to RNA. Thus, enhancement of the structural stabilities of RNA duplexes by 2'-O-methyl RNA modifications is smaller than for the corresponding LNA modifications. Indeed, our experimental measurements show that on average each 2'-O-methyl RNA and LNA substitution in a RNA duplex enhances duplex stability by 0.2 and 1.4 kcal/mol, respectively. Our computational binding free energy predictions are qualitatively in line with these results. The only exception is for the full 2'-O-methyl RNA duplex, which is overstabilized, implying that further force field revisions are needed. Collectively, the results presented in this paper explain the atomistic details of the structural and thermodynamic roles of LNA and 2'-O-methyl RNA residues in RNA hybrid duplexes, shedding light on the mechanism behind targeting endogenous micro RNA (miRNA) in order to regulate mRNA activity and inhibit gene expression in the cell.
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Affiliation(s)
- Ilyas Yildirim
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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Wu SY, Yang X, Gharpure KM, Hatakeyama H, Egli M, McGuire MH, Nagaraja AS, Miyake TM, Rupaimoole R, Pecot CV, Taylor M, Pradeep S, Sierant M, Rodriguez-Aguayo C, Choi HJ, Previs RA, Armaiz-Pena GN, Huang L, Martinez C, Hassell T, Ivan C, Sehgal V, Singhania R, Han HD, Su C, Kim JH, Dalton HJ, Kovvali C, Keyomarsi K, McMillan NAJ, Overwijk WW, Liu J, Lee JS, Baggerly KA, Lopez-Berestein G, Ram PT, Nawrot B, Sood AK. 2'-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity. Nat Commun 2014; 5:3459. [PMID: 24619206 DOI: 10.1038/ncomms4459] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 02/17/2014] [Indexed: 12/19/2022] Open
Abstract
Improving small interfering RNA (siRNA) efficacy in target cell populations remains a challenge to its clinical implementation. Here, we report a chemical modification, consisting of phosphorodithioate (PS2) and 2'-O-Methyl (2'-OMe) MePS2 on one nucleotide that significantly enhances potency and resistance to degradation for various siRNAs. We find enhanced potency stems from an unforeseen increase in siRNA loading to the RNA-induced silencing complex, likely due to the unique interaction mediated by 2'-OMe and PS2. We demonstrate the therapeutic utility of MePS2 siRNAs in chemoresistant ovarian cancer mouse models via targeting GRAM domain containing 1B (GRAMD1B), a protein involved in chemoresistance. GRAMD1B silencing is achieved in tumours following MePS2-modified siRNA treatment, leading to a synergistic anti-tumour effect in combination with paclitaxel. Given the previously limited success in enhancing siRNA potency with chemically modified siRNAs, our findings represent an important advance in siRNA design with the potential for application in numerous cancer types.
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Affiliation(s)
- Sherry Y Wu
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2]
| | - Xianbin Yang
- 1] AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, USA [2]
| | - Kshipra M Gharpure
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Hiroto Hatakeyama
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
| | - Michael H McGuire
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Archana S Nagaraja
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Takahito M Miyake
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Rajesha Rupaimoole
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Chad V Pecot
- Division of Cancer Medicine, MDACC, Houston, Texas 77054, USA
| | - Morgan Taylor
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Sunila Pradeep
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, Poland
| | - Cristian Rodriguez-Aguayo
- 1] Department of Experimental Therapeutics, MDACC, Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Hyun J Choi
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Rebecca A Previs
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Guillermo N Armaiz-Pena
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Li Huang
- Department of Cancer Biology, MDACC, Houston, Texas 77054, USA
| | - Carlos Martinez
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, USA
| | - Tom Hassell
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, USA
| | - Cristina Ivan
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Vasudha Sehgal
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | - Richa Singhania
- 1] University of Queensland Diamantina Institute, Woolloongabba, Queensland 4102, Australia [2] Centre for Biomolecular Sciences, School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Hee-Dong Han
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA [3] Department of Immunology Laboratory, School of Medicine, Konkuk University, Chungju 380-701, South Korea
| | - Chang Su
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Ji Hoon Kim
- 1] Department of Systems Biology, MDACC, Houston, Texas 77054, USA [2] Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul 136-701, Korea
| | - Heather J Dalton
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Chandra Kovvali
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, MDACC, Houston, Texas 77054, USA
| | - Nigel A J McMillan
- 1] University of Queensland Diamantina Institute, Woolloongabba, Queensland 4102, Australia [2] Griffith Health Institute and School of Medical Sciences, Griffith University, Southport, Queensland 4222, Australia
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, MDACC, Houston, Texas 77054, USA
| | - Jinsong Liu
- Department of Pathology, MDACC, Houston, Texas 77054, USA
| | - Ju-Seog Lee
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | | | - Gabriel Lopez-Berestein
- 1] Department of Experimental Therapeutics, MDACC, Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA
| | - Prahlad T Ram
- Department of Systems Biology, MDACC, Houston, Texas 77054, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, Poland
| | - Anil K Sood
- 1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA [3] Department of Cancer Biology, MDACC, Houston, Texas 77054, USA
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Pallan PS, Yang X, Sierant M, Abeydeera ND, Hassell T, Martinez C, Janicka M, Nawrot B, Egli M. Crystal structure, stability and Ago2 affinity of phosphorodithioate-modified RNAs. RSC Adv 2014. [DOI: 10.1039/c4ra10986d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The high Ago2 affinity of siRNAs with combined 2′-O-methyl and phosphorodithioate backbone modifications (MePS2) in the 3′-terminal region of the sense strand is likely the result of enhanced hydrophobic interactions with the protein's PAZ domain.
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Affiliation(s)
- Pradeep S. Pallan
- Department of Biochemistry
- Vanderbilt University
- School of Medicine
- Nashville, USA
| | | | - Malgorzata Sierant
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- Lodz, Poland
| | | | | | | | - Magdalena Janicka
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- Lodz, Poland
| | - Barbara Nawrot
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- Lodz, Poland
| | - Martin Egli
- Department of Biochemistry
- Vanderbilt University
- School of Medicine
- Nashville, USA
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Gore KR, Harikrishna S, Pradeepkumar PI. Influence of 2'-fluoro versus 2'-O-methyl substituent on the sugar puckering of 4'-C-aminomethyluridine. J Org Chem 2013; 78:9956-62. [PMID: 24016294 DOI: 10.1021/jo4012333] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Herein, we report the synthesis of 4'-C-aminomethyl-2'-deoxy-2'-fluorouridine, a therapeutically appealing RNA modification. Conformational analysis by DFT calculations and molecular dynamics simulations using trinucleotide model systems revealed that modified sugar adopts C3'-endo conformation. In this conformer, a weak intramolecular C-H···F H-bond between the hydrogen atom of the 4'-C-CH2 group and the F atom at the 2' position is observed. Comparative studies with unmodified, 2'-fluoro-, 2'-O-methyl-, and 4'-C-aminomethyl-2'-O-methyluridine showed the chemical nature of 2'-substituent dictates the sugar puckering of 2',4'-modified nucleotides.
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Affiliation(s)
- Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
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40
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Zhou J, Watt S, Wang J, Nakayama S, Sayre DA, Lam YF, Lee VT, Sintim HO. Potent suppression of c-di-GMP synthesis via I-site allosteric inhibition of diguanylate cyclases with 2'-F-c-di-GMP. Bioorg Med Chem 2013; 21:4396-404. [PMID: 23685177 DOI: 10.1016/j.bmc.2013.04.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/10/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a central regulator of bacterial behavior. Various studies have implicated c-di-GMP in biofilm formation and virulence factor production in multitudes of bacteria. Hence it is expected that the disruption of c-di-GMP signaling could provide an effective means to disrupt biofilm and/or virulence factor formation in several bacteria of clinical relevance. C-di-GMP achieves the regulation of bacterial phenotype via binding to several effector molecules including transcription factors, enzymes and riboswitches. Crystal structure analyses of c-di-GMP effector molecules, in complex with the ligand, reveal that various classes of c-di-GMP receptors recognize this dinucleotide using different sets of recognition elements. Therefore, it is plausible that different analogues of c-di-GMP could be used to selectively modulate a specific class of c-di-GMP binding receptors, and hence modulate the bacterial phenotype. Thus far only a detailed study of the differential binding of c-di-GMP analogues to riboswitches, but not proteins, has been reported. In this report, we prepared various 2'-modified analogues of c-di-GMP and studied both polymorphisms of these analogues using DOSY NMR and the binding to several effector proteins, such as PilZ-containing proteins, diguanylate cyclases (DGC) containing I-sites, and phoshphodiesterases (PDE). 2'-Modification of c-di-GMP did not adversely affect the propensity to form higher aggregates, such as octameric forms, in the presence of potassium salts. Interestingly, we find that the selective binding to different classes of c-di-GMP binding proteins could be achieved with the 2'-modified analogues and that 2'-F analogue of c-di-GMP binds to the I-site of DGCs better (four times) than the native dinucleotide, c-di-GMP, whereas c-di-GMP binds to PDEs better (10 times) than 2'-F-c-di-GMP. 2'-F-c-di-GMP potently inhibits c-di-GMP synthesis by DGCs and hence raises the potential that cell permeable analogues of 2'-F-c-di-GMP could be used to disrupt c-di-GMP signaling in bacteria.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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41
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Owczarzy R, You Y, Groth CL, Tataurov AV. Stability and mismatch discrimination of locked nucleic acid-DNA duplexes. Biochemistry 2011; 50:9352-67. [PMID: 21928795 PMCID: PMC3201676 DOI: 10.1021/bi200904e] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Locked nucleic acids (LNA; symbols of bases, +A, +C,
+G, and +T) are introduced into chemically synthesized oligonucleotides
to increase duplex stability and specificity. To understand these
effects, we have determined thermodynamic parameters of consecutive
LNA nucleotides. We present guidelines for the design of LNA oligonucleotides
and introduce free online software that predicts the stability of
any LNA duplex oligomer. Thermodynamic analysis shows that the single
strand–duplex transition is characterized by a favorable enthalpic
change and by an unfavorable loss of entropy. A single LNA modification
confines the local conformation of nucleotides, causing a smaller,
less unfavorable entropic loss when the single strand is restricted
to the rigid duplex structure. Additional LNAs adjacent to the initial
modification appear to enhance stacking and H-bonding interactions
because they increase the enthalpic contributions to duplex stabilization.
New nearest-neighbor parameters correctly forecast the positive and
negative effects of LNAs on mismatch discrimination. Specificity is
enhanced in a majority of sequences and is dependent on mismatch type
and adjacent base pairs; the largest discriminatory boost occurs for
the central +C·C mismatch within the +T+C+C sequence and the
+A·G mismatch within the +T+A+G sequence. LNAs do not affect
specificity in some sequences and even impair it for many +G·T
and +C·A mismatches. The level of mismatch discrimination decreases
the most for the central +G·T mismatch within the +G+G+C sequence
and the +C·A mismatch within the +G+C+G sequence. We hypothesize
that these discrimination changes are not unique features of LNAs
but originate from the shift of the duplex conformation from B-form
to A-form.
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Affiliation(s)
- Richard Owczarzy
- Department of Molecular Genetics and Biophysics, Integrated DNA Technologies, Coralville, Iowa 52241, United States.
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42
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Sliva K, Schnierle BS. Selective gene silencing by viral delivery of short hairpin RNA. Virol J 2010; 7:248. [PMID: 20858246 PMCID: PMC2949849 DOI: 10.1186/1743-422x-7-248] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 09/21/2010] [Indexed: 12/15/2022] Open
Abstract
RNA interference (RNAi) technology has not only become a powerful tool for functional genomics, but also allows rapid drug target discovery and in vitro validation of these targets in cell culture. Furthermore, RNAi represents a promising novel therapeutic option for treating human diseases, in particular cancer. Selective gene silencing by RNAi can be achieved essentially by two nucleic acid based methods: i) cytoplasmic delivery of short double-stranded (ds) interfering RNA oligonucleotides (siRNA), where the gene silencing effect is only transient in nature, and possibly not suitable for all applications; or ii) nuclear delivery of gene expression cassettes that express short hairpin RNA (shRNA), which are processed like endogenous interfering RNA and lead to stable gene down-regulation. Both processes involve the use of nucleic acid based drugs, which are highly charged and do not cross cell membranes by free diffusion. Therefore, in vivo delivery of RNAi therapeutics must use technology that enables the RNAi therapeutic to traverse biological membrane barriers in vivo. Viruses and the vectors derived from them carry out precisely this task and have become a major delivery system for shRNA. Here, we summarize and compare different currently used viral delivery systems, give examples of in vivo applications, and indicate trends for new developments, such as replicating viruses for shRNA delivery to cancer cells.
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Affiliation(s)
- Katja Sliva
- Paul-Ehrlich-Institute, Paul-Ehrlich-Str, 51-59, 63225 Langen, Germany.
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43
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Masaki Y, Miyasaka R, Ohkubo A, Seio K, Sekine M. Linear relationship between deformability and thermal stability of 2'-O-modified RNA hetero duplexes. J Phys Chem B 2010; 114:2517-24. [PMID: 20108976 PMCID: PMC2825091 DOI: 10.1021/jp909851j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We describe the relationship between the experimentally determined melting temperatures of 2′-O-modified-RNA/RNA duplexes and their deformability estimated from molecular dynamics simulations. To clarify this relationship, we synthesized several fully modified oligoribonucleotides such as 2′-O-cyanoethyl RNAs and 2′-O-methoxyethyl RNAs and compared the actual melting temperatures of the duplexes with their calculated deformabilities. An increase of the melting temperatures by 2′-O-modifications was found to correlate strongly with an increase of the helical elastic constants in U14/A14, (CU)7/(AG)7, and (GACU)3/(AGUC)3 sequences. Linear regression analyses could be used to estimate the melting temperature with an accuracy of ±2.0 °C in our model case. Although the strong correlation was observed in the same base sequence, the linear regression functions were different from each base sequence. Our results indicated the possibility of predicting the thermal stability of 2′-O-modified duplexes at the computer-aided molecular design stage.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan
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44
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Zhang RB, Eriksson LA. Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group. Phys Chem Chem Phys 2010; 12:3690-7. [PMID: 20358065 DOI: 10.1039/b921646d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.
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Affiliation(s)
- Ru bo Zhang
- Institute for Chemical Physics, School of Science, Beijing Institute of Technology, Beijing 100081, China
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45
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Egli M, Pallan PS. Crystallographic studies of chemically modified nucleic acids: a backward glance. Chem Biodivers 2010; 7:60-89. [PMID: 20087997 PMCID: PMC2905155 DOI: 10.1002/cbdv.200900177] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications. CNAs are also of interest in diagnostics, high-throughput genomics and target validation, nanotechnology and as model systems in investigations directed at a better understanding of the etiology of nucleic acid structure, as well as the physicochemical and pairing properties of DNA and RNA, and for probing protein-nucleic acid interactions. In this article, we review research conducted in our laboratory over the past two decades with a focus on crystal-structure analyses of CNAs and artificial pairing systems. We highlight key insights into issues ranging from conformational distortions as a consequence of modification to the modulation of pairing strength, and RNA affinity by stereoelectronic effects and hydration. Although crystal structures have only been determined for a subset of the large number of modifications that were synthesized and analyzed in the oligonucleotide context to date, they have yielded guiding principles for the design of new analogs with tailor-made properties, including pairing specificity, nuclease resistance, and cellular uptake. And, perhaps less obviously, crystallographic studies of CNAs and synthetic pairing systems have shed light on fundamental aspects of DNA and RNA structure and function that would not have been disclosed by investigations solely focused on the natural nucleic acids.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-0146, USA.
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46
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Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M, Egli M. A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution. Chem Commun (Camb) 2009:2017-9. [PMID: 19333476 PMCID: PMC2909737 DOI: 10.1039/b822781k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.
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Affiliation(s)
- Pradeep S. Pallan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
| | - Thazha P. Prakash
- Department of Medicinal Chemistry, ISIS Pharmaceuticals Inc., Carlsbad, California 92008
| | - Feng Li
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
| | - Robert L. Eoff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
| | - Muthiah Manoharan
- Department of Drug Discovery, Alnylam Pharmaceuticals Inc., Cambridge, Massachusetts 02142
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, Fax: (+) 1-615-322-7122
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Takahashi M, Minakawa N, Matsuda A. Synthesis and characterization of 2'-modified-4'-thioRNA: a comprehensive comparison of nuclease stability. Nucleic Acids Res 2009; 37:1353-62. [PMID: 19151085 PMCID: PMC2651785 DOI: 10.1093/nar/gkn1088] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We report herein the synthesis and physical and physiological characterization of fully modified 2′-modified-4′-thioRNAs, i.e. 2′-fluoro-4′-thioRNA (F-SRNA) and 2′-O-Me-4′-thioRNA (Me-SRNA), which can be considered as a hybrid chemical modification based on 2′-modified oligonucleotides (ONs) and 4′-thioRNA (SRNA). In its hybridization with a complementary RNA, F-SRNA (15mer) showed the highest Tm value (+16°C relative to the natural RNA duplex). In addition, both F-SRNA and Me-SRNA preferred RNA as a complementary partner rather than DNA in duplex formation. The results of a comprehensive comparison of nuclease stability of single-stranded F-SRNA and Me-SRNA along with 2′-fluoroRNA (FRNA), 2′-O-MeRNA (MeRNA), SRNA, and natural RNA and DNA, revealed that Me-SRNA had the highest stability with t1/2 values of > 24 h against S1 nuclease (an endonuclease) and 79.2 min against SVPD (a 3′-exonuclease). Moreover, the stability of Me-SRNA was significantly improved in 50% human plasma (t1/2 = 1631 min) compared with FRNA (t1/2 = 53.2 min) and MeRNA (t1/2 = 187 min), whose modifications are currently used as components of therapeutic aptamers. The results presented in this article will, it is hoped, contribute to the development of 2′-modified-4′-thioRNAs, especially Me-SRNA, as a new RNA molecule for therapeutic applications.
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Affiliation(s)
| | - Noriaki Minakawa
- *To whom correspondence should be addressed. Tel: +81 11 706 3228; Fax: +81 11 706 4980;
| | - Akira Matsuda
- *To whom correspondence should be addressed. Tel: +81 11 706 3228; Fax: +81 11 706 4980;
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Lebars I, Legrand P, Aimé A, Pinaud N, Fribourg S, Di Primo C. Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance. Nucleic Acids Res 2008; 36:7146-56. [PMID: 18996893 PMCID: PMC2602780 DOI: 10.1093/nar/gkn831] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In HIV-1, trans-activation of transcription of the viral genome is regulated by an imperfect hairpin, the trans-activating responsive (TAR) RNA element, located at the 5′ untranslated end of all viral transcripts. TAR acts as a binding site for viral and cellular proteins. In an attempt to identify RNA ligands that would interfere with the virus life-cycle by interacting with TAR, an in vitro selection was previously carried out. RNA hairpins that formed kissing-loop dimers with TAR were selected [Ducongé F. and Toulmé JJ (1999) RNA, 5:1605–1614]. We describe here the crystal structure of TAR bound to a high-affinity RNA aptamer. The two hairpins form a kissing complex and interact through six Watson–Crick base pairs. The complex adopts an overall conformation with an inter-helix angle of 28.1°, thus contrasting with previously reported solution and modelling studies. Structural analysis reveals that inter-backbone hydrogen bonds between ribose 2′ hydroxyl and phosphate oxygens at the stem-loop junctions can be formed. Thermal denaturation and surface plasmon resonance experiments with chemically modified 2′-O-methyl incorporated into both hairpins at key positions, clearly demonstrate the involvement of this intermolecular network of hydrogen bonds in complex stability.
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Affiliation(s)
- Isabelle Lebars
- CNRS-Université Bordeaux 1-ENITAB, UMR 5248 CBMN, Institut Européen de Chimie et Biologie, Pessac, F-33607, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, INSERM U869, Institut Européen de Chimie et Biologie, Pessac, F-33607 and Université de Bordeaux, Bordeaux, F-33076, France
| | - Pierre Legrand
- CNRS-Université Bordeaux 1-ENITAB, UMR 5248 CBMN, Institut Européen de Chimie et Biologie, Pessac, F-33607, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, INSERM U869, Institut Européen de Chimie et Biologie, Pessac, F-33607 and Université de Bordeaux, Bordeaux, F-33076, France
| | - Ahissan Aimé
- CNRS-Université Bordeaux 1-ENITAB, UMR 5248 CBMN, Institut Européen de Chimie et Biologie, Pessac, F-33607, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, INSERM U869, Institut Européen de Chimie et Biologie, Pessac, F-33607 and Université de Bordeaux, Bordeaux, F-33076, France
| | - Noël Pinaud
- CNRS-Université Bordeaux 1-ENITAB, UMR 5248 CBMN, Institut Européen de Chimie et Biologie, Pessac, F-33607, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, INSERM U869, Institut Européen de Chimie et Biologie, Pessac, F-33607 and Université de Bordeaux, Bordeaux, F-33076, France
| | - Sébastien Fribourg
- CNRS-Université Bordeaux 1-ENITAB, UMR 5248 CBMN, Institut Européen de Chimie et Biologie, Pessac, F-33607, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, INSERM U869, Institut Européen de Chimie et Biologie, Pessac, F-33607 and Université de Bordeaux, Bordeaux, F-33076, France
- *To whom correspondence should be addressed. Tel: +33 5 40 00 30 63; Fax: +33 5 40 00 30 68;
| | - Carmelo Di Primo
- CNRS-Université Bordeaux 1-ENITAB, UMR 5248 CBMN, Institut Européen de Chimie et Biologie, Pessac, F-33607, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, INSERM U869, Institut Européen de Chimie et Biologie, Pessac, F-33607 and Université de Bordeaux, Bordeaux, F-33076, France
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Watts JK, Johnston BD, Jayakanthan K, Wahba AS, Pinto BM, Damha MJ. Synthesis and biophysical characterization of oligonucleotides containing a 4'-selenonucleotide. J Am Chem Soc 2008; 130:8578-9. [PMID: 18543920 DOI: 10.1021/ja802205u] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first synthesis of oligonucleotides containing 4'-selenium-modified ribonucleotides (4'-Se-rN) is described. Four sequences containing 4'-Se-rT were successfully synthesized and compared with DNA and RNA oligonucleotides containing a dT, rT, or LNA insert in place of the 4'-Se-rT. The 4'-Se-rT behaved more like rT than dT in its effects on binding affinity, despite the DNA-like structure previously observed for the nucleoside, suggesting that a conformational switch occurs upon incorporation into an oligonucleotide. Incorporation of 4'-Se-rT into A-RNA and hybrid duplexes led to increased binding affinity, while incorporation into B-DNA destabilized the duplex to the same extent as an rT nucleotide.
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Affiliation(s)
- Jonathan K Watts
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada
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Kirk Field A, Goodchild J. Section Review: Biologicals & Immunologicals: Antisense oligonucleotides: Rational drug design for genetic pharmacology. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.4.9.799] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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